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-- Ray Luo, Ph.D. Professor of Structural Biology/Biochemistry/Biophysics, Chemical, Applied and Materials Physics, Chemical and Biomolecular Engineering, Materials Science and Engineering, and Biomedical Engineering Department of Molecular Biology and Biochemistry University of California, Irvine, CA 92697-3900 On Mon, Jul 21, 2025 at 3:02 PM Johann, Timothy via AMBER <amber.ambermd.org> wrote: > My apologies. I'm new to the mailing list. I pasted a table into my > email, and it got mangled. In summary, the value for EEL that is produced > by MMPBSA.py is -5.2417 regardless of whether epsin = 1 or epsin = 4, and > it does not change between implicit and explicit trajectories. It is also > the same for the GB and GB (GBNSR6) outputs. > > > > ________________________________ > From: Johann, Timothy via AMBER <amber.ambermd.org > Sent: Monday, July 21, 2025 5:16 PM > To: amber.ambermd.org <amber.ambermd.org> > Subject: [AMBER] MMPBSA.py results unresponsive to changes in epsin > > CAUTION: This email originated outside of Roanoke College. Do not click on > links or open attachments unless you recognize the sender and know the > content is safe. > > > Good afternoon, > > I've been analyzing protein-ligand trajectories using MMPBSA.py, and I > noticed that the results are not responsive to the value of epsin. Here's > what I'm seeing for one complex, both for an explicit solvent trajectory > and an implicit solvent trajectory. I'm only providing the EEL because I > compared changes to those calculated using mm_pbsa.pl, and EEL (ELE for > mm_pbsa.pl) was where the major difference was. > > Complex > Epsin > Method > EEL-LCPO > EEL-GBNSR6 > 4mre-imp > 1 > py > -5.2417 > -5.2417 > 4mre-imp > 4 > py > -5.2417 > -5.2417 > 4mre-exp > 1 > py > -5.2417 > -5.2417 > 4mre-exp > 4 > py > -5.2417 > -5.2417 > > Here are my input files for MMPBSA.py, pulled from the top of the > FINAL_RESULTS_MMPBSA.dat file. In putting together this data for this > post, I analyzed only one frame. I originally noticed the issue on > analysis of all 1000 frames of my trajectories. > > 4mre-imp epsin1 > |Input file: > |-------------------------------------------------------------- > |Input file for MMGBSA > |&general > | startframe=500, endframe=500, interval=1, keep_files=2, > | netcdf=1, > |/ > |&gb > | igb=66, saltcon=0.154, epsin=1, epsout=80, surften=0.005, surfoff=0, > |/ > |-------------------------------------------------------------- > > 4mre-imp epsin4 > |Input file: > |-------------------------------------------------------------- > |Input file for MMGBSA > |&general > | startframe=500, endframe=500, interval=1, keep_files=2, > | netcdf=1, > |/ > |&gb > | igb=66, saltcon=0.154, epsin=4, epsout=80, surften=0.005, surfoff=0, > |/ > |-------------------------------------------------------------- > > 4mre-exp epsin1 > |Input file: > |-------------------------------------------------------------- > |Input file for MMGBSA > |&general > | startframe=500, endframe=500, interval=1, keep_files=2, > | netcdf=1, > |/ > |&gb > | igb=66, saltcon=0.154, epsin=1, epsout=80, surften=0.005, surfoff=0, > |/ > |-------------------------------------------------------------- > > 4mre-exp epsin4 > |Input file: > |-------------------------------------------------------------- > |Input file for MMGBSA > |&general > | startframe=500, endframe=500, interval=1, keep_files=2, > | netcdf=1, > |/ > |&gb > | igb=66, saltcon=0.154, epsin=4, epsout=80, surften=0.005, surfoff=0, > |/ > |-------------------------------------------------------------- > > I started the analysis at the command line using the following syntax for > the implicit trajectory: > MMPBSA.py -O -i mmgbsa.in -cp complex.prmtop -rp protein.prmtop -lp > ligand.prmtop -y 4mre_md1.mdcrd > > I started the analysis at the command line using the following syntax for > the explicit trajectory: > MMPBSA.py -O -i mmgbsa.in -sp 4mre.top -cp complex.prmtop -rp > protein.prmtop -lp ligand.prmtop -y 4mre_md1.mdcrd > > I'm not sure if the lack of response is a bug in MMPBSA.py or an error on > my part somewhere in the process. Any help would be appreciated. I've > seen this more broadly than in just the one complex. I'm happy to provide > more data as needed. > > Cheers, > Tim > > — > > Dr. Timothy W. Johann > Professor of Chemistry > office 540-375-2364 > johann.roanoke.edu<mailto:johann.roanoke.edu> > > https://urldefense.com/v3/__http://www.calendly.com/johann-2__;!!CzAuKJ42GuquVTTmVmPViYEvSg!MCRQh-oYpkcq5P3AEDnH6Zg7rLBYvlnVH0pLRMdBR0PaC4j9U4nSu6xtsaGaupw_m3XBDZ0rmZI$ > < > https://urldefense.com/v3/__http://www.calendly.com/johann-2__;!!CzAuKJ42GuquVTTmVmPViYEvSg!MCRQh-oYpkcq5P3AEDnH6Zg7rLBYvlnVH0pLRMdBR0PaC4j9U4nSu6xtsaGaupw_m3XBDZ0rmZI$ > >< > https://urldefense.com/v3/__http://www.calendly.com/johann-2__;!!CzAuKJ42GuquVTTmVmPViYEvSg!MCRQh-oYpkcq5P3AEDnH6Zg7rLBYvlnVH0pLRMdBR0PaC4j9U4nSu6xtsaGaupw_m3XBDZ0rmZI$ > < > https://urldefense.com/v3/__http://www.calendly.com/johann-2__;!!CzAuKJ42GuquVTTmVmPViYEvSg!MCRQh-oYpkcq5P3AEDnH6Zg7rLBYvlnVH0pLRMdBR0PaC4j9U4nSu6xtsaGaupw_m3XBDZ0rmZI$ > >> > > > > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > > https://urldefense.com/v3/__http://lists.ambermd.org/mailman/listinfo/amber__;!!CzAuKJ42GuquVTTmVmPViYEvSg!MCRQh-oYpkcq5P3AEDnH6Zg7rLBYvlnVH0pLRMdBR0PaC4j9U4nSu6xtsaGaupw_m3XBatvuiJM$ > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > > https://urldefense.com/v3/__http://lists.ambermd.org/mailman/listinfo/amber__;!!CzAuKJ42GuquVTTmVmPViYEvSg!MCRQh-oYpkcq5P3AEDnH6Zg7rLBYvlnVH0pLRMdBR0PaC4j9U4nSu6xtsaGaupw_m3XBatvuiJM$ > _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Mon Jul 21 2025 - 17:00:02 PDT