error while generating trypsin-benzamidine smd input for hidr about seekr2 HOT 6 CLOSED

Following is the output to show that openmm is installed and can be imported in python3.8, thus not sure why the hidr.py script fails to import it. please do suggest. thank you.

(base) [niperg@kaberi ~]$ python3.8
\Python 3.8.13 (default, Mar 28 2022, 11:38:47)
[GCC 7.5.0] :: Anaconda, Inc. on linux
Type "help", "copyright", "credits" or "license" for more information.

import openmm

help(openmm)

Help on package openmm:

NAME
openmm

DESCRIPTION
OpenMM is a toolkit for molecular simulation. It can be used either as a
stand-alone application for running simulations, or as a library you call
from your own code. It provides a combination of extreme flexibility
(through custom forces and integrators), openness, and high performance
(especially on recent GPUs) that make it truly unique among simulation codes.

PACKAGE CONTENTS
_openmm
amd
app (package)
mtsintegrator
openmm
testInstallation
unit (package)
vec3
version

CLASSES
builtins.Exception(builtins.BaseException)
OpenMMException

class OpenMMException(builtins.Exception)
 |  This is the class used for all exceptions thrown by the C++ library.
 |  
 |  Method resolution order:
 |      OpenMMException
 |      builtins.Exception
 |      builtins.BaseException

from seekr2.

I think, I understood the problem and will post the solution if it works.

from seekr2.

I've encountered this problem before, and it's actually a bug in Parmed. You might try upgrading parmed:

pip install --upgrade parmed

However, when I first encountered this problem, I had to go into the /path/to/parmed/utils/decorators.py script and delete that line that raises the ImportError.

If you find another solution, we would be interested to hear it here.

from seekr2.

Upgrading the parmed fixed this problem.
But I'm getting errors with other AmberTools like MCBP.py and pdb4amber which are showing import error with parmed.
I've asked my student to post this error on the Amber forum, but it would be helpful if you can comment or share your experience with the same.
Thank you.
Vaibhav

from seekr2.

I don't often use MCBP.py or pdb4amber, but one idea would be to create two separate conda envs, one that has the modified parmed for SEEKR2, and the other which has the version of parmed you need for MCBP.py and pdb4amber, if its the conflicting versions that are causing the problem.

from seekr2.

Hi @vaibhavadixit, did this error ultimately get resolved?

from seekr2.