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
> > _______________________________________________
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
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>
--
Shenna Shearin
PhD candidate
Department of Computational Science & Engineering,
North Carolina A & T State University
Greensboro, NC 27411
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Received on Sun Aug 09 2015 - 05:00:02 PDT
