On Mon, Aug 4, 2014 at 9:55 PM, Hiromasa WATANABE <hi-watanabe.hpc.co.jp>
wrote:
> Dear Dr. Jason,
>
> Thank you for your rapid reply. I understood well.
>
> Could you let me know where I can find information on
> mmpbsa_py_entropy's options that can be passed from
> the MMPBSA.py command-line ?
>
You can look at the top of the mmpbsa_entropy.nab file
($AMBERHOME/AmberTools/src/mmpbsa_py). Also, if you just run
"mmpbsa_py_nabnmode" with no arguments you get a usage statement:
$ mmpbsa_py_nabnmode
Bad command-line arguments
Usage: mmpbsa_py_nabnmode {pdb} {prmtop} {maxiter} {drms} {'string of MM
options'} {nc/trj}
The "string of MM options" is a set of options defined in the AmberTools
manual. You can see the option strings that are used around the line 285
of $AMBERHOME/AmberTools/src/mmpbsa_py/MMPBSA_mods/calculation.py.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Aug 05 2014 - 07:30:03 PDT
