On Tue, Feb 19, 2013 at 8:02 AM, Saugata Hazra <saugata.iitk.gmail.com>wrote:
> Hi,
>
> I am running a binding energy calculation (MM-PBSA) for protein-ligand
> complex using Amber11 and AmberTools 1.5. I am following Ross Walker
> tutorial but have got error message during MMPBSA calculation as follows:
>
> saugata.saugata:~/Desktop/ba2291/mdrun/ba2291_atp$ $AMBERHOME/bin/MMPBSA
> -O
> -i mmpbsa.in -o FINAL_RESULTS_MMPBSA.dat -sp ba2291_atp_mg.prmtop -cp
> ba2291_com.prmtop -rp ba2291_prot.prmtop -lp atp.prmtop -y *.mdcrd
> Reading command-line arguments and input files...
> Loading and checking parameter files for compatibility...
> ptraj found! Using /home/saugata/amber11/bin/ptraj
> mmpbsa_py_energy found! Using /home/saugata/amber11/bin/mmpbsa_py_energy
> for GB calculations
> mmpbsa_py_energy found! Using /home/saugata/amber11/bin/mmpbsa_py_energy
> for PB calculations
> Preparing trajectories for simulation...
> 50 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 (core dumped)
>
Yikes. A segfault from NAB. Try upgrading to AmberTools 12 and use that
version instead. You can also try putting "use_sander=1" in the &general
section of the MMPBSA.py input file to force it to use sander instead.
Good luck,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Tue Feb 19 2013 - 06:30:03 PST
