From: Timothy Isgro (
Date: Thu Jan 25 2007 - 22:46:31 CST

Hi Guo Hao,
NAMD may certainly be of use to simulate the binding of ligand to
protein. Be aware, however, the often the conformational changes
which must take place to enable binding occur on long (more than
nanosecond) time scales, which may be impractical to simulate without
invoking methods to increase sampling in some way. Perhaps you
should direct your question to the NAMD mailing list. I am sure
there are a few experts there who may offer some advice or point you
in the right direction.

On Jan 25, 2007, at 5:52 PM, GUO HAO wrote:

> I am a new user of NAMD. Could you tell me if NAMD can simulate
> the binding process of a small molecule ligand on protein and its
> conformatonal changes during this process(the binding site of
> protein is known)? Thanks for patience! Any information will be
> appreciated!
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