Dear Jason,
Thanks for your response. I used following input. I have commented for pb
section just to test.
Sample input file for GB and PB calculation
&general
startframe=310, endframe=410, interval=5,
verbose=2, keep_files=0,
entropy=1,
/
&gb
igb=5, saltcon=0.150,
/
#&pb
istrng=0.15, fillratio=4.0
Most interesting fact is that same topology and mdcrd files are running
well for GB section on my laptop, having same OS, but giving PB bomb for
pb_aaradi.....for PB calculations.
Kshatresh
On Tue, May 7, 2013 at 12:10 AM, Jason Swails <jason.swails.gmail.com>wrote:
> W
> hat is your input file?
>
>
> On Mon, May 6, 2013 at 11:21 AM, Kshatresh Dutta Dubey
> <kshatresh.gmail.com>wrote:
>
> > Hi Chris
> >
> > I also tried that, and all topology files were generated by
> ante-MMPBSA.py
> > but unfortunately I found same error.
> >
> >
> > On Mon, May 6, 2013 at 8:48 PM, Chris Chris <alpharecept.yahoo.com>
> wrote:
> >
> > > Did you use ante-mmpbsa.py to make the topology files? If not I highly
> > > recommend you do this. It could be that your topology files are not
> > > compatible with each other MMPBSA.py is very sensitive to this issue.
> > >
> > >
> > > ________________________________
> > > From: Kshatresh Dutta Dubey <kshatresh.gmail.com>
> > > To: AMBER Mailing List <amber.ambermd.org>
> > > Sent: Monday, May 6, 2013 7:16 AM
> > > Subject: [AMBER] MMPBSA.py error
> > >
> > >
> > > Dear Users,
> > >
> > > I am running MMPBSA.py using Amber 12. I am getting an error like--
> > >
> > > *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
> > > ptraj found! Using /usr/local/amber12/bin/ptraj
> > > Preparing trajectories for simulation...
> > > 21 frames were processed by cpptraj for use in calculation.
> > >
> > > Beginning GB calculations with /usr/local/amber12/bin/mmpbsa_py_energy
> > > calculating complex contribution...
> > > calculating receptor contribution...
> > > CalcError: /usr/local/amber12/bin/mmpbsa_py_energy failed with prmtop
> > > receptor_ant.top!
> > > Exiting. All files have been retained.
> > > *
> > >
> > > I searched this problem and also followed suggestion by Jason to check
> > for
> > > -
> > > mmpbsa_py_energy -O -i _MMPBSA_pb.mdin -p <complex_prmtop> -c
> > > _MMPBSA_complex.pdb -y _MMPBSA_complex.mdcrd.0 -o output
> > >
> > > and found segmentation fault. I checked the intermediate files and
> > noticed
> > > that _MMPBSA_complex.pdb, _MMPBSA_receptor.pdb and _MMPBSA_ligand.pdb
> > > files are same. It seems that MMPBSA.py does not seperate ligand and
> > > receptor from complex.
> > >
> > > Does anyone suggest solution for it. I will deeply appreciate your
> > support.
> > >
> > >
> > >
> > > With best regards
> > >
> > >
> >
> *******************************************************************************************************************
> > > Kshatresh Dutta Dubey, PhD
> > > Post Doctoral Fellow
> > > Indian Institute of Technology Kanpur
> > > Kanpur, India
> > > _______________________________________________
> > > 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
> > >
> >
> >
> >
> > --
> > With best regards
> >
> >
> *******************************************************************************************************************
> > Kshatresh Dutta Dubey, PhD
> > Post Doctoral Fellow
> > Indian Institute of Technology Kanpur
> > Kanpur, India
> > _______________________________________________
> > 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
>
--
With best regards
*******************************************************************************************************************
Kshatresh Dutta Dubey, PhD
Post Doctoral Fellow
Indian Institute of Technology Kanpur
Kanpur, India
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Received on Mon May 06 2013 - 12:30:03 PDT
