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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 Mon, Aug 10, 2015 at 3:09 AM, Kenneth Huang <kennethneltharion.gmail.com> wrote: > Hi, > > Have you tried inp=1 with radiopt=0, and are there any other error messages > in the mdout files? I'd also suggest upgrading to Ambertools15, just to > have the latest version. > > Best, > > Kenneth > > On Sun, Aug 9, 2015 at 7:38 AM, shenna shearin <smsheari.gmail.com> wrote: > >> I am using AMBER14. When I run inp=1 or gb all is well. >> >> On Fri, Aug 7, 2015 at 11:59 PM, Ray Luo, Ph.D. <ray.luo.uci.edu> wrote: >> >> > Hi Shenna, >> > >> > It appears that you are using sander for your jobs. Which Amber >> > version are you using? Also, do you see the same error message with >> > inp=1 or gb? >> > >> > All the best, >> > Ray >> > >> > >> > All the best, >> > Ray >> > -- >> > 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/amber >> > >> >> >> >> -- >> 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 >> > > > > -- > Ask yourselves, all of you, what power would hell have if those imprisoned > here could not dream of heaven? > _______________________________________________ > 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 Aug 09 2015 - 22:30:02 PDT