AMBER Archive (2005)

Subject: Re: AMBER: Question about Lennard-Jones Parameters in Topology file

From: Germán Sciaini (gsciaini_at_qi.fcen.uba.ar)
Date: Mon Jul 04 2005 - 05:46:00 CDT

Yes, it is possible to do these kind of modifications over the topology
file but take in mind that Vij = Aij/rij^12-Bij/rij^6...You could put
different pair-pair interactions....

Good Luck
G.

At 02:15 p.m. 02/07/2005, you wrote:

>Dear Fellow Amber Users,
>
>I have an AMBER6 format topology file for a lignand-protein complex, but I
>would like to modify the 6-12 lennard-jones parameters for the ligand
>before I run molecular dynamics. Is it possible (and reasonable) to do
>that within the topology file? I read about "parameter file formats" in
>the AMBER6 manual, but I was confused by the ICO indexing. Thank you in
>advance for any help you can give me.
>
>Sincerely,
>Linda Prengaman
>Carnegie Mellon University
>Dept. of Chemistry
>Class of 2006
>
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