Dear Dr. Jason,
Thank you very much for your detailed explanation.
I found mmpbsa_py_entropy's options as you wrote.
Thank you,
WATANABE
(2014/08/05 23:10), Jason Swails wrote:
>
>
>
> On Mon, Aug 4, 2014 at 9:55 PM, Hiromasa WATANABE <hi-watanabe.hpc.co.jp <mailto: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
--
Hiromasa WATANABE
Manager, Ph.D.
HPC Dept., Technology Gr., HPC SYSTEMS Inc.
Head office: LOOP-X 8F, 3-9-15 Wangan, Minato-ku, Tokyo, Japan 108-0022.
Email: hi-watanabe.hpc.co.jp
www.hpc.co.jp
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Received on Tue Aug 05 2014 - 19:33:49 PDT
