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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 3:49 PM Chuck is Busy <chuckisbusy.gmail.com> wrote: > > Hi Ray, > > I have tried this before and I get an error/PB Bomb: > PB Bomb in pb_aaradi(): No radius assigned for atom 1 N NH3 > > I attached the full .out file as well. > > On Sat, Mar 13, 2021 at 6:32 PM Ray Luo <rluo.uci.edu> wrote: > > > Hi Chuck, > > > > If you can run your amber MD simulations and your only issue is lack > > of radii for pbsa, how about setting radiopt=1 in the mmpbsa input so > > pbsa can set the radii for you? > > > > However, the caveat is that there could be newer atom types defined > > if newer protein force fields are used. Hopefully these atom types > > have been added to pbsa in newer Amber releases. > > > > All the best, > > Ray > > -- > > 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/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 - 19:00:02 PST