Are there any error messages in the _MMPBSA_receptor_gb.mdout?
I would also suggest upgrading to the newest version of MMPBSA.py that was
released with AmberTools12 (
http://ambermd.org/#AmberTools)
-Bill
On Fri, Apr 13, 2012 at 4:05 AM, Aditya Setiajid <setiajid11.yahoo.com>wrote:
> Dear Amber Users,
>
> I faced a problem when i ran MMPBSA with my own protein and ligand after
> 200ps MD simulation. I just want to try if my way to run MMPBSA is right or
> not, apparently my job didn't worked. This error message appeared when i
> ran MMPBSA.
>
> Reading command-line arguments and input files...
> Loading and checking parameter files for compatibility...
> ptraj found! Using /home/farm/mirror/Programs/amber/amber11/bin/ptraj
> mmpbsa_py_energy found! Using
> /home/farm/mirror/Programs/amber/amber11/bin/mmpbsa_py_energy for GB
> calculations
> mmpbsa_py_energy found! Using
> /home/farm/mirror/Programs/amber/amber11/bin/mmpbsa_py_energy for PB
> calculations
> Preparing trajectories for simulation...
> 20 frames were read in and processed by
> ptraj for use in calculation.
>
> Beginning GB calculations with mmpbsa_py_energy...
> calculating complex contribution...
> calculating receptor contribution...
> Segmentation fault
> Error: mmpbsa_py_energy error during GB calculations!
> NOTE: All files have been retained for debugging purposes. Type MMPBSA.py
> --clean to erase these files.
>
>
> What's wrong with my job? what is the meaning of segmentation fault? here
> is my command to run MMPBSA:
>
> nohup MMPBSA -O -i MMPBSA.in -o 6COX_s58k_MMPBSA.dat -sp
> 6COXAsolvoct.prmtop -cp 6COXSVak_netral.prmtop -rp 6COXSonly.prmtop -lp
> s58k.prmtop -y 6COXAsolvoct_md2_ntpr2.crd > MMPBSA.log &
>
>
>
> Best Regards,
> Muhammad Aditya Setiajid
> University of Indonesia
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Bill Miller III
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-6715
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Received on Fri Apr 13 2012 - 06:00:05 PDT
