And one more information that I would like to share is that when I run the
nmode calculation with the same set of topology files, I get a different
error stating that the EXECTED NUMBER OF BOX CO-ORDINATES which is 3 or 6
DOES NOT MATCH THE CO-ORDINATES DETECTED (4). Could this again be due to
the strip_mask issue.
Please comment on this.
On Thu, Sep 18, 2014 at 4:53 AM, Jason Swails <jason.swails.gmail.com>
wrote:
> On Wed, Sep 17, 2014 at 7:18 PM, Sourav Purohit <sour000.gmail.com> wrote:
>
> > I have two ions in my dry complex trajectopy file. I run the binding
> energy
> > calculations. I get the following error:
> >
> > Loading and checking parameter files for compatibility...
> > mmpbsa_py_energy found! Using
> > /home/suman/Downloads/amber14/bin/mmpbsa_py_energy
> > cpptraj found! Using /home/suman/Downloads/amber14/bin/cpptraj
> > Preparing trajectories for simulation...
> > 3 frames were processed by cpptraj for use in calculation.
> >
> > Running calculations on normal system...
> >
> > Beginning GB calculations with
> > /home/suman/Downloads/amber14/bin/mmpbsa_py_energy
> > calculating complex contribution...
> > File "/home/suman/Downloads/amber14/bin/MMPBSA.py", line 96, in
> <module>
> > app.run_mmpbsa()
> > File "/home/suman/Downloads/amber14/bin/MMPBSA_mods/main.py", line 218,
> > in run_mmpbsa
> > self.calc_list.run(rank, self.stdout)
> > File "/home/suman/Downloads/amber14/bin/MMPBSA_mods/calculation.py",
> line
> > 79, in run
> > calc.run(rank, stdout=stdout, stderr=stderr)
> > File "/home/suman/Downloads/amber14/bin/MMPBSA_mods/calculation.py",
> line
> > 459, in run
> > self.prmtop))
> > CalcError: /home/suman/Downloads/amber14/bin/cpptraj failed with prmtop
> > 1kf1e2_vac_now.prmtop!
> > Exiting. All files have been retained.
> >
> >
> > 1kf1e2_vac_now.prmtop is the dry complex topology which has two ions.
> > Can you guess what the problem is??
> >
>
> Yes, but all I can do is guess with the information you provided. I
> suspect that you did not adjust strip_mask and MMPBSA.py stripped out the
> atoms from the solvated trajectory. So the trajectories no longer match
> the topology files.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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Received on Wed Sep 17 2014 - 16:30:04 PDT
