VMD-L Mailing List

From: Jian Dai (djpittdj_at_gmail.com)
Date: Sun Mar 29 2015 - 07:28:47 CDT

Dear all:
I intend to study a mutation of G2W by FEP, but I noticed that the total
charge of the glycine mutations are not equal to zero.
The Mutator plugin uses the topology file "top_all27_hybrid.inp" in the
plugin folder readcharmmtop1.1. When I look at the residue definition for
G2W, its total charge is 0.16. The charge is 0.16 for G2I as well.
So what's the proper dual-topology definition of G2W? Since the original
hybrid topology was based on CHARMM27 force field, is there a updated
version based on CHARMM36?
Thanks in advance.
Jian