AMBER Archive (2000)

Subject: the topology file in mutant MM-PBSA calculation?

From: Jianxin Guo (jguo_at_zeeman.unmc.edu)
Date: Wed Feb 23 2000 - 12:03:07 CST


Hello,
I am trying to do a mutant free energy calculation by amber6. I checked
the script mm_pbsa, it seems that this script only modify the coordinate
(trajectory), that means I have to prepare all of those mutanted
topology files by using either leap or rdparm. According to the papers
 J.A.C.S,1999,121,8133-8143, J.M.B.2000,295,1-6), the modifited topology
files should be done with the same script? I am not sure with that.
Thanks for your help,
Jianxin