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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 Thu, Dec 7, 2023 at 2:50 AM kefun via AMBER <amber.ambermd.org> wrote: > > Dear AMBER users, > > > I am currently utilizing Amber20 software for molecular dynamics simulations. I am writing to seek clarification and assistance concerning the SASA (Solvent Accessible Surface Area) calculation method employed by MMPBSA.py in PBSA when inp is set to 1. > In a series of calculations with MMPBSA.py, using the following input parameters: > > > &general > startframe=1, > endframe=10, > use_sander=1, > keep_files=0, > / > > > &pb > fillratio=4.0, > scale=2.0, > linit=1000, > inp=1, > radiopt=0, > cavity_surften=1, > cavity_offset=0 > / > > > &gb > igb=1, > molsurf=0, > surften=1, > > > The calculated SASA values obtained with MMPBSA.py were 277.9774 (PBSA) and 213.1704 (GBSA), respectively. > To cross-verify the results, I employed the molsurf and surf modules in cpptraj with the following input: > > > parm solution.prmtop > trajin 10.nc > molsurf molsurf :1 out molsurf.dat > surf surf :1 out surf.dat > > > The SASA values obtained using cpptraj were 127.6351 (molsurf) and 213.1675 (surf). > Upon comparing these results, it appears that in MMPBSA.py, the SASA calculation in GBSA indeed utilizes the LCPO (Linear Combination of Pairwise Overlaps) method. However, when inp is set to 1 for PBSA, the SASA calculation does not seem to align with either the molsurf method or the LCPO method. > > > I am writing to seek your expertise in confirming the SASA calculation method employed by MMPBSA.py in PBSA when inp is set to 1. It is crucial for our analysis to understand the underlying method, and your insights would greatly contribute to reconciling the observed differences in SASA values between MMPBSA.py and cpptraj calculations. > > > Thank you for your time and consideration. I look forward to your guidance on this matter. > > > > > Best wishes to you! > > > Kai-Fang Huang > > > > > > > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > https://urldefense.com/v3/__http://lists.ambermd.org/mailman/listinfo/amber__;!!CzAuKJ42GuquVTTmVmPViYEvSg!NRAm4PZwK4iEdghwulGkMtJc9VapZ_XDxWutw9h3lmydNQmo-2rlIIC57hESAX0n6pFv6NPjAkE$ _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Thu Dec 07 2023 - 11:30:02 PST