AMBER: ptraj hbond

From: Evan Kelly <>
Date: Sun, 8 Apr 2007 18:37:04 -0600

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.


Evan Kelly

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