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

From: jitrayut jitonnom <jitrayut.018.gmail.com>
Date: Tue, 13 Jun 2006 02:15:06 +0700

Dear *Thomas Steinbrecher*

Thanks again for your suggestion in steps but I suspect that what about the
trajectorie file ? Is it contained waters or not ? If "yes" Should I strip
these waters ? and how ?



---------- Forwarded message ----------
From: Thomas Steinbrecher <steinbrt.scripps.edu>
Date: 13 .. 2006, 1:50 .
Subject: Re: Fwd: AMBER: How to calculate the mmpbsa for explicit MD ?
To: jitrayut jitonnom <jitrayut.018.gmail.com>
Cc: amber.scripps.edu

Hi Jitrayut

> Thank you for your kind answer but I am still confused about MM-PBSA
> 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 mm_pbsa.pl [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 mm_pbsa.pl [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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Received on Wed Jun 14 2006 - 06:07:11 PDT
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