Re: AMBER: ptraj hbond

From: Evan Kelly <>
Date: Sun, 8 Apr 2007 20:00:29 -0600

Hi again everyone,

My apologies, but I got a little trigger happy and sent that email
too soon. I just discovered the "includeself" keyword from previous
emails to the list. Everything is working fine now!


On 8-Apr-07, at 6:37 PM, Evan Kelly wrote:

> Hi Everyone,
> I am a new user to the hbond facility within ptraj (version 9). I
> am studying a single organic molecule in TIP3P water and I want to
> use ptraj to analyze INTRAmolecular hydrogen bonding. In my
> simulations, the organic molecule is contained within a single
> residue, which poses a problem since ptraj's hbond command does not
> count intra-residue interactions. Does anyone know of a way to use
> ptraj to count intra-residue interactions? My guess is that it
> would involve a fairly simple modification to the ptraj code, so if
> anyone could help me zero in on the section that controls the
> residue restrictions in the hbond counting I would appreciate
> that. Any other suggestions would be greatly appreciated, too.
> Thanks!
> ----------------------------------
> Evan Kelly

Evan Kelly

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Received on Wed Apr 11 2007 - 06:07:12 PDT
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