[AMBER] Using mmpbsa_py_nabnmode directly

From: Liao <liaojunzhuo.aliyun.com>
Date: Mon, 15 Nov 2021 04:29:43 +0800

Dear Amber Community,

I'm trying to use mmpbsa_py_nabnmode directly instead of from MMPBSA.py. The reason for this is because I'm trying a 3-trajectory free energy calculation approach. If I use MMPBSA.py, it will calculate 3x3=9 times. Not too much a problem for enthalpies, but entropy will take too long.
Trying to run the program, I get a hint from the terminal saying "Usage: mmpbsa_py_nabnmode {pdb} {prmtop} {maxiter} {drms} {'string of MM options'} {nc/trj}" but I could not successfully fill in all the boxes properly, mainly the 'string of MM options'. Could someone maybe provide or point out a more detailed help page on how to use this program and the syntax? Or more general help on performing 3-trajectory entropy calculations would also be great!

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Received on Sun Nov 14 2021 - 13:00:05 PST
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