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?
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Received on Sun Aug 09 2015 - 12:30:02 PDT
