MMPBSA.py doesn't appear to have access to the Amber tool *parmed* used to
modify and edit prmtop files.
If it is not present in $AMBERHOME/bin/, then you need to compile it.
If it is present in the bin folder, then you are likely using the wrong
python to execute MMPBSA.py. As the message indicates, be sure you have
sourced the amber.sh (or amber.csh) file before running MMPBSA.py to ensure
the PYTHONPATH is set to point to the proper python version.
-Bill
On Mon, Oct 31, 2022 at 10:26 AM Subramanian Boopathi via AMBER <
amber.ambermd.org> wrote:
> Respected Amber users,
>
> I cooked the peptide complex using the AMBER16 package and accomplished
> some of the analysis using the cpptraj tool with the AMBER20 tool.
>
> In contrast, I have got the following error when executing the MMPBSA
> analysis (AMBER20 tool) using the command: *MMPBSA.py -O -i **mmpbsa.in
> <http://mmpbsa.in/>** -o ABTmmpbsa.dat -sp ABT.prmtop -cp com.prmtop -rp
> rec.prmtop -lp ligand.prmtop -y abt10ms100frames.mdcrd*
>
> Traceback (most recent call last):
> File
>
> "/opt/apps/amber20/lib/python3.7/site-packages/./MMPBSA.py-16.0-py3.7.egg/EGG-INFO/scripts/MMPBSA.py",
> line 41, in <module>
> File
>
> "/opt/apps/amber20/lib/python3.7/site-packages/./MMPBSA.py-16.0-py3.7.egg/MMPBSA_mods/main.py",
> line 43, in <module>
> File "/opt/apps/amber20/lib/python3.7/site-packages/./MMPBSA.py-16.0
> py3.7.egg/MMPBSA_mods/createinput.py", line 43, in <module>
> ModuleNotFoundError: No module named 'parmed'
>
>
> During handling of the above exception, another exception occurred:
>
> Traceback (most recent call last):
> File "/opt/apps/amber20/bin/MMPBSA.py", line 4, in <module>
> __import__('pkg_resources').run_script('MMPBSA.py==16.0', 'MMPBSA.py')
> File
> "/opt/apps/conda3/lib/python3.7/site-packages/pkg_resources/__init__.py",
> line 662, in run_script
> self.require(requires)[0].run_script(script_name, ns)
> File
> "/opt/apps/conda3/lib/python3.7/site-packages/pkg_resources/__init__.py",
> line 1466, in run_script
> exec(script_code, namespace, namespace)
> File
>
> "/opt/apps/amber20/lib/python3.7/site-packages/./MMPBSA.py-16.0-py3.7.egg/EGG-INFO/scripts/MMPBSA.py",
> line 48, in <module>
> ImportError: Could not import Amber Python modules. Please make sure you
> have sourced /opt/apps/amber20//amber.sh (if you are using sh/ksh/bash/zsh)
> or /opt/apps/amber20//amber.csh (if you are using csh/tcsh)
>
>
>
> I implore you to someone fix the problem by giving your valuable
> suggestion, I stay tuned for your response.
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Bill Miller III
Assistant Professor of Chemistry
Truman State University
417-549-0952
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Received on Mon Oct 31 2022 - 09:00:02 PDT
