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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 Thu, Nov 9, 2017 at 1:22 AM, Urszula Uciechowska <urszula.uciechowska.biotech.ug.edu.pl> wrote: > > Dear Amber users, > > While running mmpbsa.py (AMBER16) I am getting an error message after 50 > min of calculations that > amber16/bin/sander failed with prmtop complex.top! > > > My complex contains Zn atom for which I used Cationic Dummy Atom (CaDA) > approach. > > My input for MMPBSA is: > > &general > startframe=1, endframe=1000, interval=1, > verbose=2, keep_files=0, > / > &pb inp=1, radiopt=0, > / > > > > > If i use as a input file: > > &general > startframe=1, endframe=1000, interval=1, > verbose=2, keep_files=0, > / > &pb > / > > The error message is: PB Bomb in pb_aaradi(): No radius assigned for atom > 2735 D1 DU > > I went through the previous user lists messages, but there is no clear > answers that I could find. > > Thanks in advance for any help. > > best > Urszula > -------------------------------------------- > Urszula Uciechowska PhD > University of Gdansk and Medical Univesity of Gdansk > Department of Molecular and Cellular Biology > ul. Abrahama 58 > 80-307 Gdańsk > Poland > > > ----------------------------------------- > Ta wiadomość została wysłana z serwera Uniwersytetu Gdańskiego > http://www.ug.edu.pl/ > > > _______________________________________________ > 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 Thu Nov 09 2017 - 06:00:02 PST