[gmx-users] Hydrogen bond existence map

[andrea]

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.

best

and


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
http://www.iit.it/en/d3-people/andrea-spitaleri.html
ORCID: http://orcid.org/0000-0003-3012-3557