error while generating trypsin-benzamidine smd input for hidr

[vaibhavadixit]

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

[vaibhavadixit]

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

[vaibhavadixit]

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

[lvotapka]

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.

[vaibhavadixit]

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

[lvotapka]

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.

[lvotapka]

Hi @vaibhavadixit, did this error ultimately get resolved?