[AMBER] Clarification about Gnp settings in MM/PBSA

From: Guqin Shi <shi.293.osu.edu>
Date: Tue, 29 Aug 2017 14:35:51 -0400

Dear all,

I have a simple question that I hope somebody could clarify for me. It's
about the Gnp settings in MM/PBSA.

&pb and &gb has different namelist variables. I am using inp=1 option which
calculates Gnp linearly to SASA (gamma*SASA+b). There are different sets of
gamma and b.

In &pb namelist, I used cavity_surften (gamma) and cavity_offset (b) to
change the settings for Gnp.
(In &gb namelist, surften (gamma) and surfoff (b) are used.)

I usually ask program to print out all temporary files for me during
MM/PBSA. There is one file _MMPBSA_info which contains all input
parameters. I checked this file and noticed that both surften, surfoff,
cavity_surften, and cavity_offset are listed. surften and surfoff are their
default values (according to Amber manuals under &gb section). I am a
little bit confused. So here _MMPBSA_info file just listed all parameters
but eventually if I specified &pb, then the program will only use
cavity_surften and cavity_offset for Gnp calculation, right? I want to make
sure I pass the correct parameters to the program...

Thank you a lot!

Guqin SHI
PhD Candidate in Medicinal Chemistry and Pharmacognosy
College of Pharmacy
The Ohio State University
Columbus, OH, 43210
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Received on Tue Aug 29 2017 - 12:00:03 PDT
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