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This package runs collective molecular dynamics simulations, where collective motions from anisotropic network model normal mode analysis drive all-atom dynamics through targeted molecular dynamics simulations and energy minimization

Home Page: http://prody.csb.pitt.edu/comd/

License: MIT License

Python 1.54% Tcl 18.34% Rich Text Format 80.13%

simulations comd sampling-methods pathway-analysis anm

comd's Introduction

SYNOPSIS

ProDy is a free and open-source Python package for protein structure, dynamics, and sequence analysis. It allows for comparative analysis and modeling of protein structural dynamics and sequence co-evolution. Fast and flexible ProDy API is for interactive usage as well as application development. ProDy also comes with several analysis applications and a graphical user interface for visual analysis.

Further details are described in the ProDy papers:

Bakan A, Meireles LM, Bahar I.

ProDy: Protein Dynamics Inferred from Theory and Experiments.

Bioinformatics 2011 27(11):1575-1577.

Bakan A, Dutta A, Mao W, Liu Y, Chennubhotla C, Lezon TR, Bahar I.

Evol and ProDy for Bridging Protein Sequence Evolution and Structural Dynamics.

Bioinformatics 2014 30(18):2681-2683.

Zhang S, Krieger JM, Zhang Y, Kaya C, Kaynak B, Mikulska-Ruminska K, Doruker P, Li H, Bahar I.

ProDy 2.0: Increased Scale and Scope after 10 Years of Protein Dynamics Modelling with Python.

Bioinformatics 2021 37(20):3657-3659.

MODULES

ProDy has a modular structure with modules inside various subpackages.

The main ones are:

:mod:`~prody.atomic`` handles all :class:`~prody.atomic.Atomic` objects including :class:`~prody.atomic.AtomGroup` and :class:`.Selection`
:mod:`~prody.database` interfaces with databases such as CATH, DALI, UniProt and Pfam
:mod:`~prody.dynamics` provides all the modules for normal mode analysis with various elastic network models,

as well as PCA, SignDy (:mod:`~prody.dynamics.signature`), hybrid methods such as :mod:`~prody.dynamics.clustenm`, allosteric signal propagation methods :mod:`~prody.dynamics.perturb` (PRS) and :func:`~prody.dynamics.analysis.calcHitTime` (Markovian hitting time), and various analysis and plotting functions.

:mod:`~prody.ensemble` enables construction of heterogeneous structural ensembles for exploring dynamics from experiments and simulations
:mod:`~prody.proteins` provides various modules for parsing different kinds of protein structure files including PDB, mmCIF, MMTF and maps,

as well as tools to align and compare structures, and analysis of :mod:`~prody.proteins.interactions` within and between proteins (InSty) and find :mod:`~prody.proteins.waterbridges` (WatFinder).

:mod:`~prody.sequence` has all the sequence alignment and evolutionary analysis tools of Evol

Smaller ones include:

:mod:`~prody.chromatin` specific to chromatin dynamics (ChromDy) including :mod:`~prody.chromatin.hic` and :mod:`~prody.chromatin.cluster`
:mod:`~prody.compounds` for parsing small molecule compounds/ligands from the PDB and related databases
:mod:`~prody.domain_decomposition` for Spectrus dynamical domain decomposition
:mod:`~prody.trajectory` for trajectories in DCD format
:mod:`~prody.utilities`

GETTING PRODY

You can run ProDy on all major platforms. For download and installation instructions see:

http://prody.csb.pitt.edu/downloads

DOCUMENTATION

Homepage: http://prody.csb.pitt.edu/
Tutorials: http://prody.csb.pitt.edu/tutorials
Reference: http://prody.csb.pitt.edu/manual
Applications: http://prody.csb.pitt.edu/manual/apps
NMWiz GUI: http://prody.csb.pitt.edu/nmwiz
Changes: http://prody.csb.pitt.edu/manual/release

See also https://github.com/prody/ProDy-website for latest versions.

SOURCE CODE

Source code: https://github.com/prody/ProDy
Issue tracker: https://github.com/prody/ProDy/issues

LICENSE

ProDy is available under MIT License. See LICENSE.txt for more details.

Biopython (http://biopython.org/) KDTree and TreeConstruction modules are distributed with ProDy. Biopython is developed by The Biopython Consortium and is available under the Biopython license (http://www.biopython.org/DIST/LICENSE).

Pyparsing (https://github.com/pyparsing/pyparsing) module is distributed with ProDy. Pyparsing is developed by Paul T. McGuire and is available under the MIT license (http://www.opensource.org/licenses/mit-license.php).

CEalign module (https://pymolwiki.org/index.php/Cealign_plugin) is distributed with ProDy. The original CE method was developed by Ilya Shindyalov and Philip Bourne. The Python version which is used by ProDy is developed by Jason Vertrees and available under the New BSD license.

Hbp module: The calculation of hydrophobic interactions, solvent accessible surface area (SASA) and volume for each residue is using geometric methods based on the information of the atoms in the molecule. The methods have been programmed in C++ and can be compiled as a python module “hpb.so” which is then used by ProDy. Files for compilation are stored at prody/proteins/hpbmodule folder and required C++ and Fortran compiler. After compilation hpb.so file can be stored in prody/proteins folder in ProDy or in the local directory which is used to perform calulations. The precompiled versions for Python 2.7, 3.8, 3.9, and 3.10 are availabe in prody/proteins/hpbmodule. The user can choose the correct version of hpb.so and copy to the prody/proteins or local directory. C++ code of hpb.so was developed by Xin Cao and Fortran code by Xin Cao, Michelle H. Hummel, Bihua Yu, and Evangelos A. Coutsias (License in prody/proteins/hpbmodule folder). Details of the method can be found in the Supplementary Material of InSty manuscript (soon will be submitted for publication).

comd's People

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fongchun jamesmkrieger javimota ajimoreno snehabheemireddy thonmaker

comd's Issues

coMD - walker 2 TMD problem in comd.tcl

I would like to use coMD for pathway analysis but noticed a problem in the comd.tcl files on both the prody website and github pages...

using the comd tutorial files, if I run with either 1ake or 4ake on their own (ie same filename for initial and final) everything is fine.

However, when I use two different files to generate a pathway it fails to run TMD on walker 2 and it seems to be because the code is trying to run namd using the wrong .conf file...

line 1317 of comd.tcl currently writes to 'pro.conf'
but further down at line 1377 it tries to run namd using 'min.conf' - changing this to 'pro.conf' by analogy to the sections for Walker 1 allows everything to run and I can see the process go through several cycles fine.

However, I'm not clear about what parameters to use for ANM and TMD to complete a successful run using the tutorial files - it crashes every time after a few cycles.
Looking at the '...anmmc_log.txt' files shows that when things crashe the 6th column contains rapidly increasing values that end up as 'inf' .

Could you please post a set of values for the ANM and TMD options that should work with the tutorial ?

Thanks,

Andrew Beavil

Error with coMD in VMD re GPUs

Hi,
I was running coMD in VMD 1.9.3. The following error pops up and kills the process.

can't read "::comd::gpus_present": no such variable
can't read "::comd::gpus_present": no such variable
while executing
"if {$::comd::gpus_present} {
set processes_per_run [expr {[llength [wsplit $::comd::gpus_selection1 ","]] + 1}]

if {[info exists ::comd::num_..."
(procedure "::comd::Prepare_system" line 220)
invoked from within

"::comd::Prepare_system"
invoked from within
".comdgui.main_frame.prepare.button invoke"
("uplevel" body line 1)
invoked from within
"uplevel #0 [list $w invoke]"
(procedure "tk::ButtonUp" line 23)
invoked from within
"tk::ButtonUp .comdgui.main_frame.prepare.button"
(command bound to event)

I also tried 1.9.2 and even the ionization cannot complete.
Could you give me a clue about how to fix it? Many thanks!

Help on coMD

Hi,
I have been trying to run coMD with the old version which is available at this site (http://csb.pitt.edu/coMD/). However I am unable to figure out how to use it for my system of interest and get it running. I did write to Mert Gur as mentioned in the website but did not get any response. I would be grateful if you could help me on this.

I see in your shell script that the jobs are submitted simultaneously and queued. So my doubt is can the jobs be run serially one by one that is 1 to 10, 10 to 20 etc. This is because my computing resources are limited and I would like to know if the trajectories are interchanged among the folders as in umbrella sampling.
One of my states has Mg ion bound, so should this also be taken into account while the conformations are modelled.
Moreover how do I know decide the number of cycles and it has converged.

I am also an extensive user of ProDy, so does ProDy have the capability to perform protein-RNA + ions (ligand) ANM as in ANM 2.0 webserver. Also as I noticed in your github page that coMD is being implemented using ProDy, I would like to try even if it is in beta release.

Error with CoMD in VMD re autopsf

Hi I get this error when I prepare my system

Unable to load file 'init.pdb' using file type 'pdb'.
Unable to load file 'init.pdb' using file type 'pdb'.
while executing
"mol new init.pdb"
(procedure "::comd::Prepare_system" line 81)
invoked from within
"::comd::Prepare_system"
invoked from within
".comdgui.main_frame.prepare.button invoke"
("uplevel" body line 1)
invoked from within
"uplevel #0 [list $w invoke]"
(procedure "tk::ButtonUp" line 22)
invoked from within
"tk::ButtonUp .comdgui.main_frame.prepare.button"
(command bound to event)