Re: [AMBER] intermolecular hydrogen bonding.

From: Daniel Roe <>
Date: Tue, 17 Jan 2017 09:20:05 -0500

On Mon, Jan 16, 2017 at 5:50 AM, Saman Yousuf ali
<> wrote:
> While for second one, I got both residue-residue and residue-ligand interaction. Why results of both simulation hydrogen bond analysis is different even I have used same system and script for running these analysis. The first one results just ligand and residue interaction while other one is printing both residue-residue and residue ligand hydrogen bond.
> Where am I going wrong? Thanks in advance for any suggestions.

We need more information before we can help. Can you send me off-list
your topology as well as your output from the second run
(GHEA-quercetagetin_01.prmtop and 4hld_av_hbond.dat)? Thanks.


Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
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Received on Tue Jan 17 2017 - 06:30:05 PST
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