Are you trying to run MMPBSA on 151 frames like the output suggests? Because
your input specifies to only run on 50 frames. That would possibly suggest
some sort of prmtop/trajectory inconsistency. Regardless, you can probably
fine a more helpful error message in the standard error file or in the
_MMPBSA_complex_gb.mdout.
-Bill
On Tue, Sep 13, 2011 at 8:33 AM, 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
>
--
Bill Miller III
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-6715
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Received on Tue Sep 13 2011 - 06:30:04 PDT
