Custom Search
-- 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 Mon, Aug 23, 2021 at 7:59 AM Gilberto Pereira <gilberto.pereiraportugal.gmail.com> wrote: > > Dear members of the Amber mailing list. > > I am trying to carry out some MM/PBSA calculations in a protein-ligand > system whose simulation included a POPC membrane and explicit solvent, > carried out using GROMACS and converted to Amber format with GROMBER. The > water and membrane atoms were removed previous to the MM/PBSA calculation. > Below is the input file used to setup up the MM/PBSA run using AmberTools18. > > " > Sample input file for MMPBSA with membrane proteins > &general > use_sander=1, > startframe=1000, endframe=2000, interval=100, > keep_files=1, debug_printlevel=2 > / > &pb > radiopt=0, indi=4.0, istrng=0.150, exdi=80.0, > fillratio=1.25, ipb=1, nfocus=1, > bcopt=10, eneopt=1, cutfd=7.0, cutnb=99.0, > npbverb=1, solvopt=2, inp=1, > memopt=1, emem=1.0, mctrdz=90.31, mthick=46, poretype=1, > maxarcdot=15000, sasopt=0, > / > " > Upon submission of the calculation, the program crashes with the following > error: > > minimizing coord set # 1 > PB bomb in pb_atmlist(): MAXNEI too short > > Could you please help me to solve this issue? > > Best regards, > Gilberto Pereira > _______________________________________________ > 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 Mon Aug 23 2021 - 13:00:02 PDT