Custom Search
-- 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 7:06 AM, Urszula Uciechowska <urszula.uciechowska.biotech.ug.edu.pl> wrote: > >> So do you see any error message in the sander output when running with >> the first input, which is recommended? > > Yes after 50minutes of calculations the error is: > amber16/bin/sander failed with prmtop complex.top! > > >> >> When you use the second input, you implicitly used radiopt=1, which >> asks the program to assign radii for all atoms. However it apparently >> doesn't know anything about D1/DU, so you saw the error message. > > After using second input: the error message is: PB Bomb in pb_aaradi(): No > radius assigned for > atom > 2735 D1 DU > > How can I fix this problem, in previous versions AMBER10 and 11 I did not > have this error while running mmpbsa. > > best > Urszula > >> All the best, >> Ray >> -- >> 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/amber >> > > > > -------------------------------------------- > 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 - 14:00:03 PST