On Mon, Sep 14, 2015 at 9:40 PM, Lara rajam <lara.4884.gmail.com> wrote:
> Dear Amber
>
> I am trying to do the MMPBSA calculation , earlier I was generating the
> parameters with ff99SB and I was able to run mmpbsa.py
>
> Now I generated the prmtop using ff12SB , I was not able to run mmpbsa
> calculation, the error is as below I am running in serial mode. I again
> generated all the prmtop and did a try, the error is the same and my input
> is below
>
> INPUT file
>
> Input file for running PB and GB in serial
>
> &general
>
> endframe=50, keep_files=2,
>
> /
>
> &gb
>
> igb=2, saltcon=0.100,
>
> /
>
> &pb
>
> istrng=0.100,
>
> /
>
>
> OUT PUT ERROR !
>
> [TEST.NEMO dr2]$ $AMBERHOME/bin/MMPBSA.py -O -i mmpbsa.in -o
> FINAL_RESULTS_MMPBSA.dat -sp solvated_di.prmtop -cp complex.prmtop -rp
> protein.prmtop -lp ligand.prmtop -y *.mdcrd
>
> Loading and checking parameter files for compatibility...
>
> mmpbsa_py_energy found! Using
> /home/TEST/AMBERHOME/amber14/bin/mmpbsa_py_energy
>
> cpptraj found! Using /home/TEST/AMBERHOME/amber14/bin/cpptraj
>
> Preparing trajectories for simulation...
>
> 50 frames were processed by cpptraj for use in calculation.
>
>
> Running calculations on normal system...
>
>
> Beginning GB calculations with
> /home/TEST/AMBERHOME/amber14/bin/mmpbsa_py_energy
>
> calculating complex contribution...
>
> File "/home/TEST/AMBERHOME/amber14/bin/MMPBSA.py", line 96, in ?
>
> app.run_mmpbsa()
>
> File "/home/TEST/AMBERHOME/amber14/bin/MMPBSA_mods/main.py", line 218, in
> run_mmpbsa
>
> self.calc_list.run(rank, self.stdout)
>
> File "/home/TEST/AMBERHOME/amber14/bin/MMPBSA_mods/calculation.py", line
> 79, in run
>
> calc.run(rank, stdout=stdout, stderr=stderr)
>
> File "/home/TEST/AMBERHOME/amber14/bin/MMPBSA_mods/calculation.py", line
> 147, in run
>
> raise CalcError('%s failed with prmtop %s!' % (self.program,
>
> CalcError: /home/TEST/AMBERHOME/amber14/bin/mmpbsa_py_energy failed with
> prmtop complex.prmtop!
>
This just says the energy calculation didn't work. It doesn't have the
actual error message that says what went wrong.
Look inside _MMPBSA_complex_gb.mdout.0 to see if the error message is there.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Tue Sep 15 2015 - 07:30:06 PDT
