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-- Ray Luo, Ph.D. Professor of Structural Biology/Biochemistry/Biophysics, Chemical Physics, Biomedical Engineering, and Chemical Engineering Department of Molecular Biology and Biochemistry University of California, Irvine, CA 92697-3900 On Sat, Jul 1, 2017 at 7:19 PM, Baker, Joseph <bakerj.tcnj.edu> wrote: > Hi all, > > We've been trying to do a protein/DNA mmpbsa calculation using the > non-linear PB (so running with use_sander = 1, -make-mdins, then -use-mdins > to mmpbsa.py). We are using AmberTools17. > > We are trying to do the calculation on 50 frames over several trajectories. > After getting to about frame 8 in the analysis (for both of our > trajectories), the output from the calculation starts giving > > PBSA WARNING in pb_miccg(): CG maxitn exceeded! > > We increase the verbosity and we increased the maxitn to a very large > number (1,000,000) in one of the calcs, and still get the same problem. The > warning appears to come after the output > > Atomic solvent accessible surface area: > > in the output files consistently. Looking at the mdcrd trajectory that > mmpbsa produces for the calculation, there is no obvious difference in > between say frame 7 and 8 in the trajectory that would suggest why the > calculation is getting stuck all of sudden. > > Linear PB and GB handle the same sets of frames just fine by the way. > > I can provide more detailed information (input scripts, info about the > system, etc.) if needed. > > Thanks, > Joe > > > ------ > Joseph Baker, PhD > Assistant Professor > Department of Chemistry > C101 Science Complex > The College of New Jersey > Ewing, NJ 08628 > Phone: (609) 771-3173 > Web: http://bakerj.pages.tcnj.edu/ > _______________________________________________ > 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 Sun Jul 02 2017 - 09:00:03 PDT