AMBER Archive (2007)

Subject: Re: AMBER: ptraj hbond

From: Evan Kelly (ebkelly_at_ualberta.ca)
Date: Sun Apr 08 2007 - 21:00:29 CDT

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!

Thanks!

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
> ebkelly_at_ualberta.ca
>
>

----------------------------------
Evan Kelly
ebkelly_at_ualberta.ca

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