Re: [AMBER] Python Error in, only for PBSA on final output

From: Lennart Gundelach <>
Date: Sat, 16 Jan 2021 10:14:54 +0000


If I run only MMPBSA it works… Odd.


From: Ray Luo <>
Date: Wednesday, 13 January 2021 at 18:12
To: AMBER Mailing List <>
Subject: Re: [AMBER] Python Error in, only for PBSA on final output
CAUTION: This e-mail originated outside the University of Southampton.


What if you only run MMPBSA without GBSA or normal mode calculations?
Does it still occur?

All the best,
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 Wed, Jan 13, 2021 at 1:44 AM Lennart Gundelach
<> wrote:
> Hi,
> I am running an MMPBSA, MMGBAS and normal mode calc using in Amber16. All the calculations are performed but in the final stage, where the outputs are written to energies.csv and the summary output file, the following python error occurs right before PBSA results are written. GBSA results and NM results write without problem.
> 1294   File "/local/software/amber/amber16/bin/", line 109, in <module>
> 1295     app.write_final_outputs()
> 1296   File "/local/software/amber/amber16/lib/python2.7/site-packages/MMPBSA_mods/", line 638, in write_final_outputs
> 1297     write_binding_output(self)
> 1298   File "/local/software/amber/amber16/lib/python2.7/site-packages/MMPBSA_mods/", line 390, in write_binding_output
> 1299     davg, dstdev = sys_norm.diff(nm_sys_norm, 'DELTA TOTAL', 'Total')
> 1300   File "/local/software/amber/amber16/lib/python2.7/site-packages/MMPBSA_mods/", line 1178, in diff
> 1301     return ([key1].avg() -[key2].avg(),
> 1302 AttributeError: 'list' object has no attribute 'avg'
> 1303 Error occured on rank 0.
> 1304 Exiting. All files have been retained.
> I tried with and without explicitly loading python 2,7 module on the HPC system. Error remains unchanged. Gut feeling is that this is something to do with conflicting python versions. Any ideas?
> Thank you,
> Lennart
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