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-- 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 Thu, Dec 17, 2020 at 9:36 PM Neha Gandhi <n.gandhiau.gmail.com> wrote: > > Further to my email, here are the errors: > > Error occured on rank 3. > Exiting. All files have been retained. > calc.run(rank, stdout=stdout, stderr=stderr) > File > "/home/gandhin/amber17/lib/python2.7/site-packages/MMPBSA_mods/calculation.py", > line 431, in run > self.prmtop) + '\n\t'.join(error_list) + '\n') > CalcError: /home/gandhin/amber17/bin/sander failed with prmtop > ../../NTD/HS-9548211675/complex.prmtop! > > > Error occured on rank 5. > Exiting. All files have been retained. > calc.run(rank, stdout=stdout, stderr=stderr) > File > "/home/gandhin/amber17/lib/python2.7/site-packages/MMPBSA_mods/calculation.py", > line 431, in run > self.prmtop) + '\n\t'.join(error_list) + '\n') > CalcError: /home/gandhin/amber17/bin/sander failed with prmtop > ../../NTD/HS-9548211675/complex.prmtop! > > > Error occured on rank 9. > Exiting. All files have been retained. > calc.run(rank, stdout=stdout, stderr=stderr) > File > "/home/gandhin/amber17/lib/python2.7/site-packages/MMPBSA_mods/calculation.py", > line 431, in run > self.prmtop) + '\n\t'.join(error_list) + '\n') > CalcError: /home/gandhin/amber17/bin/sander failed with prmtop > ../../NTD/HS-9548211675/complex.prmtop! > > -------------------------------------------------------------------------------- > 4. RESULTS > -------------------------------------------------------------------------------- > > POST-PROCESSING OF TRAJECTORY ENERGIES > Cpptraj Generated trajectory > > minimizing coord set # 1 > PB bomb in pb_atmlist(): MAXNEI too short > > > > <http://www.avg.com/email-signature?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail> > Virus-free. > www.avg.com > <http://www.avg.com/email-signature?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail> > <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2> > > On Fri, 18 Dec 2020 at 07:28, Neha Gandhi <n.gandhiau.gmail.com> wrote: > > > Hi List, > > > > I tried to run gbsa and pbsa using ambertools18. Gbsa produces output > > without any issues with prmtop files. However, pbsa throws calc error with > > complex.prmtop files. I have changed the default parameter for radiopt to > > 0. > > > > How can I get this running? > > let me know if I should provide further information. > > > > Regards, > > Neha > > > > > > -- > Regards, > Dr. Neha S. Gandhi, > Vice Chancellor's Research Fellow, > Queensland University of Technology, > 2 George Street, Brisbane, QLD 4000 > Australia > LinkedIn > Research Gate > _______________________________________________ > 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 Dec 18 2020 - 16:00:02 PST