On Wed, 2014-04-30 at 09:58 +0400, James Starlight wrote:
> ... and new error during PB calculations of my test system using:
> &general
> endframe=100, keep_files=2, strip_mask=':WAT,CLA,POT,POPE,POPC'
> &pb
> istrng=0.150, inp=1, radiopt=0
>
> Beginning PB calculations
> with /home/own/Documents/simulations/amber/amber14/bin/sander
> calculating complex contribution...
> calculating receptor contribution...
> calculating receptor contribution...
> calculating receptor contribution...
> calculating receptor contribution...
> calculating ligand contribution...
> calculating ligand contribution...
> calculating ligand contribution...
> calculating ligand contribution...
You are *still* running parallel simulations incorrectly. The MMPBSA.py
tutorial (
http://ambermd.org/tutorials/advanced/tutorial3/)
What you are doing:
mpirun -np 4 MMPBSA.py -i mmpbsa.in ...
What you SHOULD be doing:
mpirun -np 4 MMPBSA.py.MPI -i mmpbsa.in ...
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Wed Apr 30 2014 - 04:30:02 PDT
