[gmx-users] Hydrogen bond existence map

andrea andrea.spitaleri at iit.it
Thu Jun 19 12:37:11 CEST 2014

Hi Nidhi,

I have something that does what you are looking for. It works in vmd and 
it is written in tcl. contact me by email if you want test it.



On 19/06/2014 12:24, Erik Marklund wrote:
> Hi Nidhi,
> Only with post processing of named files I'm afraid.
> Kind regards,
> Erik
> On 19 Jun 2014, at 10:48, Nidhi Katyal <nidhikatyal1989 at gmail.com> wrote:
>> Hi all
>> I would like to create hydrogen bond existence map for interaction of each
>> residue with my ligand. I am aware that -hbm and -hbn option of g_hbond
>> along with index file would serve the purpose. But the resulting output
>> file is giving existence map for each atom of the residue. Instead, I want
>> one map for residue as a whole. Example if any residue of protein is
>> forming hydrogen bond with my ligand for certain time through bond A but
>> for the remaining time it forms through bond B, then I want the map to show
>> presence of hydrogen bond through one single line during the entire course
>> of simulation. Is it possible with gromacs?
>> Thanks in advance
>> Nidhi
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Andrea Spitaleri PhD
D3 - Drug Discovery & Development
Istituto Italiano di Tecnologia
Via Morego, 30 16163 Genova
cell: +39 3485188790
ORCID: http://orcid.org/0000-0003-3012-3557

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