Re: [AMBER] -make-mdins does not work with nmode

From: Jason Swails <>
Date: Tue, 5 Aug 2014 10:10:37 -0400

On Mon, Aug 4, 2014 at 9:55 PM, Hiromasa WATANABE <>

> 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 command-line ?

​You can look at the top of the 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/


Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Tue Aug 05 2014 - 07:30:03 PDT
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