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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, Mar 13, 2021 at 3:05 PM Chuck is Busy <chuckisbusy.gmail.com> wrote: > > So...CHARMM-GUI converts the structure to the Amber format with prmtop and > rst7. I used those files to run my simulation, and I used that same prmtop > file to create my complex, receptor, and ligand prmtop file with cpptraj. > At the time, I didn't realize that my CHARMM-GUI prmtop file doesn't have > any radii defined. After I create my 3 topology files to run sander, I get > that error because none of those files have a radii mentioned. Then I go > back and set mbondi as my radii for my 3 topology files and I guess I'm > overestimating my values. > > If my simulation was run without defining a radii, what radii or what > values can I set for my 3 topology files to get reasonable values with > sander? > Or can I use cpptraj to trajout a trajectory with new radii? > > > On Sat, Mar 13, 2021 at 5:08 PM David A Case <david.case.rutgers.edu> wrote: > > > On Sat, Mar 13, 2021, Chuck is Busy wrote: > > > > > >Do you have any better insight on how I can define the 1-4 EEL and 1-4 VDW > > >scale factors so I can run PBSA calculations on my protein system? The > > >protein membrane system was built in CHARMM-GUI and the CHARMM force field > > >but simulated using AMBER. > > > > If you ran the simulation with Amber, you have prmtop files with the > > appropriate values of SCEE and SCNB in them (as highlighted here from your > > output): > > > > >| Note: 1-4 EEL scale factors are being read from the topology file. > > >| Note: 1-4 VDW scale factors are being read from the topology file. > > > > >If I set my radii to mbondi with parmed.py and set scnb and scee to 1. I > > >can get MMPBSA to run this way using sander, but after doing my > > >subtractions I get extremely positive values like 1200 to 1700. Wondering > > >if there is a more appropriate way to do this.. > > > > Why are you changing scnb and scee with parmed? Setting the radii makes > > sense to me, but I'm not sure why you want to change scnb and scee. > > > > ...hoping the others on the list will correct any mistakes above. > > > > ....dac > > > > > > _______________________________________________ > > 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/amber _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Sat Mar 13 2021 - 16:00:01 PST