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-- Ray Luo, Ph.D. Professor Biochemistry, Molecular Biophysics, Chemical Physics, Chemical and Biomedical Engineering University of California, Irvine, CA 92697-3900 On Sat, Aug 8, 2015 at 8:33 AM, shenna shearin <smsheari.gmail.com> wrote: > Hi Amber community! > > I am trying to run mmpbsa using pbsa=2 on 300 frames of the last 50ns of > trajectory but am continuously encountering problems. Your input is greatly > appreciated. My input file is below followed by the errow statement. > > PBSA with PARSE RADII > &general > startframe=1, endframe=9999, interval=1, netcdf=1, > ligand_mask=":336-678", receptor_mask=":1-335", > use_sander=1, > / > &pb > inp=2, radiopt=1, istrng=0.100, > > > CalcError: /home/divi/gccamber/bin/sander failed with prmtop complex.top! > > calc.run(rank, stdout=stdout, stderr=stderr) > Error occured on rank 7. > Exiting. All files have been retained. > File > "/home/divi/gccamber/lib/python2.6/site-packages/MMPBSA_mods/calculation.py", > line 431, in run > calc.run(rank, stdout=stdout, stderr=stderr) > File > "/home/divi/gccamber/lib/python2.6/site-packages/MMPBSA_mods/calculation.py", > line 431, in run > CalcError: /home/divi/gccamber/bin/sander failed with prmtop complex.top! > > > [cli_7]: aborting job: > application called MPI_Abort(MPI_COMM_WORLD, 1) - process 7 > Error occured on rank 13. > Exiting. All files have been retained. > self.prmtop) + '\n\t'.join(error_list) + '\n') > self.prmtop) + '\n\t'.join(error_list) + '\n') > CalcError: /home/divi/gccamber/bin/sander failed with prmtop complex.top! > > -- > Shenna Shearin > PhD candidate > Department of Computational Science & Engineering, > North Carolina A & T State University > Greensboro, NC 27411 > _______________________________________________ > 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 Fri Aug 07 2015 - 21:30:02 PDT