From: ydhuang2727 (ydhuang2727_at_163.com)
Date: Tue Aug 11 2009 - 08:29:25 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,
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