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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 Wed, Sep 8, 2021 at 4:35 AM Lennart Gundelach <L.Gundelach.soton.ac.uk> wrote: > > Hi, > > I have been running MMPBSA.py with a couple of explicit waters defined as part of the complex. This worked fine when working with trajectories (and .prmtop) that had been generated using ff14SB + TIP3P but seems to no longer work when using trajectories generated with ff19SB + OPC. > > Both the complex and receptor calculations yield ‘nan’ for VdW and EEL while the ligand calculation works just fine (since it has not waters). The only change made to setup is new trajectories generated with ff19SB + OPC instead of ff14SB + TIP3P. > > Could it be, that due to the 4 point setup of OPC, MMPBSA.py does not know how to handle the 4th point, which does not directly correspond to an atom? > > From topology files: > TIP3P: OW HW HW > OPC: OW HW HW EP > > Could this be the issues? Anny suggestions how to proceed? > > Thanks, > > Lennart > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Wed Sep 08 2021 - 09:00:03 PDT