Re: AMBER: hbond ptraj

From: Chris Moth <>
Date: Thu, 17 May 2007 07:14:31 -0500 (CDT)

> I was expecting that I could get the same results with both ptraj input
> file, however, i was wrong. It seems to me that I need to list out all
> the
> potential hbonding partners of the drug in the ptraj file? Isn't?

Yes, all potential pairs must be listed.

> One more question regarding hbond is I could like to monitor a
> intramolecular hbond WITHIN the drug, can I do it will ptraj commands too?

So long as the donor and acceptor are listed, I think youi will get these.


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Received on Sun May 20 2007 - 06:07:20 PDT
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