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
kindly help me in resolving it.
Thanks & Regards
On 2014-03-28 16:44, Jason Swails wrote:
> 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.
--
Arun Kumar Somavarapu
Project Fellow,
Dr. Pawan Gupta Lab,
Protein Science and Engineering Dept,
Institute of Microbial Tecnology,
Sec 39-A, Chandigarh - 160036.
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Received on Wed Apr 02 2014 - 02:30:02 PDT
