> On Jul 17, 2015, at 5:46 AM, Albert <mailmd2011.gmail.com> wrote:
>
> Hello:
>
> I am following tutorial on
>
> http://ambermd.org/tutorials/advanced/tutorial3/py_script/section4.htm
>
> However, there is no FINAL_RESULTS_MMPBSA.dat
> <http://ambermd.org/tutorials/advanced/tutorial3/py_script/files/FINAL_RESULTS_MMPBSA_parallel.dat>
> generated.
>
> Here is my input file:
> &general
> endframe=100, verbose=1,
> /
> &gb
> igb=2, saltcon=0.150
> /
> &pb
> istrng=0.150, fillratio=4.0
> /
>
> and I submit job with command:
>
>
> mpirun -np 16 MMPBSA.py.MPI -O -i 06-mmpbsa.in -o
> FINAL_RESULTS_MMPBSA.dat -sp sol.prmtop -cp com.prmtop -rp rec.prmtop
> -lp lig.prmtop -y prod*.mdcrd > progre
> ss.log&
>
>
> here is the progress.log file:
>
> mmpbsa_py_energy found! Using
> /home/albert/install/amber14/bin/mmpbsa_py_energy
> cpptraj found! Using /home/albert/install/amber14/bin/cpptraj
> Preparing trajectories for simulation...
> 100 frames were processed by cpptraj for use in calculation.
>
> Running calculations on normal system...
>
> Beginning GB calculations with
> /home/albert/install/amber14/bin/mmpbsa_py_energy
> calculating complex contribution...
Are you sure the calculations finished? This message seems to suggest that it didn't finish.
Also, I suggest trying a couple frames in serial if it turns out that there is an error. Then look at some of the intermediate mdout files for an error if it turns out that MMPBSA.py failed for some reason.
The error message is often printed there.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Fri Jul 17 2015 - 13:00:04 PDT
