seekrcentral / seekr2 Goto Github PK

Simulation-Enabled Estimation of Kinetic Rates - Version 2

License: MIT License

Shell 0.11% Python 93.96% Rich Text Format 5.93%

seekr2-openmm-plugin openmm namd2 md-simulations conda

seekr2's Introduction

seekr2

##########################################      ########
   ###   ######  ######  ### ###  #####      ####      ####
  #####   ##  #   ##  #   ##  #    ##  #    ##           ###
  ##      ##      ##      ## #     ##  #     ##           ##
   ##     ####    ####    ###      ##  #                 ###
    ##    ##      ##      ###     #####                ####
  #####   ##  #   ##  #   ## #     ##  #            ###
   ###   ######  ######  ###  ##  ###  #         ## 
##########################################    ##
         #######   #  #      ###           ##            #
       ##       #########       ##       ##  ####    #####
         ###      #  #   #######        ##       #######

Simulation-Enabled Estimation of Kinetic Rates - Version 2

Overview

Fast and versatile multiscale milestoning to compute molecular thermodynamics and kinetics.

Prepare and run milestoning calculations in the OpenMM, NAMD, and/or Browndye2 simulation engines to obtain the kinetics and thermodynamics of molecular processes such as: ligand-receptor binding and unbinding, membrane permeability, internal molecular dynamics, and many other potential situations.

This README is only a quickstart guide to get SEEKR2 up and running as soon as possible. To see more detailed instructions and tutorials, please see https://seekr2.readthedocs.io/en/latest or the docs/ subfolder.

Quick Install

Dependencies

Many of the dependencies for SEEKR2 will be installed alongside SEEKR2, but some must be installed separately, and are installed first, before SEEKR2.

OpenMM (recommended)

OpenMM is recommended for the molecular dynamics (MD) stage of SEEKR2. SEEKR2 also needs the SEEKR2 OpenMM Plugin in order to use OpenMM for MD simulations.

The easiest, quickest way to install the SEEKR2 OpenMM Plugin is to use Conda. If you don't already have Conda installed, Download Conda with Python version 3.8 from https://conda.io/en/latest/miniconda.html and run the downloaded script and fill out the prompts.

With Conda working, install the SEEKR2 OpenMM Plugin:

conda install -c conda-forge seekr2_openmm_plugin

One can test the installation by opening a Python terminal and typing:

import seekr2plugin

If there is a problem related to not being able to find libOpenMM8.1, one can try specifying the OpenMM version:

conda install -c conda-forge seekr2_openmm_plugin openmm=8.1

If there is an error such as "No module named seekr2plugin", one can always try installing an older version of OpenMM and CUDA:

conda install -c conda-forge seekr2_openmm_plugin cudatoolkit=10.2 openmm=7.7

Alternatively, NAMD2 may be used for MD if desired. See the NAMD2 section below for installation instructions.

Browndye2 (optional; required for k-on calculations)

SEEKR2 needs Browndye2 if Brownian dynamics (BD) simulations will be run (necessary for k-on calculations). Please see (https://browndye.ucsd.edu/) for Browndye2 installation instructions.

NAMD2 (optional, required if not using OpenMM)

If OpenMM is not desirable or available for the MD simulations, SEEKR2 may use NAMD2 in order to run MD simulations. NAMD2 is frequently already available on shared computing resources like clusters and supercomputers. Not all SEEKR2 options may be available using NAMD2.

If you wish to install NAMD2 yourself, please see http://www.ks.uiuc.edu/Research/namd/ for instructions to install NAMD.

Install SEEKR2

Once the dependencies are installed, we may install SEEKR2. First, clone this repository and install the package:

git clone https://github.com/seekrcentral/seekr2.git
cd seekr2
python -m pip install .

Testing SEEKR2 (Optional)

To test SEEKR2, run the following command in the seekr2/ directory:

pytest

Additional continuous integration tests may be run from the Python scripts in the seekr2/seekr2/continuous_integration/ directory.

Run

A SEEKR2 calculation needs a "Model Input File" to run. Several examples may be found in seekr2/seekr2/data. Execute the following commands within the seekr2/seekr2/ directory to run a sample calculation on the host-guest system:

(It is assumed that both Browndye2 and the the SEEKR2 OpenMM Plugin have already been installed).

python prepare.py data/sample_input_mmvt_openmm.xml
python run.py any ~/test_mmvt_openmm/model.xml
python converge.py ~/test_mmvt_openmm/model.xml
python analyze.py ~/test_mmvt_openmm/model.xml

Important Options and Hints

In general, SEEKR2 programs can be run with the '-h' argument to see all available options. Please see https://seekr2.readthedocs.io/en/latest for a detailed description of programs and options.
the run.py program accepts an INSTRUCTION as its first argument, and the following options are available:
- "any" - run any MD or BD calculation that still needs to be run.
- "any_md" - run any MD calculation that still needs to be run.
- "any_bd" - run any BD calculation that still needs to be run.
- INTEGER - run the MD anchor whose index is INTEGER. Examples: "0", "1", etc.
- "b_surface" - run BD simulations starting at the b-surface.
When an option must be modified, it is usually necessary to make the change in the input file and not the model file, and then re-run prepare.py to make a new model file. In some exceptions, the model file may be directly (and carefully) modified.

Authors and Contributors

The following people have contributed directly to the coding and validation efforts of SEEKR2 (listed an alphabetical order of last name). Thanks also to everyone who has helped or will help improve this project by providing feedback, bug reports, or other comments.

Rommie Amaro (principal investigator)
Ilker Deveci (developer)
Hilliary Frank (contributor)
Sasha Heyneman (contributor)
Ben Jagger (developer)
Anand Ojha (developer)
Andy Stokely (developer)
Natalie Timms (contributor)
Lane Votapka (lead developer)
Jeff Wagner (contributor)

Citing SEEKR2

If you use SEEKR2, please cite the following paper:

Votapka, L. W.; Stokely, A. M.; Ojha, A. A.; Amaro, R. E. SEEKR2: Versatile Multiscale Milestoning Utilizing the OpenMM Molecular Dynamics Engine. J. Chem. Inf. Mod. 2022 62 (13), 3253-3262. DOI: 10.1021/acs.jcim.2c00501

You may also optionally cite the following papers:

Votapka, L. W.; Jagger, B. R.; Heyneman, A. L.; Amaro, R. E. SEEKR: Simulation Enabled Estimation of Kinetic Rates, A Computational Tool to Estimate Molecular Kinetics and Its Application to Trypsin–Benzamidine Binding. J. Phys. Chem. B 2017, 121 (15), 3597–3606. https://doi.org/10.1021/acs.jpcb.6b09388.
Jagger, B. R.; Ojha, A. A.; Amaro, R. E. Predicting Ligand Binding Kinetics Using a Markovian Milestoning with Voronoi Tessellations Multiscale Approach. J. Chem. Theory Comput. 2020. https://doi.org/10.1021/acs.jctc.0c00495.
Jagger, B. R.; Lee, C. T.; Amaro, R. E. Quantitative Ranking of Ligand Binding Kinetics with a Multiscale Milestoning Simulation Approach. J. Phys. Chem. Lett. 2018, 9 (17), 4941–4948. https://doi.org/10.1021/acs.jpclett.8b02047.
Votapka LW, Amaro RE (2015) Multiscale Estimation of Binding Kinetics Using Brownian Dynamics, Molecular Dynamics and Milestoning. PLOS Computational Biology 11(10): e1004381. https://doi.org/10.1371/journal.pcbi.1004381

Copyright

Acknowledgements

Project based on the Computational Molecular Science Python Cookiecutter version 1.5.

seekr2's People

Contributors

Stargazers

Watchers

Forkers

astokely cartercanedy jabruniessner tienmphan

seekr2's Issues

attribute error in analyze.py

Hi Lane,
I tried to use analyze.py on some seerk2 directories but everytime I observe a weird error:

#Input
python ~/Software/seekr2-conda/seekr2/analyze.py model.xml

#Output
Traceback (most recent call last):
File "/home/g035896/Software/seekr2-conda/seekr2/analyze.py", line 801, in
image_directory = common_analyze.make_image_directory(
AttributeError: module 'seekr2.modules.common_analyze' has no attribute 'make_image_directory'

Before executing analyze.py, I have pulled the latest seekr2-code by 'git pull' and 'python setup.py install'. I also regenerated the model-file by 'prepare.py' but observed no change.

From looking into the code, I assume these two lines are causing the error:

model = base.load_model(model_file)
image_directory = common_analyze.make_image_directory(
model, image_directory)

'image_directory' seems to fail because it is missing the 'model' attribute.

Issue running OpenMM in the tutorial

Hi Lane,
I was running the tutorial file 'sample_input_mmvt_openmm.xml' and observed the following error while running:

python run.py any /path/to/model.xml

#########Output: ##############
mark0
anchor 0 has not run the minimum number of steps 0 of 100000
anchor 1 has not run the minimum number of steps 0 of 100000
anchor 2 has not run the minimum number of steps 0 of 100000
anchor 3 has not run the minimum number of steps 0 of 100000
anchor 4 has not run the minimum number of steps 0 of 100000
anchor 5 has not run the minimum number of steps 0 of 100000
anchor 6 has not run the minimum number of steps 0 of 100000
anchor 7 has not run the minimum number of steps 0 of 100000
anchor 8 has not run the minimum number of steps 0 of 100000
anchor 9 has not run the minimum number of steps 0 of 100000
anchor 10 has not run the minimum number of steps 0 of 100000
anchor 11 has not run the minimum number of steps 0 of 100000
anchor 12 has not run the minimum number of steps 0 of 100000
running anchor_index: 0 restart: False total_simulation_length: 100000 num_transitions: 0
Traceback (most recent call last):
File "run.py", line 872, in
run(model, instruction, min_total_simulation_length,
File "run.py", line 605, in run
run_openmm(model, anchor_index, restart,
File "run.py", line 484, in run_openmm
sim_openmm_obj = mmvt_sim_openmm.create_sim_openmm(
File "/home/g035896/Software/anaconda3/envs/seekr2/lib/python3.8/site-packages/seekr2-0+untagged.130.gc6773e3.dirty-py3.8.egg/seekr2/modules/mmvt_sim_openmm.py", line 168, in create_sim_openmm
add_simulation(sim_openmm, model, topology, positions, box_vectors)
File "/home/g035896/Software/anaconda3/envs/seekr2/lib/python3.8/site-packages/seekr2-0+untagged.130.gc6773e3.dirty-py3.8.egg/seekr2/modules/mmvt_sim_openmm.py", line 101, in add_simulation
sim_openmm.simulation = openmm_app.Simulation(
File "/home/g035896/Software/anaconda3/envs/seekr2/lib/python3.8/site-packages/simtk/openmm/app/simulation.py", line 105, in init
self.context = mm.Context(self.system, self.integrator, platform, platformProperties)
File "/home/g035896/Software/anaconda3/envs/seekr2/lib/python3.8/site-packages/simtk/openmm/openmm.py", line 13232, in init
_openmm.Context_swiginit(self, _openmm.new_Context(*args))
simtk.openmm.OpenMMException: Specified a Platform for a Context which does not support all required kernels

############################

I installed openmm (7.5.1) by 'conda install -c conda-forge openmm' in a clean conda-environment with python 3.8.10. I tested my seekr2 install and it passed all the tests (except for the NAMD-test because I didn't exported the path to the binary). I also tested my OpenMM installation and environment by running a simulation using the same environment and observe no issues there. I used the simulateAmber.py file from the example-folder in the OpenMM installation.

I also tested the 'sample_input_mmvt_namd.xml' file with my installation. After exporting the path to the namd-executable, I can run 'python run.py any /path/to/model.xml' flawlessly.

+-----------------------------------------------------------------------------+
| Processes: |
| GPU GI CI PID Type Process name GPU Memory |
| ID ID Usage |
|=============================================================================|
| No running processes found |
+-----------------------------------------------------------------------------+

Do you have any idea what is causing this issue?

Thank you in advance and best regards
Jens Wilbert

Convergence Check

Dear SEEKR2 team,

I recently ran some SEEKR2 simulations of a protein looking at Ca binding to different EF hands. I came across a few issues when it comes to analyzing the results. They are described below and your help will be very much appreciated.

For one of the EF hand simulations, after running converge.py, koff did not converge well, meaning it fluctuates across several orders of magnitude. Meanwhile, it did not return any output for the kon statictics. Running analyze.py returned this error "All post-simulation checks passed.
Printing results from MMVT SEEKR calculation
k_off (1/s): (5.8 ± 23.0) * 10^-22
k_ons :
k_on (1/s * 1/M) to state 0 : (0.0 ± 0.0) * 10^+00
Traceback (most recent call last):
File "/home/xfang2/Apps/seekr2/seekr2/analyze.py", line 763, in
analysis.print_results()
File "/home/xfang2/Apps/seekr2/seekr2/analyze.py", line 602, in print_results
delta_G_err = diss_constant_err*common_analyze.GAS_CONSTANT
TypeError: unsupported operand type(s) for *: 'NoneType' and 'float'
"
For another EF hand simulations, after running convergy.py, koff did not converge well either. Meanwhile kon showed nice convergence.
For the SMD simulations, it seems that it did not provide directional bias. Therefore, one thing I noticed is that while Ca was pulled away from the binding site, Ca actually moved closer to other parts of the protein.

So I was wondering:

For the koff convergence issue, does it suggest longer simulation of the MD stage is needed?
For the kon issue, what would be an appropriate way to fix it?
After running analyze.py, several images were generated. For 'pi_alpha.png', 'p_i.png', and images under dirs 'N_ij' and 'R_i', I tried to look for descriptions on the website and the paper but no luck on that. Could you provide some explanations or sources to read up on them?
Regarding the SMD simulations, would it matter if the ligand is interacting with other parts of the protein even though it is away from the binding site? If so, is there a way to perform more sophisticated SMD simulations to a certain direction?

Thanks!
Xuan

AttributeError running Browndye2

Hi Lane,
I have a weird issue running the browndye simulations in seekr2.

#Using this command:
python /path/to /seekr2/run.py any_bd model.xml

#I observe the following error:
Traceback (most recent call last):
File "/home/g035896/Software/seekr2-conda/seekr2/run.py", line 877, in
run(model, instruction, min_total_simulation_length,
File "/home/g035896/Software/seekr2-conda/seekr2/run.py", line 652, in run
bd_milestone_info_to_run = choose_next_simulation_browndye2(
File "/home/g035896/Software/seekr2-conda/seekr2/run.py", line 62, in choose_next_simulation_browndye2
bd_transition_counts = data_sample.bd_transition_counts
AttributeError: 'NoneType' object has no attribute 'bd_transition_counts'

In order to identify the issue, I added the following lines to run.py which print data_sample_list and model():
print(*data_sample_list)
print(model)

#In the output:
None None None None None None None None None None None None None None None None None None None None None None None None None None None None None None None None None None None None None None None None None None None None None None None None None None None None None None None None None None None None None None None None None None None None None None None None None None None None None None None None None None None None None None None None None None None None None None None None None None None None
<seekr2.modules.common_base.Model object at 0x1552d10e23d0>

For me it seams as if the contents of the model file are not picked up by seekr2 but I don*t fully understand how this is done in the code.

I observed this issue with all of my prepared inputs but also once running tutorial files. I also have this behavior if I run on one node with 1 or multiple threads or if I use multiple nodes.

Do you have any idea what is wrong or what I could test to identify the issue?

Best regards
Jens

presimulation check failures and Model Input File

Hi SEEKR2 team,
For the trypsin-benzamidine tutorial, I reached the stage of creating a "Model Input File" to run the "prepare.py, run.py, converge.py and analyze.py" scripts.
I've copied the input_tryp_ben_mmvt.xml file from seekr2/seekr2/data/trypsin_benzamidine_files.
Then, I gave the full path for all the anchor pdb files (smd_atXXX.pdb) in this xml file?
Then I reorder the numbers given in anchor-radius to match the smd file names. This did not give any error, thus I'm assuming this is correct, is it? PDB files created during all earlier steps are shown below.

in the input preparation step, I forgot to mention that antechamber failed with benzamidine pdb file and I added the missing polar hydrogen using GaussView5 to make benzamidiine +vely charged after which it ran correctly. Thus you may want to check the structure available on the tutorial (or pdb website) page and its behavior during parameter generation.

Please let me know if this step is likely to be the cause of errors in the presimulation checks.
If that is the case, then I will have to restart from the first step of the tutorial, right?
I am unable to attached sample files that I'm using here.
I can send them over the email in case it is required to do some checking at your end.
Please let me know if it is ok to simply use the "-s" flag to skip these check (I think it might not be a good idea).
Looking forward to your valuable suggestions.
Thank you and best regards, Vaibhav

(SEEKR) [exx@c107739 trypsin-benzamidine]$ ls -arlth *.pdb
-rw-rw-r--. 1 exx exx 250K Sep 4 16:07 3ptb_processed.pdb
-rw-rw-r--. 1 exx exx 711 Sep 4 18:00 BEN.pdb
-rw-rw-r--. 1 exx exx 1.9K Sep 4 18:13 BEN-H.pdb
-rw-rw-r--. 1 exx exx 1.9K Sep 4 18:14 BEN-H1.pdb
-rw-rw-r--. 1 exx exx 1.4K Sep 4 18:15 sqm.pdb
-rw-rw-r--. 1 exx exx 1.6K Sep 4 19:43 tryp_ben_ligand_one_resid_nonprot.pdb
-rw-rw-r--. 1 exx exx 243M Sep 5 02:38 equilibration_trajectory.pdb
-rw-rw-r--. 1 exx exx 1.8M Sep 8 12:12 tryp_ben.pdb
-rw-rw-r--. 1 exx exx 1.8M Sep 8 12:13 equilibrated.pdb
-rw-rw-r--. 1 exx exx 1.8M Sep 8 12:45 smd_at0.15.pdb
-rw-rw-r--. 1 exx exx 1.8M Sep 8 13:08 smd_at0.25.pdb
-rw-rw-r--. 1 exx exx 1.8M Sep 8 13:26 smd_at0.35.pdb
-rw-rw-r--. 1 exx exx 1.8M Sep 8 13:53 smd_at0.45.pdb
-rw-rw-r--. 1 exx exx 1.8M Sep 8 14:57 smd_at0.75.pdb
-rw-rw-r--. 1 exx exx 1.8M Sep 8 15:20 smd_at0.85.pdb
-rw-rw-r--. 1 exx exx 1.8M Sep 8 16:28 smd_at1.15.pdb
-rw-rw-r--. 1 exx exx 1.8M Sep 8 16:55 smd_at1.25.pdb
-rw-rw-r--. 1 exx exx 1.8M Sep 8 18:03 smd_at1.55.pdb
-rw-rw-r--. 1 exx exx 1.8M Sep 8 18:21 smd_at1.65.pdb
-rw-rw-r--. 1 exx exx 1.8M Sep 8 19:34 smd_at1.95.pdb
-rw-rw-r--. 1 exx exx 173M Sep 8 19:34 smd_trajectory.pdb

(SEEKR) [exx@c107739 trypsin-benzamidine]$ python3.8 /home/exx/Downloads/seekr2/seekr2/prepare.py input_tryp_ben_mmvt.xml
Vpmg_ctor2:
Warning: External energies are not used in BCFL_MAP calculations!
Vpmg_ctor2:
Warning: External energies are not used in BCFL_MAP calculations!
CHECK FAILURE: BD simulation has significantly different
ionic strength of 0.120 Me^2 than MD simulation ionic strength of
0.061 Me^2 for anchor 0. Please check the ion concentrations in the
BD simulation settings, and also count the number of ions
in the MD simulations. Counterions added to neutralize the protein in an
MD simulation may also trigger this failure. If that is the case, simply
skip this check.
One or more fatal pre-simulation checks failed. It is highly recommended that you address and correct each of these problems. However, you can force SEEKR to skip these checks by using the --skip_checks (-s) argument on prepare.py.
Traceback (most recent call last):
File "/home/exx/Downloads/seekr2/seekr2/prepare.py", line 86, in
check.check_pre_simulation_all(model)
File "/home/exx/anaconda3/envs/SEEKR/lib/python3.8/site-packages/seekr2-0+untagged.144.ge74fc0f-py3.8.egg/seekr2/modules/check.py", line 749, in check_pre_simulation_all
raise Exception("The SEEKR2 calculation can not proceed due "
Exception: The SEEKR2 calculation can not proceed due to failed pre-simulation checks.
(SEEKR) [exx@c107739 trypsin-benzamidine]$

simtk.openmm.OpenMMException: Error loading CUDA module: CUDA_ERROR_INVALID_PTX (218)

Dear Lane and SEEKR2 team,
After successful installation, I'm tried running the examples given on this github page, but I'm getting the subject error in the run.py step (details below).
This problem seems to be similar to one reported on the openmm issue page, but not being an expert I thought it's better to take your advice before trying to upgrade anything in CUDA installation.
This cuda version is working well with Amber18.
Can you please have a look and let me know how to try and fix this problem and proceed further?
Looking forward to hearing from you and the team.
thank you and best regards.
Dr Vaibhav A. Dixit, Asst. Prof., BITS Pilani, Pilani, India.

relevant openmm issue page

openmm/openmm#2251

(SEEKR) [exx@c107739 seekr2]$ which nvcc
/usr/local/cuda/bin/nvcc
(SEEKR) [exx@c107739 seekr2]$ nvcc --version
nvcc: NVIDIA (R) Cuda compiler driver
Copyright (c) 2005-2019 NVIDIA Corporation
Built on Sun_Jul_28_19:07:16_PDT_2019
Cuda compilation tools, release 10.1, V10.1.243
(SEEKR) [exx@c107739 seekr2]$

(SEEKR) [exx@c107739 seekr2]$ python3.8 run.py any ~/test_mmvt_openmm/model.xml
anchor 0 has not run the minimum number of steps 0 of 100000
anchor 1 has not run the minimum number of steps 0 of 100000
anchor 2 has not run the minimum number of steps 0 of 100000
anchor 3 has not run the minimum number of steps 0 of 100000
anchor 4 has not run the minimum number of steps 0 of 100000
anchor 5 has not run the minimum number of steps 0 of 100000
anchor 6 has not run the minimum number of steps 0 of 100000
anchor 7 has not run the minimum number of steps 0 of 100000
anchor 8 has not run the minimum number of steps 0 of 100000
anchor 9 has not run the minimum number of steps 0 of 100000
anchor 10 has not run the minimum number of steps 0 of 100000
anchor 11 has not run the minimum number of steps 0 of 100000
anchor 12 has not run the minimum number of steps 0 of 100000
running anchor_index: 0 restart: False total_simulation_length: 100000 num_transitions: 0
Traceback (most recent call last):
File "run.py", line 742, in
run(model, instruction, min_total_simulation_length,
File "run.py", line 515, in run
run_openmm(model, anchor_index, restart,
File "run.py", line 404, in run_openmm
sim_openmm_obj = mmvt_sim_openmm.create_sim_openmm(
File "/home/exx/anaconda3/envs/SEEKR/lib/python3.8/site-packages/seekr2-0+untagged.144.ge74fc0f-py3.8.egg/seekr2/modules/mmvt_sim_openmm.py", line 168, in create_sim_openmm
add_simulation(sim_openmm, model, topology, positions, box_vectors)
File "/home/exx/anaconda3/envs/SEEKR/lib/python3.8/site-packages/seekr2-0+untagged.144.ge74fc0f-py3.8.egg/seekr2/modules/mmvt_sim_openmm.py", line 101, in add_simulation
sim_openmm.simulation = openmm_app.Simulation(
File "/home/exx/anaconda3/envs/SEEKR/lib/python3.8/site-packages/simtk/openmm/app/simulation.py", line 105, in init
self.context = mm.Context(self.system, self.integrator, platform, platformProperties)
File "/home/exx/anaconda3/envs/SEEKR/lib/python3.8/site-packages/simtk/openmm/openmm.py", line 13232, in init
_openmm.Context_swiginit(self, _openmm.new_Context(*args))
simtk.openmm.OpenMMException: Error loading CUDA module: CUDA_ERROR_INVALID_PTX (218)
(SEEKR) [exx@c107739 seekr2]$

seekr2 testing error on HPC

Dear Lane,
I'm now trying to install seekr2 on an HPC system and I followed the recommended procedure to create an environment, then install seekr2_openmm_plugin using python3.8.
The installation step went well, but in the testing phase, I'm getting the following error.
Where can I get the seekr2plugin? I couldn't find a page, conda or git command for the same.
Please suggest how to fix this.
Thank you and best regards.

(myseekr2) [root@node1 software]# cd seekr2
(myseekr2) [root@node1 seekr2]# python setup.py test
/home/software/miniconda3/envs/myseekr2/lib/python3.8/site-packages/setuptools/installer.py:27: SetuptoolsDeprecationWarning: setuptools.installer is deprecated. Requirements should be satisfied by a PEP 517 installer.
warnings.warn(
running pytest
running egg_info
writing seekr2.egg-info/PKG-INFO
writing dependency_links to seekr2.egg-info/dependency_links.txt
writing requirements to seekr2.egg-info/requires.txt
writing top-level names to seekr2.egg-info/top_level.txt
reading manifest file 'seekr2.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no previously-included files matching 'pycache' found anywhere in distribution
warning: no previously-included files matching '*.so' found anywhere in distribution
adding license file 'LICENSE'
writing manifest file 'seekr2.egg-info/SOURCES.txt'
running build_ext
=========================================================== test session starts ============================================================
platform linux -- Python 3.8.13, pytest-7.1.2, pluggy-1.0.0
rootdir: /home/software/seekr2
collecting ... Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
collected 0 items / 1 error

================================================================== ERRORS ==================================================================
______________________________________________________ ERROR collecting test session _______________________________________________________
../miniconda3/envs/myseekr2/lib/python3.8/importlib/init.py:127: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
:1014: in _gcd_import
???
:991: in _find_and_load
???
:975: in _find_and_load_unlocked
???
:671: in _load_unlocked
???
../miniconda3/envs/myseekr2/lib/python3.8/site-packages/pytest-7.1.2-py3.8.egg/_pytest/assertion/rewrite.py:168: in exec_module
exec(co, module.dict)
seekr2/tests/conftest.py:13: in
import seekr2.prepare as prepare
seekr2/prepare.py:15: in
import seekr2.modules.check as check
seekr2/modules/check.py:59: in
import seekr2.modules.mmvt_sim_openmm as mmvt_sim_openmm
seekr2/modules/mmvt_sim_openmm.py:18: in
import seekr2plugin
E ModuleNotFoundError: No module named 'seekr2plugin'
========================================================= short test summary info ==========================================================
ERROR - ModuleNotFoundError: No module named 'seekr2plugin'
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Interrupted: 1 error during collection !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
============================================================= 1 error in 0.94s =============================================================

error in SMD step trypsin-benzamidine tutorial

Dear SEEKR team,
I started to reproduce the tutorial given here, which ran well till the equilibration step.
But I got the following error in the SMD calculation which looks like something wrong in the setup of SMD in opemm (I maybe wrong).
Can you please suggest to me how to approach this error to find a solution?
I'm an intermediate level expert in Amber, but never used openmm as standalone MD package, thus not sure what to try to fix this.
Looking forward to your valuable suggestions.
thanks and best regards. Vaibhav

(SEEKR) [exx@c107739 trypsin-benzamidine]$ python3.8 tryp_ben_smd.py > smd.log &
[1] 6806
(SEEKR) [exx@c107739 trypsin-benzamidine]$
(SEEKR) [exx@c107739 trypsin-benzamidine]$ Traceback (most recent call last):
File "tryp_ben_smd.py", line 164, in
distance, positions = run_window(window_radius, state_filename, i)
File "tryp_ben_smd.py", line 129, in run_window
simulation.step(steps_per_window)
File "/home/exx/anaconda3/envs/SEEKR/lib/python3.8/site-packages/simtk/openmm/app/simulation.py", line 132, in step
self._simulate(endStep=self.currentStep+steps)
File "/home/exx/anaconda3/envs/SEEKR/lib/python3.8/site-packages/simtk/openmm/app/simulation.py", line 197, in _simulate
self.integrator.step(10) # Only take 10 steps at a time, to give Python more chances to respond to a control-c.
File "/home/exx/anaconda3/envs/SEEKR/lib/python3.8/site-packages/simtk/openmm/openmm.py", line 15833, in step
return _openmm.LangevinIntegrator_step(self, steps)
simtk.openmm.OpenMMException: Particle coordinate is nan

[1]+ Exit 1 python3.8 tryp_ben_smd.py > smd.log
(SEEKR) [exx@c107739 trypsin-benzamidine]$ tail smd.log
start_radius: 0.03647575518727076
simulating steered MD in windows from 0.03647575518727076 to 2.05 in increments of 0.02013524244812729
running window: 0.03647575518727076
(SEEKR) [exx@c107739 trypsin-benzamidine]$

errors in seekr2 test

Dear Seekr2 team,
I finally got access to a GPU in my new location and tried to install seekr2, but I'm getting the following failed, error and warning messages in the testing phase. The installation seems to have been completed without a noticeable error or major warnning.

It seems like some input files were not found in the expected location.
Please point me to a location where these might be available so that I can copy and try to rerun these tests.
Since it has been almost a year since I last tried seekr2, I may have forgotten something that you told me earlier.

Please have a look and suggest if I can proceed with the trypsin-benzamidine tutorial?
Thank you and best regards,
Vaibhav

seekr2/tests/test_run.py::test_run_planar
/home/niperg/Downloads/seekr2/seekr2/modules/check.py:239: UserWarning: Empty mmvt trajectories were found in anchor: 1.
warnings.warn("Empty mmvt trajectories were found in "\

-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
===================================================================================== short test summary info =====================================================================================
FAILED seekr2/tests/test_common_analyze.py::test_browndye_run_compute_rate_constant - subprocess.CalledProcessError: Command 'compute_rate_constant < /home/niperg/Downloads/seekr2/seekr2/tests...
FAILED seekr2/tests/test_common_prepare.py::test_move_add_delete_input_anchors - AssertionError: Problem running make_apbs_input - APBS input files not found: receptor*.in
FAILED seekr2/tests/test_common_prepare.py::test_modify_model - AssertionError: Problem running make_apbs_input - APBS input files not found: receptor*.in
FAILED seekr2/tests/test_common_sim_browndye2.py::test_make_and_run_apbs - AssertionError: Problem running make_apbs_input - APBS input files not found: receptor*.in
FAILED seekr2/tests/test_run.py::test_choose_next_simulation_namd - AssertionError: Problem occurred running namd: results file(s) was not generated.
FAILED seekr2/tests/test_run.py::test_normal_run_namd - AssertionError: Problem occurred running namd: results file(s) was not generated.
FAILED seekr2/tests/test_run.py::test_normal_restart_namd - AssertionError: Problem occurred running namd: results file(s) was not generated.
FAILED seekr2/tests/test_runner_namd.py::test_cleanse_anchor_outputs - AssertionError: Problem occurred running namd: results file(s) was not generated.
ERROR seekr2/tests/test_common_analyze.py::test_Data_sample_parse_browndye_results - AssertionError: Problem running make_apbs_input - APBS input files not found: receptor*.in
ERROR seekr2/tests/test_common_base.py::test_model_get_type - AssertionError: Problem running make_apbs_input - APBS input files not found: receptor*.in
ERROR seekr2/tests/test_common_base.py::test_model_get_timestep - AssertionError: Problem running make_apbs_input - APBS input files not found: receptor*.in
ERROR seekr2/tests/test_common_converge.py::test_analyze_bd_only - AssertionError: Problem running make_apbs_input - APBS input files not found: receptor*.in
ERROR seekr2/tests/test_common_cv.py::test_assign_state_points_hostguest - AssertionError: Problem running make_apbs_input - APBS input files not found: receptor*.in
ERROR seekr2/tests/test_common_sim_openmm.py::test_create_openmm_system - AssertionError: Problem running make_apbs_input - APBS input files not found: receptor*.in
ERROR seekr2/tests/test_common_sim_openmm.py::test_add_platform_cuda - AssertionError: Problem running make_apbs_input - APBS input files not found: receptor*.in
ERROR seekr2/tests/test_converge.py::test_converge_default_bd_only_mmvt - AssertionError: Problem running make_apbs_input - APBS input files not found: receptor*.in
ERROR seekr2/tests/test_converge.py::test_converge_default_bd_only_elber - AssertionError: Problem running make_apbs_input - APBS input files not found: receptor*.in
ERROR seekr2/tests/test_elber_base.py::test_create_elber_model - AssertionError: Problem running make_apbs_input - APBS input files not found: receptor*.in
ERROR seekr2/tests/test_elber_sim_openmm.py::test_elber_sim_openmm_amber - AssertionError: Problem running make_apbs_input - APBS input files not found: receptor*.in
ERROR seekr2/tests/test_mmvt_base.py::test_MMVT_anchor_id_from_alias - AssertionError: Problem running make_apbs_input - APBS input files not found: receptor*.in
ERROR seekr2/tests/test_mmvt_base.py::test_MMVT_anchor_alias_from_id - AssertionError: Problem running make_apbs_input - APBS input files not found: receptor*.in
ERROR seekr2/tests/test_mmvt_base.py::test_MMVT_anchor_alias_from_neighbor_id - AssertionError: Problem running make_apbs_input - APBS input files not found: receptor*.in
ERROR seekr2/tests/test_mmvt_base.py::test_MMVT_anchor_get_ids - AssertionError: Problem running make_apbs_input - APBS input files not found: receptor*.in
ERROR seekr2/tests/test_mmvt_base.py::test_check_openmm_context_within_boundary - AssertionError: Problem running make_apbs_input - APBS input files not found: receptor*.in
ERROR seekr2/tests/test_mmvt_sim_openmm.py::test_mmvt_sim_openmm_amber - AssertionError: Problem running make_apbs_input - APBS input files not found: receptor*.in
ERROR seekr2/tests/test_mmvt_sim_openmm.py::test_check_if_state_in_anchor - AssertionError: Problem running make_apbs_input - APBS input files not found: receptor*.in
ERROR seekr2/tests/test_run.py::test_choose_next_simulation_browndye2 - AssertionError: Problem running make_apbs_input - APBS input files not found: receptor*.in
ERROR seekr2/tests/test_runner_browndye2.py::test_make_browndye_input_xml - AssertionError: Problem running make_apbs_input - APBS input files not found: receptor*.in
ERROR seekr2/tests/test_runner_browndye2.py::test_make_browndye_reaction_xml - AssertionError: Problem running make_apbs_input - APBS input files not found: receptor*.in
ERROR seekr2/tests/test_runner_browndye2.py::test_modify_variables - AssertionError: Problem running make_apbs_input - APBS input files not found: receptor*.in
ERROR seekr2/tests/test_runner_browndye2.py::test_runner_browndye2_b_surface_mmvt - AssertionError: Problem running make_apbs_input - APBS input files not found: receptor*.in
ERROR seekr2/tests/test_runner_browndye2.py::test_runner_browndye2_b_surface_elber - AssertionError: Problem running make_apbs_input - APBS input files not found: receptor*.in
ERROR seekr2/tests/test_runner_namd.py::test_search_for_state_to_load - AssertionError: Problem running make_apbs_input - APBS input files not found: receptor*.in
ERROR seekr2/tests/test_runner_namd.py::test_Runner_namd_default - AssertionError: Problem running make_apbs_input - APBS input files not found: receptor*.in
ERROR seekr2/tests/test_runner_namd.py::test_Runner_namd_load_state - AssertionError: Problem running make_apbs_input - APBS input files not found: receptor*.in
ERROR seekr2/tests/test_runner_namd.py::test_Runner_namd_save_states - AssertionError: Problem running make_apbs_input - APBS input files not found: receptor*.in
ERROR seekr2/tests/test_runner_namd.py::test_Runner_namd_save_states_until_all_bounds - AssertionError: Problem running make_apbs_input - APBS input files not found: receptor*.in
ERROR seekr2/tests/test_runner_openmm.py::test_saveCheckpoint - AssertionError: Problem running make_apbs_input - APBS input files not found: receptor*.in
ERROR seekr2/tests/test_runner_openmm.py::test_Runner_openmm_default - AssertionError: Problem running make_apbs_input - APBS input files not found: receptor*.in
ERROR seekr2/tests/test_runner_openmm.py::test_Runner_openmm_default_cuda - AssertionError: Problem running make_apbs_input - APBS input files not found: receptor*.in
ERROR seekr2/tests/test_runner_openmm.py::test_Runner_openmm_load_state - AssertionError: Problem running make_apbs_input - APBS input files not found: receptor*.in
ERROR seekr2/tests/test_runner_openmm.py::test_runner_openmm_elber - AssertionError: Problem running make_apbs_input - APBS input files not found: receptor*.in
ERROR seekr2/tests/test_runner_openmm.py::test_runner_openmm_save_states - AssertionError: Problem running make_apbs_input - APBS input files not found: receptor*.in
ERROR seekr2/tests/test_runner_openmm.py::test_runner_openmm_save_states_until_all_bounds - AssertionError: Problem running make_apbs_input - APBS input files not found: receptor*.in
ERROR seekr2/tests/test_runner_openmm.py::test_mmvt_swarm - AssertionError: Problem running make_apbs_input - APBS input files not found: receptor*.in
========================================================== 8 failed, 117 passed, 4 skipped, 18 warnings, 37 errors in 441.12s (0:07:21) ===========================================================
(base) [niperg@kaberi seekr2]$

Importance of Target vulnerability for binding kinetics

Dear Seekr2 team,
I have a pharmacology and drug discovery-oriented question regarding binding kinetics.
I hope this is appropriate for this forum because I'm guessing that the developers are working on similar projects and would have made decisions on similar lines.

So here is the question.
I've learned from some literature that the importance of kinetic selectivity in drug discovery also depends on the target vulnerability (Peter Tonge ACS Chem. Neurosci.2018, 9, 29−39., DOI:10.1021/acschemneuro.7b00185).
In short, for targets that have a low vulnerability (high turnover or other means), kinetic selectivity is less likely to be of major importance in drug design and candidate selection. Only for high vulnerability targets, kinetic selectivity would play a role in drug efficacy, and thus using seerk2-like methods for estimation of kon, koff and kinetic Kd makes sense.

Especially, I want to understand if it would make sense to run complicated SEEKR2 calculations in the absence of information on target vulnerability. Because for a given target if only the thermodynamic selectivity plays a role in drug efficacy then binding kinetics assessment is not expected to correlate with selectivity and efficacy (even if predictions agree with measurements of kon/koff from SPR experiments or other methods).

Thus I'm curious to know if you are considering these aspects while you are making predictions on kon/koff for different targets of interest.
Looking forward to valuable suggestions and comments from this group.
Thank you and best regards.
Dr. Vaibhav A. Dixit

How to use multiple GPU ?

Hello Mr. Lane Janvi here,
I wanted to use multiple GPU Card for running my command instead of using "any".
According to your previous comments on following issue "BD or MD first with run.py any #21"

I tried using
" python /home/software/seekr2/seekr2/run.py 0 model.xml -f -c 0 &
python /home/software/seekr2/seekr2/run.py 1 model.xml -f -c 1 &
python /home/software/seekr2/seekr2/run.py 2 model.xml -f -c 2 &
python /home/software/seekr2/seekr2/run.py 3 model.xml -f -c 3 &
wait"

but it didn't work, also I used following command , I am getting empty out file and error files.

" python "/home/software/seekr2new/seekr2/seekr2/run.py" any "/home/msmeity/JANVI/SEEKR/tryp_ben_hidr_tutorial3/model.xml" -f -c '1,2' & ".
error file is empty here as well.

can you please suggest ?

Non-Uniform Discretization

Dear SEEKR2 team,

Recently I ran into an issue when using SEEKR2 to simulate Ca binding to a EF-hand protein with 0.5 A increment between anchors. After running the simulations of each anchor, I got this error message when trying to analyze the results: "seekr2.modules.common_analyze.MissingStatisticsError: Anchor(s) [0, 2, 5] are missing sufficient statistics. Consider running simulations of anchor(s) [0, 2] for longer time scales or readjust anchor locations to make transitions more frequent."

I thought this was because of lack of smooth transition as suggested by the message. So I used small increments (0.25 A) in distance for the problematic anchors 2 (i.e. I added two anchors between anchor 0 and 3). I then concatenated these new simulations with the original ones and modified the model.xml for analysis. However, this gave the error "seekr2.modules.common_analyze.MissingStatisticsError: Anchor(s) [0, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17] are missing sufficient statistics.". Is this because I have different distance spaces between anchors? If so, is there ia way to run non-uniform discretization for cases like this?

Thanks!

Xuan

converge step failure

Hi Lane,
On the in-house HPC (A100), the MD part of the simulation is over and took 2 days less than the single A4000 card.
Now I just ran the converge step. I got the following output from this step.
There is convergence failure in 3 steps.
Is it recommended to rerun these anchors with a higher number of steps and/or some other modifications in the input before proceeding to the analysis step?
Please suggest. thank you

On the tutorial website, I think you have removed this step.
Thus curious to know your opinion about this step.

https://seekr2.readthedocs.io/en/latest/running_calculations.html

(base) [vaibhav@param_embryo seekr2-tutorial]$ cat job.156.out
All available options for --k_on_state include: [0]
No BD milestone has been provided for k_on_state. The BD milestone 0 has been chosen by default.
Processing interval 0 of 100
Processing interval 10 of 100
Processing interval 20 of 100
Processing interval 30 of 100
Processing interval 40 of 100
Processing interval 50 of 100
Processing interval 60 of 100
Processing interval 70 of 100
Processing interval 80 of 100
Processing interval 90 of 100
All plots have been saved to: /home/vaibhav/seekr2-tutorial/images_and_plots/
Molecular dynamics results:

Anchor 0:
Milestone transitions: 0->0 : 580072,
Milestone avg. transition time (ps): 0 : 0.431,
Convergence value: 8.6777e-02.
Converged? True
Anchor 1:
Milestone transitions: 0->1 : 76, 1->0 : 77,
Milestone avg. transition time (ps): 0 : 3126.789, 1 : 16.014,
Convergence value: 9.9907e-02.
Converged? False
Anchor 2:
Milestone transitions: 1->2 : 3487, 2->1 : 3487,
Milestone avg. transition time (ps): 1 : 59.639, 2 : 12.046,
Convergence value: 4.4408e-02.
Converged? True
Anchor 3:
Milestone transitions: 2->3 : 5877, 3->2 : 5877,
Milestone avg. transition time (ps): 2 : 33.158, 3 : 9.358,
Convergence value: 1.0377e-01.
Converged? False
Anchor 4:
Milestone transitions: 3->4 : 127, 4->3 : 127,
Milestone avg. transition time (ps): 3 : 1279.104, 4 : 563.341,
Convergence value: 7.3745e-02.
Converged? True
Anchor 5:
Milestone transitions: 4->5 : 936, 5->4 : 937,
Milestone avg. transition time (ps): 4 : 167.988, 5 : 98.718,
Convergence value: 2.3719e-02.
Converged? True
Anchor 6:
Milestone transitions: 5->6 : 622, 6->5 : 623,
Milestone avg. transition time (ps): 5 : 87.694, 6 : 313.408,
Convergence value: 8.0206e-02.
Converged? True
Anchor 7:
Milestone transitions: 6->7 : 1188, 7->6 : 1187,
Milestone avg. transition time (ps): 6 : 102.850, 7 : 107.059,
Convergence value: 7.5754e-02.
Converged? True
Anchor 8:
Milestone transitions: 7->8 : 395, 8->7 : 395,
Milestone avg. transition time (ps): 7 : 60.049, 8 : 569.117,
Convergence value: 1.0529e-01.
Converged? False
Anchor 9:
Milestone transitions: 8->9 : 1789, 9->8 : 1789,
Milestone avg. transition time (ps): 8 : 89.347, 9 : 49.790,
Convergence value: 8.6231e-02.
Converged? True
Anchor 10:
Milestone transitions: 9->10 : 2609, 10->9 : 2609,
Milestone avg. transition time (ps): 9 : 44.651, 10 : 50.262,
Convergence value: 2.2274e-02.
Converged? True
Brownian dynamics results:
b-surface reaction counts:
to milestone 10: 26946
to milestone 9: 9463
escaped: 990537
stuck: 0
total: 1000000

Regarding the external HPC, I'm struggling with OpenMM installation due to the complicated configuration required in ccmake steps which is giving errors in the make step. I'll post the details in that thread after trying to fix it myself.

Thank you and best regards.
Vaibhav

error at the convergence step

Hi,
On the A4000 workstation that I mentioned earlier, the run.py step has completed successfully.
Then I tried the converge.py step but got the following error.
I'm somewhat surprised to see this error. It did run both BD and MD parts, thus can't understand why it is giving this error now.
Can you please suggest what might be wrong here?
thank you.

(base) [xxxx@xxxx seekr2]$ python3.8 converge.py /home/niperg/tryp_ben_hidr_tutorial/model.xml
Traceback (most recent call last):
File "/home/niperg/miniconda3/lib/python3.8/site-packages/seekr2-0+untagged.226.g094afe7-py3.8.egg/seekr2/modules/elber_base.py", line 15, in
import openmm
ModuleNotFoundError: No module named 'openmm'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "converge.py", line 13, in
import seekr2.modules.common_converge as common_converge
File "/home/niperg/miniconda3/lib/python3.8/site-packages/seekr2-0+untagged.226.g094afe7-py3.8.egg/seekr2/modules/common_converge.py", line 19, in
import seekr2.analyze as analyze
File "/home/niperg/miniconda3/lib/python3.8/site-packages/seekr2-0+untagged.226.g094afe7-py3.8.egg/seekr2/analyze.py", line 21, in
import seekr2.modules.check as check
File "/home/niperg/miniconda3/lib/python3.8/site-packages/seekr2-0+untagged.226.g094afe7-py3.8.egg/seekr2/modules/check.py", line 57, in
import seekr2.modules.elber_base as elber_base
File "/home/niperg/miniconda3/lib/python3.8/site-packages/seekr2-0+untagged.226.g094afe7-py3.8.egg/seekr2/modules/elber_base.py", line 17, in
import simtk.openmm as openmm
File "/home/niperg/miniconda3/lib/python3.8/site-packages/simtk/init.py", line 1, in
import openmm
ModuleNotFoundError: No module named 'openmm'

Error running hidr.py

Hello Mr. Lane, Janvi here, Today I am performing calculations for another system. I got an error as follows , while running hidr.py script:

Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
Traceback (most recent call last):
File "/home/software/seekrtools/seekrtools/hidr/hidr.py", line 366, in
hidr(model, destination, pdb_files, dry_run, equilibration_steps,
File "/home/software/seekrtools/seekrtools/hidr/hidr.py", line 88, in hidr
hidr_base.assign_pdb_file_to_model(model, pdb_file)
File "/home/software/miniconda3/envs/myseekr2/lib/python3.8/site-packages/seekrtools-0+untagged.65.g549ac37-py3.8.egg/seekrtools/hidr/hidr_base.py", line 352, in assign_pdb_file_to_model
result = cv.check_mdtraj_within_boundary(traj, milestone.variables,
File "/home/software/miniconda3/envs/myseekr2/lib/python3.8/site-packages/seekr2-0+untagged.239.gcaa21a8-py3.8.egg/seekr2/modules/mmvt_base.py", line 365, in check_mdtraj_within_boundary
radius = self.get_mdtraj_cv_value(traj, frame_index)
File "/home/software/miniconda3/envs/myseekr2/lib/python3.8/site-packages/seekr2-0+untagged.239.gcaa21a8-py3.8.egg/seekr2/modules/mmvt_base.py", line 349, in get_mdtraj_cv_value
traj2 = traj.atom_slice(self.group2)
File "/home/software/miniconda3/envs/myseekr2/lib/python3.8/site-packages/mdtraj-1.9.7-py3.8-linux-x86_64.egg/mdtraj/core/trajectory.py", line 1821, in atom_slice
return Trajectory(xyz=xyz, topology=topology, time=time,
File "/home/software/miniconda3/envs/myseekr2/lib/python3.8/site-packages/mdtraj-1.9.7-py3.8-linux-x86_64.egg/mdtraj/core/trajectory.py", line 1226, in init
self.xyz = xyz
File "/home/software/miniconda3/envs/myseekr2/lib/python3.8/site-packages/mdtraj-1.9.7-py3.8-linux-x86_64.egg/mdtraj/core/trajectory.py", line 939, in xyz
value = ensure_type(value, np.float32, 3, 'xyz', shape=shape,
File "/home/software/miniconda3/envs/myseekr2/lib/python3.8/site-packages/mdtraj-1.9.7-py3.8-linux-x86_64.egg/mdtraj/utils/validation.py", line 148, in ensure_type
raise error
ValueError: xyz must be shape (Any, 32, 3). You supplied (1, 33, 3)

Please help me understanding what is wrong here ?

Build Seekr2 Plugin from source fails

Hi - Having issues with the SEEKR2 Plugin, after SEEKR2 install from source successfully installs.
I'm using REHL (rocky linux 8.6) distribution of linux, and have my build notes below...

For some reason, when I issue the "make" command for the plugin - the git repository seems to have the files we need, but the make file is trying to find the headers files in the wrong place?

here is a screenshot of trying to do the make command after configuring the ccmake ..

Build Notes for SEEKER and dependencies and addons

AmberTools Dependencies:

yum -y install tcsh make
gcc gcc-gfortran gcc-c++
which flex bison patch bc
libXt-devel libXext-devel
perl perl-ExtUtils-MakeMaker util-linux wget
bzip2 bzip2-devel zlib-devel tar

AmberTools Compile:

# downloaded tar to /var/AMBERTOOLS/AmberTools22.tar.bz2

tar -xvf AmberTools22.tar.bz2
cd /var/AMBERTOOLS/amber22_src/build
# edit run_cmake - INSTALL_PREFIX to be /var/AMBERTOOLS
./run_cmake
make install
source /var/AMBERTOOLS/amber22/amber.sh

Install BrownDye

dnf install make lapack

OpenMM & OpenMM Plugin Install from Source Notes:

https://github.com/seekrcentral/seekr2_openmm_plugin#readme

Install Prerequisits:

conda create --name SEEKR2 python=3.8
conda activate SEEKR2 #go into the enivronment you want this installed in
conda install numpy scipy netcdf4 mpi4py
sudo dnf -y install cmake-gui #this step used DNF instead of APT-GET (ubuntu)
conda install -c conda-forge doxygen
conda install swig
pip install --upgrade cython # needed at later step, but better to do sooner

#SOURCE BUILD for OpenMM
cd /var/OpenMM/

or we put it where utot user can edit: /home/utot/.conda/envs/SEEKR2/openmm

git clone https://github.com/openmm/openmm.git
cd openmm
mkdir build
cd build
ccmake ..

cmake options come up, press "c", then "e", then "Enter" fill in info:

CMAKE_INSTALL_PREFIX /var/OpenMM/ #or /home/utot/.conda/envs/SEEKR2/openmm

press "Enter" then save via "c", "e", then generate "g" then done

make
make install
make PythonInstall
make test

test openmm

python -m openmm.testInstallation

REQUIRED Install Plugin from Source

cd /home/utot/.conda/envs/SEEKR2/Plugin
git clone https://github.com/seekrcentral/seekr2_openmm_plugin.git
cd seekr2_openmm_plugin/seekr2plugin
mkdir build
cd build
ccmake ..

cmake options come up, press "c", then "e", then "Enter" fill in info:

CMAKE_INSTALL_PREFIX /home/utot/.conda/envs/SEEKR2/Plugin
OPENMM_DIR /home/utot/.conda/envs/SEEKR2/openmm

press "Enter" then save via "c", "e", then generate "g" then done

make

Facing problem in analyze.py step

Hello, Janvi here, I have performed seekr2 calculation and got following error at analyze step :

" The center of masses of atom group1 and atom group2 were found to be 1.0000 nm apart. This distance falls
outside of the milestone boundary at 1.0000 nm.
CHECK FAILURE: The MMVT trajectory(ies) for anchor 7 do not lie within the anchor boundaries. This could be
caused by incorrect modification of files or the model.xml file, or possibly a bug.
One or more fatal post-simulation checks failed. It is highly recommended that you address and correct each of
these problems. However, you can force SEEKR to skip these checks by using the --skip_checks (-s) argument on
analyze.py. " can you suggest ?

error setting up seekr2 calculation with Heme protein

Dear Seekr2 team,
We (myself and @pulkit2907 ) have been attempting to run seekr2 on new systems (after successful training with tutorial).
We closely followed the procedure used for trypsin-benzamidine system realizing that there ought to be major differences.

Our system is oxygen bound to Heme-Fe, but we parameterized Heme without O2 bound and separately parameterized O2 in G16-antechamber.
In the 1st prepare.py step, we defined group 1 as Heme only Hydrogen atoms and Fe (which gave an error, thus removing Fe from the list).
In group 2, only two O atoms were kept.
Now we are getting the following error. regarding failure to generate apbs receptor*.in input file.
We are unable to identify any difference between the tutorial and our input html file that might be the reason for the error (diff output below).

Thus, we're requesting you to please have a look at these and suggest how to fix the same.
thank you and best regards.
Vaibhav

[jrfnsm@param_embryo 1mbo_seekr2]$ tail job.775.err
model, xml_path = prepare(model_input, force_overwrite)
File "/home/software/seekr2/seekr2/prepare.py", line 42, in prepare
common_prepare.generate_bd_files(model, root_directory)
File "/home/software/miniconda3/envs/myseekr2/lib/python3.8/site-packages/seekr2-0+untagged.239.gcaa21a8-py3.8.egg/seekr2/modules/common_prepare.py", line 961, in generate_bd_files
runner_browndye2.make_browndye_input_xml(
File "/home/software/miniconda3/envs/myseekr2/lib/python3.8/site-packages/seekr2-0+untagged.239.gcaa21a8-py3.8.egg/seekr2/modules/runner_browndye2.py", line 175, in make_browndye_input_xml
debye_length = sim_browndye2.make_and_run_apbs(
File "/home/software/miniconda3/envs/myseekr2/lib/python3.8/site-packages/seekr2-0+untagged.239.gcaa21a8-py3.8.egg/seekr2/modules/common_sim_browndye2.py", line 975, in make_and_run_apbs
assert len(glob.glob(apbs_input_glob)), "Problem running "
AssertionError: Problem running make_apbs_input - APBS input files not found: receptor*.in

[jrfnsm@param_embryo 1mbo_seekr2]$ diff input_Mb_OXY_hidr1.xml trypsin-input.xml
8c8
< 300.0

<temperature>298.0</temperature>

11c11
< <root_directory>~/mb_oxy_hidr_tutorial/</root_directory>

<root_directory>/home/vaibhav/seekr2-tutorial</root_directory>

21,24c21,24
< [438, 442, 443, 444, 691, 1050, 1052, 1099, 1100, 1103, 1104, 1105, 1749, 1750, 1751, 2499, 2500, 2528]
< [2533, 2534]
< <bd_group1>[438, 442, 443, 444, 691, 1050, 1052, 1099, 1100, 1103, 1104, 1105, 1749, 1750, 1751, 2499, 2500, 2528]</bd_group1>
< <bd_group2>[0, 1]</bd_group2>

        <group1>[2478, 2489, 2499, 2535, 2718, 2745, 2769, 2787, 2794, 2867, 2926]</group1>
        <group2>[3221, 3222, 3223, 3224, 3225, 3226, 3227, 3228, 3229]</group2>
        <bd_group1>[2478, 2489, 2499, 2535, 2718, 2745, 2769, 2787, 2794, 2867, 2926]</bd_group1>
        <bd_group2>[0, 1, 2, 3, 4, 5, 6, 7, 8]</bd_group2>

31c31
< <prmtop_filename>1mbo_solv_oxy.prmtop</prmtop_filename>

                    <prmtop_filename>tryp_ben.prmtop</prmtop_filename>

43c43
< <prmtop_filename>1mbo_solv_oxy.prmtop</prmtop_filename>

                    <prmtop_filename>tryp_ben.prmtop</prmtop_filename>

55c55
< <prmtop_filename>1mbo_solv_oxy.prmtop</prmtop_filename>

                    <prmtop_filename>tryp_ben.prmtop</prmtop_filename>

67c67
< <prmtop_filename>1mbo_solv_oxy.prmtop</prmtop_filename>

                    <prmtop_filename>tryp_ben.prmtop</prmtop_filename>

79c79
< <prmtop_filename>1mbo_solv_oxy.prmtop</prmtop_filename>

                    <prmtop_filename>tryp_ben.prmtop</prmtop_filename>

91c91
< <prmtop_filename>1mbo_solv_oxy.prmtop</prmtop_filename>

                    <prmtop_filename>tryp_ben.prmtop</prmtop_filename>

103c103
< <prmtop_filename>1mbo_solv_oxy.prmtop</prmtop_filename>

                    <prmtop_filename>tryp_ben.prmtop</prmtop_filename>

115c115
< <prmtop_filename>1mbo_solv_oxy.prmtop</prmtop_filename>

                    <prmtop_filename>tryp_ben.prmtop</prmtop_filename>

127c127
< <prmtop_filename>1mbo_solv_oxy.prmtop</prmtop_filename>

                    <prmtop_filename>tryp_ben.prmtop</prmtop_filename>

139c139
< <prmtop_filename>1mbo_solv_oxy.prmtop</prmtop_filename>

                    <prmtop_filename>tryp_ben.prmtop</prmtop_filename>

151c151
< <prmtop_filename>1mbo_solv_oxy.prmtop</prmtop_filename>

                    <prmtop_filename>tryp_ben.prmtop</prmtop_filename>

163c163
< <prmtop_filename>1mbo_solv_oxy.prmtop</prmtop_filename>

                    <prmtop_filename>tryp_ben.prmtop</prmtop_filename>

175,176c175,176
< <receptor_pqr_filename>mb_oxy_receptor.pqr</receptor_pqr_filename>
< <ligand_pqr_filename>mb_oxy_ligand.pqr</ligand_pqr_filename>

    <receptor_pqr_filename>tryp_ben_receptor.pqr</receptor_pqr_filename>
    <ligand_pqr_filename>tryp_ben_ligand.pqr</ligand_pqr_filename>

warnings in prepare.py step

dear developers
i ran the try_benz tutorial in my workstataion. while running prepare.py the following warining came. Please suggest whether these errors can safely avoidable and does not affect the final kon, koff values to a large extent. in case of large effect please suggest the source of error and possible way to avoid these errors.
(SEEKR) cadd-sys3@caddsys3:~/Documents/seekr_tutorial$ python /home/cadd-sys3/setupfiles/seekr2/seekr2/prepare.py input_tryp_ben_hidr.xml
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
Vpmg_ctor2:
Warning: External energies are not used in BCFL_MAP calculations!

Vpmg_ctor2:
Warning: External energies are not used in BCFL_MAP calculations!
MGparm_check: you're using a very small nlev (1) and therefore
MGparm_check: will not get the optimal performance of the multigrid

thanking you in anticipation

Question/Issue: Index Error running BD-Milestone

Hi Lane,
I come across another issue running the BD-simulations in seekr2. First, I would like to ask if running the BD-milestone in seekr2 requires a converged MD-part?

Anyway, I have the following issue running the BD-milestone after the b_surface simulations are finished. I am not sure, if the lower error is independent from the MissingStatiscsError or a consequence of the "-s" option not working in this case.

Running command:
python ~/Software/seekr2/seekr2/run.py any_bd model.xml -s

Output:
Traceback (most recent call last):
File "/home/bensebaer/Software/conda/envs/SEEKR2/lib/python3.8/site-packages/seekr2-0+untagged.144.ge74fc0f.dirty-py3.8.egg/seekr2/modules/common_converge.py", line 142, in analyze_kinetics
sufficient_statistics = analysis.check_extraction()
File "/home/bensebaer/Software/conda/envs/SEEKR2/lib/python3.8/site-packages/seekr2-0+untagged.144.ge74fc0f.dirty-py3.8.egg/seekr2/analyze.py", line 301, in check_extraction
result = self.mmvt_check_anchor_stats(silent)
File "/home/bensebaer/Software/conda/envs/SEEKR2/lib/python3.8/site-packages/seekr2-0+untagged.144.ge74fc0f.dirty-py3.8.egg/seekr2/analyze.py", line 228, in mmvt_check_anchor_stats
raise common_analyze.MissingStatisticsError(
seekr2.modules.common_analyze.MissingStatisticsError: Anchor(s) [1, 3] are missing sufficient statistics. Consider running simulations of anchor(s) [1, 3] for longer time scales or readjust anchor locations to make transitions more frequent. You may skip this check with the --skip_checks (-s) option.

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/home/bensebaer/Software/seekr2/seekr2/run.py", line 742, in
run(model, instruction, min_total_simulation_length,
File "/home/bensebaer/Software/seekr2/seekr2/run.py", line 553, in run
bd_milestone_info_to_run = choose_next_simulation_browndye2(
File "/home/bensebaer/Software/seekr2/seekr2/run.py", line 50, in choose_next_simulation_browndye2
data_sample_list = converge.converge(model)
File "/home/bensebaer/Software/conda/envs/SEEKR2/lib/python3.8/site-packages/seekr2-0+untagged.144.ge74fc0f.dirty-py3.8.egg/seekr2/converge.py", line 29, in converge
= common_converge.check_milestone_convergence(
File "/home/bensebaer/Software/conda/envs/SEEKR2/lib/python3.8/site-packages/seekr2-0+untagged.144.ge74fc0f.dirty-py3.8.egg/seekr2/modules/common_converge.py", line 333, in check_milestone_convergence
k_on, k_off, N_ij, R_i = analyze_kinetics(
File "/home/bensebaer/Software/conda/envs/SEEKR2/lib/python3.8/site-packages/seekr2-0+untagged.144.ge74fc0f.dirty-py3.8.egg/seekr2/modules/common_converge.py", line 164, in analyze_kinetics
data_sample.parse_browndye_results()
File "/home/bensebaer/Software/conda/envs/SEEKR2/lib/python3.8/site-packages/seekr2-0+untagged.144.ge74fc0f.dirty-py3.8.egg/seekr2/modules/common_analyze.py", line 470, in parse_browndye_results
browndye_run_compute_rate_constant(os.path.join(
File "/home/bensebaer/Software/conda/envs/SEEKR2/lib/python3.8/site-packages/seekr2-0+untagged.144.ge74fc0f.dirty-py3.8.egg/seekr2/modules/common_analyze.py", line 241, in browndye_run_compute_rate_constant
dest = int(name[1])
IndexError: list index out of range

#I also checked the contents of name[] and apparently, name[1] is empty and name[0]=['7'].

#From the results1.xml file:

<n_trajectories> 1000000 </n_trajectories>
0
999944

7
56

Thank you very much for your help
Jens

installing seekr2 on HPC via user account

Hello Seekr2 team,
After some success with installing seekr2 locally and in-house HPC, I am looking for options with a higher GPU computing facility.
But I have only regular user account access and don't have admin privileges on such a system.

Is it possible to install seekr2 and all of its dependencies in such an environment?
And after install/testing, do I need to explicitly control the GPU nodes to which the jobs are submitted or slurm can manage it for me?
Please suggest based on your developmental and end-user experiences.
Looking forward to your valuable suggestions.
Thank you and best regards.
Vaibhav

Facing an issue in running seekr2 in the HIDR step on trypsin-benzamidine system

Hello, Janvi here.
I am a master student at National Institute of Pharmaceutical Education & Research, Guwahati India. Working under
Dr Vaibhav Dixit. I am using trypsin-benzamidine tutorials for seeker2 on HPC installation and I am able to generate the results till step of constructing the SEEKR2 Model Input File.
After generating an empty modeI I'm stuck at "Running HIDR on the new Model", job error shows

"you should atleast have OpenMM 6.3 installed ",

whereas my system is already having OpenMM 7.7 installed ,
what could be the remedy?

Please suggest so that I can move forward in the tutorial and then apply SEEKR2 methodology to my project work.
Thank you and Best regards.

error in prepare step due to ambpdb output

Dear Seekr2 team,
Just noticed that the ambpdb adds an additional line (CRYST1...) at the top of pqr files which causes the following error during the seekr2 prepare.py step (given here). After manually removing this line the calculation proceeds as expected.
Just thought to let you know in case it requires a bug fix.
Thank you

Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
Fatal error: exception Failure("wrong number of tokens at CRYST1 71.811 71.811 71.811 109.47 109.47 109.47")
terminate called after throwing an instance of 'Browndye::Jam_Exception'
what(): Parse error at line 2 : no element found in file tryp_ben_receptor.xml
sh: line 1: 1226044 Aborted (core dumped) make_apbs_inputs /home/vaibhav/tryp_ben_hidr_tutorial/b_surface/apbs_input.xml > /home/vaibhav/tryp_ben_hidr_tutorial/b_surface/input.xml
Traceback (most recent call last):
File "/home/software/seekr2/seekr2/prepare.py", line 75, in
model, xml_path = prepare(model_input, force_overwrite)
File "/home/software/seekr2/seekr2/prepare.py", line 42, in prepare
common_prepare.generate_bd_files(model, root_directory)
File "/home/software/miniconda3/envs/myseekr2/lib/python3.8/site-packages/seekr2-0+untagged.239.gcaa21a8-py3.8.egg/seekr2/modules/common_prepare.py", line 961, in generate_bd_files
runner_browndye2.make_browndye_input_xml(
File "/home/software/miniconda3/envs/myseekr2/lib/python3.8/site-packages/seekr2-0+untagged.239.gcaa21a8-py3.8.egg/seekr2/modules/runner_browndye2.py", line 175, in make_browndye_input_xml
debye_length = sim_browndye2.make_and_run_apbs(
File "/home/software/miniconda3/envs/myseekr2/lib/python3.8/site-packages/seekr2-0+untagged.239.gcaa21a8-py3.8.egg/seekr2/modules/common_sim_browndye2.py", line 975, in make_and_run_apbs
assert len(glob.glob(apbs_input_glob)), "Problem running "
AssertionError: Problem running make_apbs_input - APBS input files not found: receptor*.in

query about tutorial simulation time trypsin-benzamidine

Dear @lvotapka and SEEKR2 team,
I resubmitted the tutorial calculation with -t 500000 flag so that MD runs for only 1ns (as a test).
Now It seems like SEEKR2 has been running the BD part for ~6 hrs with n_threads=6.
Since I've limited experience in both BD and milestoning, it will be good to know how long one can expect the BD component to run.
What is the default sequence in SEEKR for the BD and MD simulations? If I understood correctly, the MD and BD runs are not explicitly dependent on each other (MD for active site and BD from protein surface to g-surface i.e. infinity).
Thus is it possible to run both simultaneously BD on CPU and MD on GPUs to save time?

For newer protein-ligand systems, in testing mode, will it make sense to reduce the MD convergence criteria and other parameters in addition to the -t flag, in order to first check whether the simulation step is ok or not?

The output of the command is below at the end.
Looking forward to your valuable suggestions and comments.
thank you and best regards, Vaibhav

PID USER PR NI VIRT RES SHR S %CPU %MEM TIME+ COMMAND
13163 exx 20 0 477940 41396 2620 S 601.0 0.1 1890:57 nam_simulation receptor_ligand_simulation.xml

(SEEKR) [exx@c107739 trypsin-benzamidine]$ python3.8 /home/exx/Downloads/seekr2/seekr2/run.py any model.xml -t 500000 > runstep-output.log &
(SEEKR) [exx@c107739 trypsin-benzamidine]$ cat runstep-output.log
command surface_spheres -probe_radius 1.5 < tryp_ben_receptor.xml > receptor_surface.xml
command inside_points -spheres tryp_ben_receptor.xml -surface receptor_surface.xml -egrid receptor1.dx > receptor_inside.xml
command hydro_params < receptor_inside.xml > receptor_hydro_params.xml
command test_charges < tryp_ben_receptor.xml > receptor_charges.xml
command lumped_charges -pts receptor_charges.xml > receptor_cheby.xml
command make_surface_sphere_list -surface receptor_surface.xml -spheres tryp_ben_receptor.xml -rxn rxns.xml -group receptor -core receptor > receptor_surface_atoms.xml
command mpole_grid_fit -dx receptor0.dx -solvdi 78 -debye 8.75563 > receptor_mpole.xml
command born_integral -in receptor_inside.xml -oeps 78 -debye 8.75563 -ieps 4.000000 > receptor_born.dx
command compute_charges_squared < receptor_charges.xml > receptor_charges_squared.xml
command lumped_charges -pts receptor_charges_squared.xml > receptor_squared_cheby.xml
command surface_spheres -probe_radius 1.5 < tryp_ben_ligand.xml > ligand_surface.xml
command inside_points -spheres tryp_ben_ligand.xml -surface ligand_surface.xml -egrid ligand2.dx > ligand_inside.xml
command hydro_params < ligand_inside.xml > ligand_hydro_params.xml
command test_charges < tryp_ben_ligand.xml > ligand_charges.xml
command lumped_charges -pts ligand_charges.xml > ligand_cheby.xml
command make_surface_sphere_list -surface ligand_surface.xml -spheres tryp_ben_ligand.xml -rxn rxns.xml -group ligand -core ligand > ligand_surface_atoms.xml
command mpole_grid_fit -dx ligand0.dx -solvdi 78 -debye 8.75563 > ligand_mpole.xml
command born_integral -in ligand_inside.xml -oeps 78 -debye 8.75563 -ieps 4.000000 > ligand_born.dx
command compute_charges_squared < ligand_charges.xml > ligand_charges_squared.xml
command lumped_charges -pts ligand_charges_squared.xml > ligand_squared_cheby.xml

error while generating trypsin-benzamidine smd input for hidr

Dear Seekr2 team,
I installed seekr2 on a new system with A4000 GPU card.
While trying the tryp-benz tutorial, I'm getting the following error.
I think I've openmm latest version installed correctly via conda, even then it is giving me the following error.
Can you please suggest how to fix the same?
thank you and best regards.
Vaibhav

(base) [niperg@kaberi tryp_ben_hidr_tutorial]$ python /home/niperg/Downloads/seekrtools-master/seekrtools/hidr/hidr.py any model.xml -M SMD -p tryp_ben.pdb
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
Assigning pdb file tryp_ben.pdb to anchor 0
The following procedure will be executed:
SMD force constant is 90000.0 kJ/(nm2 mol)
SMD from anchor 0 to anchor 1
SMD force constant is 90000.0 kJ/(nm2 mol)
SMD from anchor 1 to anchor 2
SMD force constant is 90000.0 kJ/(nm2 mol)
SMD from anchor 2 to anchor 3
SMD force constant is 90000.0 kJ/(nm2 mol)
SMD from anchor 3 to anchor 4
SMD force constant is 90000.0 kJ/(nm2 mol)
SMD from anchor 4 to anchor 5
SMD force constant is 90000.0 kJ/(nm2 mol)
SMD from anchor 5 to anchor 6
SMD force constant is 90000.0 kJ/(nm2 mol)
SMD from anchor 6 to anchor 7
SMD force constant is 90000.0 kJ/(nm2 mol)
SMD from anchor 7 to anchor 8
SMD force constant is 90000.0 kJ/(nm2 mol)
SMD from anchor 8 to anchor 9
SMD force constant is 90000.0 kJ/(nm2 mol)
SMD from anchor 9 to anchor 10
Estimated total simulation time: 165.000 ns
running SMD from anchor 0 to anchor 1
running_window: (0.00865611727496281,) steps_in_window: 706719
running_window: (0.022790505547466526,) steps_in_window: 706719
running_window: (0.036924893819970245,) steps_in_window: 706719
running_window: (0.05105928209247396,) steps_in_window: 706719
running_window: (0.06519367036497767,) steps_in_window: 706719
running_window: (0.07932805863748138,) steps_in_window: 706719
running_window: (0.0934624469099851,) steps_in_window: 706719
running_window: (0.10759683518248882,) steps_in_window: 706719
running_window: (0.12173122345499253,) steps_in_window: 706719
running_window: (0.13586561172749625,) steps_in_window: 706719
running_window: (0.14999999999999997,) steps_in_window: 706719
Benchmark: 0.0 ns/day
Traceback (most recent call last):
File "/home/niperg/Downloads/seekrtools-master/seekrtools/hidr/hidr.py", line 366, in
hidr(model, destination, pdb_files, dry_run, equilibration_steps,
File "/home/niperg/Downloads/seekrtools-master/seekrtools/hidr/hidr.py", line 190, in hidr
hidr_simulation.run_SMD_simulation(
File "/home/niperg/miniconda3/lib/python3.8/site-packages/seekrtools-0+unknown-py3.8.egg/seekrtools/hidr/hidr_simulation.py", line 534, in run_SMD_simulation
parm = parmed.openmm.load_topology(topology, system)
File "/home/software/amber22/lib/python3.9/site-packages/parmed/utils/decorators.py", line 30, in new_fcn
raise ImportError('You must have at least OpenMM 6.3 installed')
ImportError: You must have at least OpenMM 6.3 installed

unable to locate trypsin-benzamidine tutorial page

Dear Seekr2 team,
I wanted to repeat the subject tutorial using the tutorial website that I used last year.
But strangely enough, I'm unable to get to the required webpage.
thus it will be really helpful if you can share the link to this tutorial which uses AmberTools to prepare prmtop/inpcrd files.
Thanks in advance and best regards.
Vaibhav

assumptions related to milestoning size/shape interactions in MD region

Dear seekr2 team,
I'm reading the assumptions of milestoning theory here.
This paper, as expected, is a bit math/stat oriented, thus I might have misunderstood something and thus I'm requesting you to comment.

On page 4 in "A. Isocommittor surfaces as optimal milestones" section, it is mentioned that one of the main assumptions is the following.
sets of optimal milestones satisfying property (P1') and, hence, (P1), exist. Where (P1') the probability to reach first Sj from Si is the same from any starting point on Si.

My question is related to the size, the shape of the active site and associated different interactions that a ligand may encounter during its transit in/out of the binding site.

Now, considering the different size/shape of the active sites of different protein how is it possible that the above statement remains correct? I would expect that (except for small ligands like O2, NO etc) many points starting on Si would have different types of interactions and different Es between ligand and protein and thus (P1') would be different for these points. This would invalidate the assumption above.

If these arguments are correct then what care one must take while setting up the optimum milestones during seekr2 calculations for proteins with different sizes, shapes and interactions across the active site region (the MD region)? For e.g. some proteins have shallow active sites, while others have mostly buried active sites with all kinds of shapes (V, L, Y etc) and others in between these two extermes.

Looking forward to your useful comments and suggestions.
Thank you and best regards.
Vaibhav

Import Error During Installation

Hi,

I'm getting the following error while trying to import "seekr2plugin",

====================================== short test summary info ======================================
ERROR - ImportError: libOpenMM.so.7.7: cannot open shared object file: No such file or directory
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Interrupted: 1 error during collection !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
========================================= 1 error in 0.77s ==========================================

Please let me know how to get rid of this error.

Sincerely,
Sutanu

BD or MD first with run.py any

Hi,
We have started running the trypsin-benz tutorial and I've a question regarding the run.py step.
When I ran this on A4000 GPU on a workstation I'm getting the following output, but when I ran on the HPC it is running the nam_simulation (i.e. Browndyne2) first.
Thus I'm curious to know if it is possible to run the separate (BD and MD) calculations simultaneously.
Please comment on this for my better understanding.
Thank you and best regards.
Vaibhav

A4000 output
(base) [xxxx@yyyy seekr2]$ python3.8 run.py any /home/niperg/tryp_ben_hidr_tutorial/model.xml
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
anchor 0 has not run the minimum number of steps 0 of 125000000 in swarm index None
anchor 1 has not run the minimum number of steps 0 of 125000000 in swarm index None
anchor 2 has not run the minimum number of steps 0 of 125000000 in swarm index None
anchor 3 has not run the minimum number of steps 0 of 125000000 in swarm index None
anchor 4 has not run the minimum number of steps 0 of 125000000 in swarm index None
anchor 5 has not run the minimum number of steps 0 of 125000000 in swarm index None
anchor 6 has not run the minimum number of steps 0 of 125000000 in swarm index None
anchor 7 has not run the minimum number of steps 0 of 125000000 in swarm index None
anchor 8 has not run the minimum number of steps 0 of 125000000 in swarm index None
anchor 9 has not run the minimum number of steps 0 of 125000000 in swarm index None
anchor 10 has not run the minimum number of steps 0 of 125000000 in swarm index None
running anchor_index: 0 restart: False total_simulation_length: 125000000 num_transitions: 0 swarm index: None
#"Step","Potential Energy (kJ/mole)","Temperature (K)","Box Volume (nm^3)"
1250000,-250376.41525536962,296.89521240530155,177.84127115140652
2500000,-251816.960299053,300.7401145559686,177.84127115140652
3750000,-249775.08480032883,297.9072758462745,177.84127115140652
5000000,-251141.35327599244,297.6162308596486,177.84127115140652
6250000,-250886.5529175289,294.8508385438355,177.84127115140652
7500000,-251429.59675331693,297.38012520319904,177.84127115140652
8750000,-250864.39621214918,296.1578648834993,177.84127115140652
10000000,-251011.7579468072,295.76070438850223,177.84127115140652
11250000,-250754.05444069766,297.1850567116118,177.84127115140652
12500000,-250880.8638553978,295.8717125853891,177.84127115140652
13750000,-251361.46465320792,302.357790197908,177.84127115140652
15000000,-251751.39429811202,299.9408218258437,177.84127115140652
16250000,-249909.23492376693,297.9641657593563,177.84127115140652
17500000,-250831.85557753057,297.31015841402126,177.84127115140652
18750000,-250872.648794075,299.0403939308773,177.84127115140652
20000000,-251404.7889921791,297.7748683698601,177.84127115140652
21250000,-250549.96409982583,301.07466638268477,177.84127115140652
22500000,-250308.76190222194,299.49519508510076,177.84127115140652
23750000,-249980.19527490553,297.75345978110516,177.84127115140652
25000000,-250624.00605515996,302.3343559508517,177.84127115140652
26250000,-250507.18145670742,301.4777494536038,177.84127115140652
27500000,-250228.3289753215,297.5157977352142,177.84127115140652
28750000,-250618.3579239829,299.9698301611076,177.84127115140652
30000000,-251083.14304677257,298.0573303543426,177.84127115140652
31250000,-251045.4935685862,296.4738785135786,177.84127115140652
32500000,-250732.25450399006,300.618752740865,177.84127115140652
33750000,-250150.650192847,296.68024535972495,177.84127115140652
35000000,-251843.7443778594,300.2775982225485,177.84127115140652
36250000,-250836.95118905604,298.35247101304157,177.84127115140652
37500000,-250730.25663781445,297.32925657065,177.84127115140652
38750000,-250681.76350122364,297.8295673493248,177.84127115140652
40000000,-250602.82712599728,301.8936784618029,177.84127115140652
41250000,-250908.67839316884,291.74930158738516,177.84127115140652
42500000,-250592.08901361236,296.4671783286221,177.84127115140652
43750000,-250205.9630815657,299.62388927715705,177.84127115140652
45000000,-251191.23436955502,299.895703373847,177.84127115140652
46250000,-251312.6290877089,295.9285451245737,177.84127115140652
47500000,-250885.78268891945,296.78113468776826,177.84127115140652
48750000,-251039.89442682546,299.17780628575764,177.84127115140652
50000000,-250586.59940173826,293.56036419906906,177.84127115140652
51250000,-251341.73434409965,297.40858264131396,177.84127115140652
52500000,-250785.1078860676,296.41169807661623,177.84127115140652
53750000,-250548.55212000664,299.82566753647023,177.84127115140652
55000000,-251336.17954663094,297.700648296592,177.84127115140652
56250000,-251493.64182420238,297.4044061539442,177.84127115140652
57500000,-250436.24132813164,297.64335069479813,177.84127115140652
58750000,-250900.1289494743,297.87782575301594,177.84127115140652
60000000,-251365.70957936766,299.9146946657265,177.84127115140652
61250000,-251739.93011926254,298.8694927949889,177.84127115140652
62500000,-251018.5306754359,300.8728575753887,177.84127115140652
63750000,-250989.5727051692,301.2254064441114,177.84127115140652
65000000,-251151.17498785816,300.28418159681985,177.84127115140652
66250000,-250811.2604660911,297.125632003862,177.84127115140652
67500000,-250745.48249687115,301.95650385173224,177.84127115140652
68750000,-250896.07283422747,301.1085610457348,177.84127115140652
70000000,-250620.20485602436,299.3786922707276,177.84127115140652
71250000,-249668.51900003082,299.38797967742096,177.84127115140652
72500000,-250026.44720053556,296.880736328326,177.84127115140652
73750000,-251382.91487488337,293.0451477013571,177.84127115140652
75000000,-250798.74752313131,301.3031975570151,177.84127115140652
76250000,-251841.08711535623,300.24075164395157,177.84127115140652
77500000,-250607.52170097549,299.82053728140306,177.84127115140652
78750000,-251339.97406868823,300.0053381759625,177.84127115140652
80000000,-251620.8250389523,298.3618845607552,177.84127115140652
81250000,-251612.2944833946,298.2132969679813,177.84127115140652
82500000,-250558.90810871706,299.03952799174374,177.84127115140652
83750000,-250634.8499758104,300.8930652191651,177.84127115140652
85000000,-251014.51466802903,294.7870487439599,177.84127115140652
86250000,-250786.990156529,295.9250767611833,177.84127115140652
87500000,-251009.94473820366,299.3163430049137,177.84127115140652
88750000,-250342.0269576956,302.3439476150922,177.84127115140652
90000000,-250707.24345579604,294.5966184916818,177.84127115140652
91250000,-250763.4695239584,297.27304561892134,177.84127115140652
92500000,-251729.84289589804,298.48210669852375,177.84127115140652
93750000,-250918.35286462284,296.7007638691411,177.84127115140652
95000000,-251102.30022457894,296.47653030568483,177.84127115140652
96250000,-251151.94991578627,294.0330664425347,177.84127115140652
97500000,-249825.05061047943,300.7539475266632,177.84127115140652
98750000,-251913.89867717726,295.9855820395087,177.84127115140652
100000000,-250226.26716483058,297.799287179786,177.84127115140652
101250000,-249982.53791840328,298.08416196314124,177.84127115140652
102500000,-251413.05335161253,301.5823982733784,177.84127115140652
103750000,-250439.35385266365,297.79579694683963,177.84127115140652
105000000,-250791.20807962585,299.55582695186314,177.84127115140652
106250000,-250653.68977421243,297.91695645628715,177.84127115140652
107500000,-250195.73558695614,295.0807334628034,177.84127115140652
108750000,-251093.61188615602,296.53038741796996,177.84127115140652
110000000,-251480.1944490187,304.1390419674086,177.84127115140652
111250000,-250769.3652417278,294.8156741931179,177.84127115140652
112500000,-250157.7076921661,296.331567877692,177.84127115140652
113750000,-250983.5466161277,300.3119088244567,177.84127115140652
115000000,-250947.34169258294,299.686376747694,177.84127115140652
116250000,-250522.54435569188,301.2849067322041,177.84127115140652
117500000,-250931.10059117898,294.7009081382181,177.84127115140652
118750000,-250664.06582189025,303.4956653291268,177.84127115140652
120000000,-251064.59574373765,297.32083267079287,177.84127115140652
121250000,-251606.44924361142,296.75987865226944,177.84127115140652
122500000,-250993.6611946551,298.8907556879082,177.84127115140652
123750000,-250197.03636861872,295.25539555555633,177.84127115140652
125000000,-249612.35455580102,295.8961460193411,177.84127115140652
Benchmark (ns/day): 282.6259063385334
running anchor_index: 1 restart: False total_simulation_length: 125000000 num_transitions: 0 swarm index: None
#"Step","Potential Energy (kJ/mole)","Temperature (K)","Box Volume (nm^3)"
1250000,-251259.4426750599,294.6629526592754,177.84127115140652
2500000,-250765.72184476117,299.36995856663737,177.84127115140652
3750000,-250848.54080326902,296.31244688110917,177.84127115140652
5000000,-250384.19994499488,293.4496098255166,177.84127115140652
6250000,-250924.3924683323,300.2378917470994,177.84127115140652
7500000,-250770.1583597092,298.09511762078046,177.84127115140652
8750000,-251455.48746547895,297.8792693442864,177.84127115140652
10000000,-250859.59599494375,295.0429203120194,177.84127115140652
11250000,-250136.3151631034,298.3075320749688,177.84127115140652
12500000,-251009.68614812754,294.2744449183289,177.84127115140652
13750000,-250640.44650838315,296.8044192410573,177.84127115140652
15000000,-250418.59393999376,293.78215103701274,177.84127115140652
16250000,-251351.28738953965,297.4008396898686,177.84127115140652
17500000,-251294.72341999668,299.531905809816,177.84127115140652
18750000,-250463.3308101648,303.73813319121285,177.84127115140652
20000000,-250427.12095736945,297.52910853449305,177.84127115140652
21250000,-250973.74070397043,300.3789704509949,177.84127115140652
22500000,-250579.21751565533,298.7562571851669,177.84127115140652
23750000,-251432.9784859363,301.49303895725274,177.84127115140652
25000000,-251110.66937395255,301.46464267108837,177.84127115140652
26250000,-251251.63167706504,299.49951037430156,177.84127115140652
27500000,-250572.44890967244,296.89380434480745,177.84127115140652
28750000,-250140.19067218387,301.1059178934554,177.84127115140652
30000000,-251199.66560487263,294.17380927028927,177.84127115140652
31250000,-250043.40207134187,300.95852182176037,177.84127115140652
32500000,-250791.76140220044,296.47326886836913,177.84127115140652
33750000,-250442.05083427997,301.998836962379,177.84127115140652
35000000,-250590.44339945703,300.5902666019184,177.84127115140652
36250000,-251071.2009507832,300.9992785430724,177.84127115140652
37500000,-251506.3604732894,297.49571766768435,177.84127115140652
38750000,-250895.8533184596,301.5968664245832,177.84127115140652
40000000,-250883.29082193132,298.26300253227936,177.84127115140652
41250000,-251651.47171014082,307.73439340465194,177.84127115140652
42500000,-250305.12439275743,298.0143337338997,177.84127115140652
43750000,-250613.1140536156,297.4515498466713,177.84127115140652
45000000,-250868.51864006324,298.561895048489,177.84127115140652
46250000,-250564.8245985997,297.99240701222277,177.84127115140652
47500000,-251012.72356958687,300.39938744525585,177.84127115140652
48750000,-250392.43096753443,298.58242407492764,177.84127115140652
50000000,-251035.1473082339,296.14095207941426,177.84127115140652
51250000,-251227.71490027197,302.4036548209542,177.84127115140652
52500000,-250522.53721845592,296.81303077479197,177.84127115140652
53750000,-250826.29571607313,298.405325878737,177.84127115140652
55000000,-250120.66219415353,298.0081225182074,177.84127115140652
56250000,-251105.63211397594,297.82980884685645,177.84127115140652
57500000,-250323.36232781573,297.5810193031567,177.84127115140652
58750000,-250623.39771179738,297.0397373693085,177.84127115140652
60000000,-251313.26762351906,292.3351538455054,177.84127115140652
61250000,-250154.16336838342,297.08175895943714,177.84127115140652
62500000,-252308.72308942117,299.07260160561094,177.84127115140652
63750000,-250594.4323346382,301.9754779054601,177.84127115140652
65000000,-251859.11473322287,299.6608428151863,177.84127115140652
66250000,-251087.2070069802,299.6953884748485,177.84127115140652
67500000,-251802.10227993852,297.0937701070965,177.84127115140652
68750000,-251570.61608901946,299.7394249148812,177.84127115140652
70000000,-251306.4699697583,300.08195487568383,177.84127115140652
71250000,-251280.58563445345,298.52583806825453,177.84127115140652
72500000,-250737.1717557311,301.9037488948244,177.84127115140652
73750000,-251257.2719639868,297.70835995995475,177.84127115140652
75000000,-250454.95606256882,300.76403074623505,177.84127115140652
76250000,-251292.47676609014,303.15305000858115,177.84127115140652
77500000,-251573.22319973866,296.6073573182158,177.84127115140652
78750000,-250386.25605534436,302.42128964907766,177.84127115140652
80000000,-250751.07752651232,302.4641231108624,177.84127115140652
81250000,-251387.76963990787,293.865031217276,177.84127115140652
82500000,-250100.21676361188,300.00358798050877,177.84127115140652
83750000,-250601.57886954676,301.3720101791027,177.84127115140652
85000000,-250235.0574428863,295.74220956424205,177.84127115140652
86250000,-251469.80277535156,300.77650223503815,177.84127115140652
87500000,-249988.65012317477,296.276116870113,177.84127115140652
88750000,-250502.05432189978,296.1010129234983,177.84127115140652
90000000,-251968.39292710647,296.60859281762686,177.84127115140652
91250000,-250791.86354266037,295.8910847277333,177.84127115140652
92500000,-250404.56387520768,298.9048408840197,177.84127115140652
93750000,-251154.475504898,296.99560105670747,177.84127115140652
95000000,-251359.19246092672,299.51372660792583,177.84127115140652
96250000,-250764.11982902559,298.4252684757289,177.84127115140652
97500000,-251484.33265610877,299.40898474185764,177.84127115140652
98750000,-250935.99084728095,300.932682078628,177.84127115140652
100000000,-251445.2858629264,301.49998914194157,177.84127115140652
101250000,-250187.6698401617,297.4103964713417,177.84127115140652
102500000,-251637.72404296696,297.3061071492267,177.84127115140652
103750000,-250904.40802089963,300.4314819328267,177.84127115140652
105000000,-251078.05117556825,296.9107071906265,177.84127115140652
106250000,-250952.78594076866,297.01861025279345,177.84127115140652
107500000,-250802.97160940943,296.9837422883592,177.84127115140652
108750000,-250144.81036504335,295.5391186771401,177.84127115140652
110000000,-250408.76959471265,299.5920144289264,177.84127115140652
111250000,-251265.48837245023,298.6026394090152,177.84127115140652
112500000,-251187.4663939576,299.35775457542996,177.84127115140652
113750000,-251361.33346678014,295.0478388167673,177.84127115140652
115000000,-251394.21021181066,301.3376359074994,177.84127115140652
116250000,-251057.08305738913,296.7607983850883,177.84127115140652
117500000,-250673.4803463628,295.2263131829163,177.84127115140652
118750000,-250833.26661640173,299.1149224913304,177.84127115140652
120000000,-251410.9140135313,300.213790546652,177.84127115140652
121250000,-250332.92606316763,298.6392307175874,177.84127115140652
122500000,-251197.99922959972,298.6720200794495,177.84127115140652
123750000,-251727.90174243366,295.2262481836339,177.84127115140652
125000000,-250838.0265258979,298.9726168252748,177.84127115140652
Benchmark (ns/day): 281.221144219288
running anchor_index: 10 restart: False total_simulation_length: 125000000 num_transitions: 0 swarm index: None
#"Step","Potential Energy (kJ/mole)","Temperature (K)","Box Volume (nm^3)"
1250000,-250963.61889972934,297.8796832262577,177.84127115140652
2500000,-251100.75729331374,297.7754051036002,177.84127115140652
3750000,-250787.89210539637,297.1841722775951,177.84127115140652
5000000,-250622.71299585304,297.06264123069576,177.84127115140652
6250000,-250821.9841966941,295.32203814155105,177.84127115140652
7500000,-249772.9566296395,297.2846601329349,177.84127115140652
8750000,-251087.09847757034,294.96687104952366,177.84127115140652
10000000,-250296.20332069322,297.50360697497297,177.84127115140652
11250000,-251053.39524247777,297.7810223006985,177.84127115140652
12500000,-250609.3133067037,301.9160241174032,177.84127115140652
13750000,-250654.74175767647,299.9137915559968,177.84127115140652
15000000,-251246.0571761001,297.5900131046811,177.84127115140652
16250000,-249805.84242308652,296.1516417954397,177.84127115140652
17500000,-250385.3948628693,293.95899986085556,177.84127115140652
18750000,-250870.40786798252,300.92852254107123,177.84127115140652
20000000,-250905.67367758462,296.4416548335448,177.84127115140652
21250000,-250707.01590270572,298.4641538897293,177.84127115140652
22500000,-251103.76571191382,298.0251731412272,177.84127115140652
23750000,-250857.61640539858,298.2536600109732,177.84127115140652
25000000,-250574.95729532233,297.43102224900605,177.84127115140652
26250000,-251082.92657866422,298.13251092741314,177.84127115140652
27500000,-251642.8137897672,297.66562113432065,177.84127115140652
28750000,-250673.8559527225,300.2280735890014,177.84127115140652
30000000,-250993.53902922152,299.61717458412096,177.84127115140652
31250000,-251593.71903408505,303.1971113478435,177.84127115140652
32500000,-250612.1940932686,296.17957592455355,177.84127115140652
33750000,-251109.1292685545,297.87972097528217,177.84127115140652
35000000,-251504.09697998967,301.89775846431866,177.84127115140652
36250000,-250624.9054595204,299.6020381533652,177.84127115140652
37500000,-250196.6593948789,297.58610478306593,177.84127115140652
38750000,-250772.68634288735,295.9347013668348,177.84127115140652
40000000,-251121.43306054547,300.965484540292,177.84127115140652
41250000,-251319.9035094534,298.1519555442378,177.84127115140652
42500000,-252062.46652876912,299.81752553831586,177.84127115140652
43750000,-250913.95741329156,297.09971023855746,177.84127115140652
45000000,-251023.71011325298,297.6121898078329,177.84127115140652
46250000,-251156.1582629932,301.21430667652606,177.84127115140652
47500000,-250973.7799685821,301.2418667839347,177.84127115140652
48750000,-250061.98426671792,295.67015589823285,177.84127115140652
50000000,-250858.78900723904,300.39840964216665,177.84127115140652
51250000,-249833.1550544314,300.04648956517707,177.84127115140652
52500000,-250755.61106327875,297.6282421147988,177.84127115140652
53750000,-250633.77985838032,296.68933906938247,177.84127115140652
55000000,-249208.43697069818,297.18976749075216,177.84127115140652
56250000,-251849.91741440422,300.7844392343469,177.84127115140652
57500000,-250662.8009897722,297.99908109997284,177.84127115140652
58750000,-250871.8564283948,295.70531975683423,177.84127115140652
60000000,-251025.46409789985,297.01312224961515,177.84127115140652
61250000,-250437.04213957582,297.8969129060293,177.84127115140652
62500000,-250929.3088880726,301.3655435105789,177.84127115140652
63750000,-251365.3793179521,300.7234767423653,177.84127115140652
65000000,-250499.15234704735,300.0873309512295,177.84127115140652
66250000,-250928.9496843838,295.9500399191102,177.84127115140652
67500000,-251202.30126014398,298.7874974974075,177.84127115140652
68750000,-251216.94150573667,294.6608167870472,177.84127115140652
70000000,-250390.27349948348,297.23256132492077,177.84127115140652
71250000,-251404.40668005217,297.1052465295271,177.84127115140652
72500000,-250735.0252188514,295.83046509164376,177.84127115140652
73750000,-250352.66381779732,296.40474659807165,177.84127115140652
75000000,-251743.92527426593,298.4225979534454,177.84127115140652
76250000,-251675.50774102146,296.45510815031645,177.84127115140652
77500000,-251600.76772023272,296.54512463258675,177.84127115140652
78750000,-251342.93648028607,293.5898786595307,177.84127115140652
80000000,-251557.576574611,298.3036344967419,177.84127115140652
81250000,-250827.78162114602,298.6237527864562,177.84127115140652
82500000,-251362.96318814694,294.70286897441025,177.84127115140652
83750000,-250847.04300829396,300.2560358190567,177.84127115140652
85000000,-250414.343118208,299.48662507907414,177.84127115140652
86250000,-251087.53326319717,299.710353431438,177.84127115140652
87500000,-250474.6633588774,302.65096347009177,177.84127115140652
88750000,-250881.799825656,299.5173791444326,177.84127115140652
90000000,-251291.59384958865,300.02986660417866,177.84127115140652
91250000,-251566.37239163462,295.7179376227423,177.84127115140652
92500000,-250634.69581886218,295.28119503196945,177.84127115140652
93750000,-251367.401673167,298.4655400438071,177.84127115140652
95000000,-250645.225053536,299.2935865258229,177.84127115140652
96250000,-250860.34303405532,298.6747387437222,177.84127115140652

HPC output
[vaibhav@node1 seekr2-tutorial]$ cat job.50.out
command surface_spheres -probe_radius 1.5 < tryp_ben_receptor.xml > receptor_surface.xml
command inside_points -spheres tryp_ben_receptor.xml -surface receptor_surface.xml -egrid receptor3.dx > receptor_inside.xml
command hydro_params < receptor_inside.xml > receptor_hydro_params.xml
command test_charges < tryp_ben_receptor.xml > receptor_charges.xml
command lumped_charges -pts receptor_charges.xml > receptor_cheby.xml
command make_surface_sphere_list -surface receptor_surface.xml -spheres tryp_ben_receptor.xml -rxn rxns.xml -group receptor -core receptor > receptor_surface_atoms.xml
command mpole_grid_fit -dx receptor0.dx -solvdi 78 -debye 1.79769e+308 > receptor_mpole.xml
command born_integral -in receptor_inside.xml -oeps 78 -debye 1.79769e+308 -ieps 4.000000 > receptor_born.dx
command compute_charges_squared < receptor_charges.xml > receptor_charges_squared.xml
command lumped_charges -pts receptor_charges_squared.xml > receptor_squared_cheby.xml
command surface_spheres -probe_radius 1.5 < tryp_ben_ligand.xml > ligand_surface.xml
command inside_points -spheres tryp_ben_ligand.xml -surface ligand_surface.xml -egrid ligand2.dx > ligand_inside.xml
command hydro_params < ligand_inside.xml > ligand_hydro_params.xml
command test_charges < tryp_ben_ligand.xml > ligand_charges.xml
command lumped_charges -pts ligand_charges.xml > ligand_cheby.xml
command make_surface_sphere_list -surface ligand_surface.xml -spheres tryp_ben_ligand.xml -rxn rxns.xml -group ligand -core ligand > ligand_surface_atoms.xml
command mpole_grid_fit -dx ligand0.dx -solvdi 78 -debye 1.79769e+308 > ligand_mpole.xml
command born_integral -in ligand_inside.xml -oeps 78 -debye 1.79769e+308 -ieps 4.000000 > ligand_born.dx
command compute_charges_squared < ligand_charges.xml > ligand_charges_squared.xml
command lumped_charges -pts ligand_charges_squared.xml > ligand_squared_cheby.xml

OpenMM Incompatibility

Dear SEEKR2 team,

We recently updated OpenMM to 8.0.0 and now when I tried to run SEEKR2 for simulations (preparation is fine), I get the following error:
openmm.OpenMMException: Specified a Platform for a Context which does not support all required kernels

Is this due to a incompatibility issue?

Thank you!

seekrcentral / seekr2 Goto Github PK

seekr2's Introduction

seekr2

Overview

Quick Install

Dependencies

OpenMM (recommended)

Browndye2 (optional; required for k-on calculations)

NAMD2 (optional, required if not using OpenMM)

Install SEEKR2

Testing SEEKR2 (Optional)

Run

Important Options and Hints

Authors and Contributors

Citing SEEKR2

Copyright

Acknowledgements

seekr2's People

Contributors

Stargazers

Watchers

Forkers

seekr2's Issues

relevant openmm issue page

Build Notes for SEEKER and dependencies and addons

AmberTools Dependencies:

AmberTools Compile:

Install BrownDye

OpenMM & OpenMM Plugin Install from Source Notes:

Install Prerequisits:

or we put it where utot user can edit: /home/utot/.conda/envs/SEEKR2/openmm

cmake options come up, press "c", then "e", then "Enter" fill in info:

press "Enter" then save via "c", "e", then generate "g" then done

test openmm

REQUIRED Install Plugin from Source

cmake options come up, press "c", then "e", then "Enter" fill in info:

press "Enter" then save via "c", "e", then generate "g" then done

[jrfnsm@param_embryo 1mbo_seekr2]$ diff input_Mb_OXY_hidr1.xml trypsin-input.xml 8c8 < 300.0

11c11 < <root_directory>~/mb_oxy_hidr_tutorial/</root_directory>

21,24c21,24 < [438, 442, 443, 444, 691, 1050, 1052, 1099, 1100, 1103, 1104, 1105, 1749, 1750, 1751, 2499, 2500, 2528] < [2533, 2534] < <bd_group1>[438, 442, 443, 444, 691, 1050, 1052, 1099, 1100, 1103, 1104, 1105, 1749, 1750, 1751, 2499, 2500, 2528]</bd_group1> < <bd_group2>[0, 1]</bd_group2>

31c31 < <prmtop_filename>1mbo_solv_oxy.prmtop</prmtop_filename>

43c43 < <prmtop_filename>1mbo_solv_oxy.prmtop</prmtop_filename>

55c55 < <prmtop_filename>1mbo_solv_oxy.prmtop</prmtop_filename>

67c67 < <prmtop_filename>1mbo_solv_oxy.prmtop</prmtop_filename>

79c79 < <prmtop_filename>1mbo_solv_oxy.prmtop</prmtop_filename>

91c91 < <prmtop_filename>1mbo_solv_oxy.prmtop</prmtop_filename>

103c103 < <prmtop_filename>1mbo_solv_oxy.prmtop</prmtop_filename>

115c115 < <prmtop_filename>1mbo_solv_oxy.prmtop</prmtop_filename>

127c127 < <prmtop_filename>1mbo_solv_oxy.prmtop</prmtop_filename>

139c139 < <prmtop_filename>1mbo_solv_oxy.prmtop</prmtop_filename>

151c151 < <prmtop_filename>1mbo_solv_oxy.prmtop</prmtop_filename>

163c163 < <prmtop_filename>1mbo_solv_oxy.prmtop</prmtop_filename>

175,176c175,176 < <receptor_pqr_filename>mb_oxy_receptor.pqr</receptor_pqr_filename> < <ligand_pqr_filename>mb_oxy_ligand.pqr</ligand_pqr_filename>

Recommend Projects

Recommend Topics

Recommend Org

[jrfnsm@param_embryo 1mbo_seekr2]$ diff input_Mb_OXY_hidr1.xml trypsin-input.xml
8c8
< 300.0

11c11
< <root_directory>~/mb_oxy_hidr_tutorial/</root_directory>

21,24c21,24
< [438, 442, 443, 444, 691, 1050, 1052, 1099, 1100, 1103, 1104, 1105, 1749, 1750, 1751, 2499, 2500, 2528]
< [2533, 2534]
< <bd_group1>[438, 442, 443, 444, 691, 1050, 1052, 1099, 1100, 1103, 1104, 1105, 1749, 1750, 1751, 2499, 2500, 2528]</bd_group1>
< <bd_group2>[0, 1]</bd_group2>

31c31
< <prmtop_filename>1mbo_solv_oxy.prmtop</prmtop_filename>

43c43
< <prmtop_filename>1mbo_solv_oxy.prmtop</prmtop_filename>

55c55
< <prmtop_filename>1mbo_solv_oxy.prmtop</prmtop_filename>

67c67
< <prmtop_filename>1mbo_solv_oxy.prmtop</prmtop_filename>

79c79
< <prmtop_filename>1mbo_solv_oxy.prmtop</prmtop_filename>

91c91
< <prmtop_filename>1mbo_solv_oxy.prmtop</prmtop_filename>

103c103
< <prmtop_filename>1mbo_solv_oxy.prmtop</prmtop_filename>

115c115
< <prmtop_filename>1mbo_solv_oxy.prmtop</prmtop_filename>

127c127
< <prmtop_filename>1mbo_solv_oxy.prmtop</prmtop_filename>

139c139
< <prmtop_filename>1mbo_solv_oxy.prmtop</prmtop_filename>

151c151
< <prmtop_filename>1mbo_solv_oxy.prmtop</prmtop_filename>

163c163
< <prmtop_filename>1mbo_solv_oxy.prmtop</prmtop_filename>

175,176c175,176
< <receptor_pqr_filename>mb_oxy_receptor.pqr</receptor_pqr_filename>
< <ligand_pqr_filename>mb_oxy_ligand.pqr</ligand_pqr_filename>