Dear Amber
The error message was
PB Bomb in pb_aaradi(): No radius assigned for atom 7 CB 2C
I went through the earlier post and changed my input files as below
input file for running PB and GB
&general
endframe=5000, keep_files=2,
/
&gb
igb=2, saltcon=0.100,
/
&pb
istrng=0.100,inp=1,radiopt=0,
/
The programing is working .
I have a question if one need to calculate the binding energy (ligand ,
Protein) is these inputs are enough if not what else to be added
thank you
On Tue, Sep 15, 2015 at 10:27 AM, Jason Swails <jason.swails.gmail.com>
wrote:
> 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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>
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Received on Tue Sep 15 2015 - 10:00:03 PDT
