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??
On Thu, Sep 18, 2014 at 4:38 AM, Jason Swails <jason.swails.gmail.com>
wrote:
> On Wed, Sep 17, 2014 at 6:46 PM, Sourav Purohit <sour000.gmail.com> wrote:
>
> > Hi all,
> >
> > What happens if one has ions in the complex (dry) prmtop file? Will it
> lead
> > to an error?
> >
>
> If you do not change strip_mask to prevent it from stripping out the ions
> that are still in the complex dry file, then yes you will get an error.
>
> As long as coordinate files match topology files after MMPBSA.py processes
> the trajectory, MMPBSA.py should run.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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> AMBER.ambermd.org
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>
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Received on Wed Sep 17 2014 - 16:30:02 PDT
