Re: [AMBER] MMPBSA module error

From: Ray Luo <rluo.uci.edu>
Date: Sat, 16 Apr 2022 07:58:45 -0700

Ryan,

Here is my suggestion, download and install AmberTools 2021 and make sure
all tests, especially the mmpbsa.py tests pass. Note sander is part of
AmberTools, so mmpbsa should be able to run even if you don't have an Amber
license.

All the best,
Ray 
--
Ray Luo, Ph.D.
Professor of Structural Biology/Biochemistry/Biophysics,
Chemical and Materials Physics, Chemical and Biomolecular Engineering,
Biomedical Engineering, and Materials Science and Engineering
Department of Molecular Biology and Biochemistry
University of California, Irvine, CA 92697-3900
On Thu, Apr 14, 2022 at 6:26 PM Ryan Pavlovicz <pavlovicz.7.osu.edu> wrote:
> Hi,
>
> I am trying to run an MMPBSA calculation on a trajectory that was generated
> via OpenMM with an Amber force field:
>
> cpptraj found! Using /opt/conda/envs/AmberTools21/bin/cpptraj
>
> mmpbsa_py_energy found! Using
> /opt/conda/envs/AmberTools21/bin/mmpbsa_py_energy
>
> Preparing trajectories for simulation...
>
>   File "/opt/conda/envs/AmberTools21/bin/MMPBSA.py", line 4, in <module>
>
>     __import__('pkg_resources').run_script('MMPBSA.py==16.0', 'MMPBSA.py')
>
>   File
>
> "/opt/conda/envs/AmberTools21/lib/python3.9/site-packages/pkg_resources/__init__.py",
> line 662, in run_script
>
>     self.require(requires)[0].run_script(script_name, ns)
>
>   File
>
> "/opt/conda/envs/AmberTools21/lib/python3.9/site-packages/pkg_resources/__init__.py",
> line 1466, in run_script
>
>     exec(script_code, namespace, namespace)
>
>   File
>
> "/opt/conda/envs/AmberTools21/lib/python3.9/site-packages/MMPBSA.py-16.0-py3.9.egg/EGG-INFO/scripts/MMPBSA.py",
> line 99, in <module>
>
>   File
>
> "/opt/conda/envs/AmberTools21/lib/python3.9/site-packages/MMPBSA.py-16.0-py3.9.egg/MMPBSA_mods/main.py",
> line 167, in file_setup
>
>     self.mut_str, mutant_residue = make_mutant_trajectories(INPUT, FILES,
>
>   File
>
> "/opt/conda/envs/AmberTools21/lib/python3.9/site-packages/MMPBSA.py-16.0-py3.9.egg/MMPBSA_mods/make_trajs.py",
> line 298, in make_mutant_trajectories
>
>     from alamdcrd import MutantMdcrd, GlyMutantMdcrd
>
> ModuleNotFoundError: No module named 'alamdcrd'
>
> I have AmberTools installed via conda but do not have an Amber/sander
> install (no license). Should I be able to successfully run MMPBSA.py with
> only an AmberTools installation?
>
> Thanks,
>
> ryan
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Received on Sat Apr 16 2022 - 08:00:02 PDT
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