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
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>
--
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 - 08:30:05 PDT
