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-- Ray Luo, Ph.D. Professor, Biochemistry, Molecular Biophysics, Chemical Physics, Chemical and Biomedical Engineering University of California, Irvine, CA 92697-3900 On Tue, Jun 23, 2015 at 8:00 AM, Norbert GARNIER <norbert.garnier.cnrs-orleans.fr> wrote: > sorry but it is npopt=1 > In the trj files i dont keep water > Thank you > Norbert > > Le 23/06/2015 14:37, Jason Swails a écrit : >> On Tue, Jun 23, 2015 at 8:26 AM, Norbert GARNIER < >> norbert.garnier.cnrs-orleans.fr> wrote: >> >>> Dear Amber Users >>> >>> I have performed 10 ns of MD simulations on a DNA-Protein-Ligand-Na+ and >>> a zinc atom complex with Amber11. >>> I would like to calculate the binding free energy of the ligand with the >>> DNA-Protein part using MMPBSA.py. >>> >>> My input file is the following: >>> >>> &general >>> startframe=1, interval=5, endframe=5000, keep_files=2 >>> receptor_mask=':1-299', ligand_mask=':300', >>> strip_mdcrd=1, strip_mask=':Na+:ZNA', >>> entropy=1, >>> / >>> &pb >>> nopot=1, cavity_surften=0.0378, cavity_offset=-0.5692, >>> fillratio=4, scale=2.0, >>> linit=1000, prbrad=1.4, radiopt=0, >>> / >>> >>> >> Is this input file is correct? >> What is nopot? That doesn't look like any MMPBSA.py variable I'm aware >> of... And your strip_mask only strips Na+ and ZNA residues. Did you not >> have explicit solvent? >> >> Also, what version of AmberTools are you using? >> > > -- > Dr. Norbert GARNIER > Assistant Professor of physics - Orléans University > > « DNA repair: structural and functional approaches» > Centre de Biophysique Moléculaire, UPR4301, CNRS > Rue Charles Sadron > CS 80054 > 45071 Orléans cedex 2 > Tel: +33 (0)2 38 25 76 68 > Web site : http://cbm.cnrs-orleans.fr/ > > _______________________________________________ > 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 Tue Jun 23 2015 - 11:00:02 PDT