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 - 16:30:03 PDT
