On Wed, 2014-04-02 at 14:41 +0530, Arun Kumar Somavarapu wrote:
>
> Dear Sir,
>
> Sorry for the delay in replying the mail.
>
> while calculating entropy i used to remove the comment.
>
> I am able to calculate values successfully with out entropy, but when I
> switch on the entropy (entropy = 1) I was getting that error.
>
> I have done MD by using amber11 and I am calculating MMPBSA with
> ambertools13.
>
> I have taken care of environment variables as fallows
>
> export AMBERHOME=/home/user/amber12
> export PATH=$PATH:/home/user/amber12/bin:/home/user/amber11/bin
>
> later, I have changed "igb" from 5 to 2, this time i am getting the
> fallowing error
>
> Loading and checking parameter files for compatibility...
> mmpbsa_py_energy found! Using /home/braf/md/amber12/bin/mmpbsa_py_energy
> cpptraj found! Using /home/braf/md/amber12/bin/cpptraj
> ptraj found! Using /home/braf/md/amber12/bin/ptraj
> Preparing trajectories for simulation...
> 50 frames were processed by cpptraj for use in calculation.
>
> Running calculations on normal system...
>
> Beginning GB calculations with
> /home/braf/md/amber12/bin/mmpbsa_py_energy
> calculating complex contribution...
> calculating receptor contribution...
> calculating ligand contribution...
>
> Beginning PB calculations with
> /home/braf/md/amber12/bin/mmpbsa_py_energy
> calculating complex contribution...
> calculating receptor contribution...
> calculating ligand contribution...
>
> Beginning quasi-harmonic calculations with
> /home/braf/md/amber12/bin/ptraj
> CalcError: /home/braf/md/amber12/bin/ptraj failed with prmtop
> ../complex-gas.prmtop!
> Exiting. All files have been retained.
> application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
Whenever calculations in MMPBSA.py fail (that is, when MMPBSA.py does
_not_ detect some sort of problem in the setup), then error messages
printed by MMPBSA.py usually just tell you that something went wrong,
but it never tells you exactly what. You need to look at the output
files that were generated to determine what went wrong.
I suggest removing the &gb and &pb sections of your input file and JUST
running a quasi-harmonic entropy calculation. Then look for any error
messages in the _MMPBSA_* output files that were generated (specifically
_MMBPSA_cpptraj_entropy.out, for instance). That said, 50 frames is far
too few to actually run a quasi-harmonic entropy calculation.
Quasi-harmonic calculations are notoriously difficult to converge, since
it requires a very large number of frames for analysis. I would suggest
looking at the relevant literature to see how quasi-harmonic entropy
calculations have been used in the past (and how effective it was) and
look for tips about how to use it effectively.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Wed Apr 02 2014 - 05:00:08 PDT
