I think it is is a fault in the mmpa code. May be you have to write your own
code
On Tue, Sep 13, 2011 at 6:03 PM, Devlina Chakravarty <
devlina.chakravarty.gmail.com> wrote:
> Hullo,
>
> I am trying to calculate the binding free energy of Tubulin when it
> binds with colchicine using mmpbsa.py. I thought of carrying out the
> binding energy calculation using both the MM-GBSA method and the
> MM-PBSA method for comparison. I am using Amber tools 1.5. In a folder
> I have the .top files for the solvated complex,complex in vacuum,
> protein in vacuum and the drug in vacuum. Also the .crd files for the
> complex , the starting structure generated from leap, the structure
> after equilibration, and the structure after 10 ns of simulation.
>
> The input file for mmpbsa:
> Input file for running PB and GB in serial
> &general
> endframe=50, keep_files=2,
> /
> &gb
> igb=1, saltcon=0.100,
> /
> &pb
> istrng=0.100,
> /
>
> Then I type in the command to run mmpbsa:
> MMPBSA -O -i mmpbsa.in -o FINAL_RESULTS_MMPBSA.dat -sp
> 1sa0-water.prmtop -cp 1sa0.prmtop -rp 1sa0_b.top -lp cn2.prmtop -y
> *crd
>
> The program stops after giving this error message:
>
> Reading command-line arguments and input files...
> Loading and checking parameter files for compatibility...
> ptraj found! Using /home/pinak/amber11/bin/ptraj
> mmpbsa_py_energy found! Using /home/pinak/amber11/bin/mmpbsa_py_energy
> for GB calculations
> mmpbsa_py_energy found! Using /home/pinak/amber11/bin/mmpbsa_py_energy
> for PB calculations
> Preparing trajectories for simulation...
> 151 frames were read in and processed by ptraj for use in calculation.
>
> Beginning GB calculations with mmpbsa_py_energy...
> calculating complex contribution...
> Error: mmpbsa_py_energy error during GB calculations!
>
> I don't know where is it going wrong. Any help would be appreciated.
>
> Thanks in advance,
> --
> Devlina Chakravarty
> JRF
> Bose Institute
> Kolkata
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
R.Dhilip kumar
Computational Biophysics Lab
Department of Biotechnology
IIT Madras
Chennai-600036
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Sep 13 2011 - 06:30:06 PDT
