Thank you
This is only what is in the _MMPBSA_complex_pb.mdout.0. file. I don't see
an error msg there.
Reading parm file (../complex.prmtop)
title:
default_name
mm_options: e_debug=3
mm_options: ipb=2
mm_options: inp=2
mm_options: epsin=1.000000
mm_options: epsout=80.000000
mm_options: smoothopt=1
mm_options: istrng=100.000000
mm_options: radiopt=1
mm_options: dprob=1.400000
mm_options: iprob=2.000000
mm_options: npbopt=0
mm_options: solvopt=1
mm_options: accept=0.001000
mm_options: maxitn=1000
mm_options: fillratio=4.000000
mm_options: space=0.500000
mm_options: nfocus=2
mm_options: fscale=8
mm_options: bcopt=5
mm_options: eneopt=2
mm_options: cutnb=0.000000
mm_options: sprob=0.557000
mm_options: cavity_surften=0.037800
mm_options: cavity_offset=-0.569200
Processing ASCII trajectory (_MMPBSA_complex.mdcrd.0)
Processing frame 1
iter Total bad vdW elect nonpolar EPB
frms
On Wed, Mar 27, 2013 at 11:48 AM, Jason Swails <jason.swails.gmail.com>wrote:
> The error message will be found in _MMPBSA_complex_pb.mdout.0.
>
> If you google the error message you get, it should take you to previous
> discussions on the mailing list where people have asked that question and
> received answers.
>
> Good luck,
> Jason
>
> On Wed, Mar 27, 2013 at 12:08 PM, Chinthaka Ratnaweera <cnr88.msstate.edu
> >wrote:
>
> > Hi
> > I am getting following error when calculating the MMPBSA energies with
> > MMPBSA.py. But GBSA works fine. Error msg and input files are paste
> below.
> > Thank you in advanced.
> >
> > Reading command-line arguments and input files...
> > Loading and checking parameter files for compatibility...
> > mmpbsa_py_energy found! Using /usr/local/amber12/bin/mmpbsa_py_energy
> > cpptraj found! Using /usr/local/amber12/bin/cpptraj
> > Preparing trajectories for simulation...
> > 50 frames were processed by cpptraj for use in calculation.
> >
> > Beginning PB calculations with /usr/local/amber12/bin/mmpbsa_py_energy
> > calculating complex contribution...
> > CalcError: /usr/local/amber12/bin/mmpbsa_py_energy failed with prmtop
> > ../complex.prmtop!
> >
> >
> > Exiting. All files have been retained.
> >
> > ...................
> >
> > input file
> >
> > input file for running PB and GB in serial
> > &general
> > endframe=50, keep_files=2,
> > /
> > &gb
> > igb=2, saltcon=0.100,
> > /
> > &pb
> > istrng=0.100,
> > /
> >
> >
> > --
> > Chinthaka Nadun Ratnaweera
> > Mississippi State University
> > 310 Presidents Circle
> > Starkville, MS 39762
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Chinthaka Nadun Ratnaweera
Hand Lab Rm 1126
Mississippi State University
310 Presidents Circle
Starkville, MS 39762
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Received on Wed Mar 27 2013 - 11:00:02 PDT
