AMBER Archive (2007)

Subject: Re: AMBER: hbond ptraj

From: Chris Moth (chris.moth_at_vanderbilt.edu)
Date: Thu May 17 2007 - 07:14:31 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.

Chris

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