AMBER Archive (2006)

Subject: Re: Fwd: AMBER: How to calculate the mmpbsa for explicit MD ?

From: Thomas Steinbrecher (
Date: Mon Jun 12 2006 - 13:50:30 CDT

Hi Jitrayut

> Thank you for your kind answer but I am still confused about MM-PBSA script
> that you say strips waters and counterions from the trajectorie. Please
> explain in more specific details or how I can do with this script.

When I did MM-PBSA calculations, I always did two steps one after the

For the processing of your trajectory set GC=1 and AS,DC,MM,GB,PB,MS=0 in
your input script and insert the details of your trajectory into the
@MAKECRD section (see amber 9 manual p273 for the meaning of the
parameters in MAKECRD) as well as the filename of your crd-file at

run [your input file] > mm_pbsa.log

This creates a lot of coordinate files in your directory.
Create a second input script in which you set GC=0 and e.g. MM=1, PB=1

run [your second input file]

and it should process your snapshots.

You have to set COMPT,RECPT and LIGPT to the filenames of your parameter
files without water molecules.


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