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-- 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 Sat, Jan 16, 2021 at 2:17 AM Lennart Gundelach <L.Gundelach.soton.ac.uk> wrote: > > Hi, > > If I run only MMPBSA it works… Odd. > > Lennart > > From: Ray Luo <rluo.uci.edu> > Date: Wednesday, 13 January 2021 at 18:12 > To: AMBER Mailing List <amber.ambermd.org> > Subject: Re: [AMBER] Python Error in MMPBSA.py, only for PBSA on final output > CAUTION: This e-mail originated outside the University of Southampton. > > Lennart, > > What if you only run MMPBSA without GBSA or normal mode calculations? > Does it still occur? > > 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 Wed, Jan 13, 2021 at 1:44 AM Lennart Gundelach > <L.Gundelach.soton.ac.uk> wrote: > > > > Hi, > > > > I am running an MMPBSA, MMGBAS and normal mode calc using MMPBSA.py.MPI 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/MMPBSA.py.MPI", line 109, in <module> > > 1295 app.write_final_outputs() > > 1296 File "/local/software/amber/amber16/lib/python2.7/site-packages/MMPBSA_mods/main.py", line 638, in write_final_outputs > > 1297 write_binding_output(self) > > 1298 File "/local/software/amber/amber16/lib/python2.7/site-packages/MMPBSA_mods/output_file.py", 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/amber_outputs.py", line 1178, in diff > > 1301 return (self.data[key1].avg() - other.data[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 > > _______________________________________________ > > AMBER mailing list > > AMBER.ambermd.org > > https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Flists.ambermd.org%2Fmailman%2Flistinfo%2Famber&data=04%7C01%7CL.Gundelach%40soton.ac.uk%7Ca027a51352b841e1f05008d8ba8a4082%7C4a5378f929f44d3ebe89669d03ada9d8%7C0%7C0%7C637464450241852287%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=tiB8heauoZfYNf1XSskQzSG8IVgMfYyR%2BKtXTvKsXzk%3D&reserved=0 > > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Flists.ambermd.org%2Fmailman%2Flistinfo%2Famber&data=04%7C01%7CL.Gundelach%40soton.ac.uk%7Ca027a51352b841e1f05008d8ba8a4082%7C4a5378f929f44d3ebe89669d03ada9d8%7C0%7C0%7C637464450241852287%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=tiB8heauoZfYNf1XSskQzSG8IVgMfYyR%2BKtXTvKsXzk%3D&reserved=0 > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Flists.ambermd.org%2Fmailman%2Flistinfo%2Famber&data=04%7C01%7CL.Gundelach%40soton.ac.uk%7Ca027a51352b841e1f05008d8ba8a4082%7C4a5378f929f44d3ebe89669d03ada9d8%7C0%7C0%7C637464450241852287%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=tiB8heauoZfYNf1XSskQzSG8IVgMfYyR%2BKtXTvKsXzk%3D&reserved=0 _______________________________________________ AMBER mailing list AMBER.ambermd.org https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Flists.ambermd.org%2Fmailman%2Flistinfo%2Famber&data=04%7C01%7CL.Gundelach%40soton.ac.uk%7Ca027a51352b841e1f05008d8ba8a4082%7C4a5378f929f44d3ebe89669d03ada9d8%7C0%7C0%7C637464450241852287%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=tiB8heauoZfYNf1XSskQzSG8IVgMfYyR%2BKtXTvKsXzk%3D&reserved=0 _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Fri Jan 22 2021 - 04:30:02 PST