a question about NAMD TI

From: 林星雨 (linxingyu1986_at_gmail.com)
Date: Sun Jun 20 2010 - 22:26:48 CDT

Hi dear all,
I have a question about NAMD TI
It seems that in NAMD TI it can only calculate the derivatives of vdw and
ele, but if I want to mutate a fragment of a ligand and for these two
ligands they change the protein side-chain diherdral angle differently, then
the free enegy change must be associated with this side-chain. So how can I
use NAMD to get the free energy change?
Many Thanks!

Xingyu Lin
National Institute of Biological Sciences, Beijing
Dr. Niu Huang's Lab
Tel: 80726688-8572
Address: Beijing ZhongGuanCun Life Science Park, NO.7 Science Park East
Road, NIBS B427
Postcode: 102206

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