How to do a complex dynamics simulation

From: ydhuang2727 (ydhuang2727_at_163.com)
Date: Wed Aug 05 2009 - 03:25:10 CDT

Hi, everyone,
I want to do a simulation of a complex, like protein and chemical molecule complex.
Can anybody share his or her experience?
Herein i firstly introduce the methods so far as i know.
I originally used Xplorn3851 to generate .psf file of both protein and ligand, the parameter and topology files of the ligand is from HIC-Up. But, the ligand doesn't have hydrogen atoms and the HIC-Up have make X-H, i.e. O-H, a single atom. Therefore the O atom's mass is 17 and zero charge. I don't know why they deal with these small molecules like that because it's hydrogens who always have non-bond interactions with protein atoms.
Desperately hope that someone have ever used Xplor generating input files for namd.
 
best,
Yandong,
 

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 05:22:16 CST