On Fri, 2014-03-28 at 10:32 +0530, Arun Kumar Somavarapu wrote:
>
> Dear Sir,
>
> I was trying to calculate MMPBSA to a protein-ligand complex by
> switching on entropy, but I am getting the fallowing error
>
> 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...
> CalcError: /home/braf/md/amber12/bin/ptraj failed with prmtop
What version of Amber are you using? This message doesn't make much
sense since ptraj is not used for anything except the quasi-harmonic
entropy calculation (which your input file has commented out below).
I also need to know how many updates have been applied. So what is the
output of
$AMBERHOME/update_amber --version
??
> ../complex-gas.prmtop!
> Error occured on rank 18.
This tells you that you should look in _MMPBSA_receptor_gb.mdout.18 for
the error message.
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Fri Mar 28 2014 - 04:30:02 PDT
