AMBER Archive (2005)

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

From: Linda Prengaman (lindap_at_cmu.edu)
Date: Sat Jul 02 2005 - 13:15:51 CDT

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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