[gmx-users] Number of H bonds formed between ligand and amino acid residues

[Erik Marklund]

Hi Amali,


gmx hbond identifies typical acceptor and donor groups by default. In fact, analysing non-standard donors/acceptors is a bit underdeveloped. What the program basically does, if memory serves me right, is to identify N and O with H bound to them, or optionally without H in case of acceptors. If you wish to analyse the hbonds separated by residue number you may wan to either run vmx bond multiple times with one group being a single residue and the other the ligand, or you can run it once with the -hbm and -hbn options and extract the information from the resulting matrix.

Kind regards,
Erik


> On 28 Jun 2016, at 08:59, Amali Guruge <amaligg2010 at gmail.com> wrote:
> 
> Thank you very much for the answer. How we identify residues involving in H
> bonds? In index file do we have to specify them?
> 
> On Tue, Jun 28, 2016 at 11:45 AM, Subhomoi Borkotoky <subhomoy.bk at gmail.com>
> wrote:
> 
>> Hello,
>> 
>> Please use the "hbond"  utility in gromacs.
>> 
>> gmx hbond [-f [<.xtc/.trr/...>]] [-s [<.tpr/.tpb/...>]] [-n
>> [<.ndx>]][-num [<.xvg>]
>> 
>> 
>> On Tue, Jun 28, 2016 at 11:24 AM, Amali Guruge <amaligg2010 at gmail.com>
>> wrote:
>> 
>>> Dear Gromacs users,
>>> 
>>> I carried out 20 ns long MD simulation for my receptor-ligand complex
>> using
>>> Gromacs software. Now I want to calculate number of hydrogen bonds formed
>>> in the ligand and receptor corresponding to the residue number. Can
>> anyone
>>> help me?
>>> 
>>> 
>>> Thank you.
>>> --
>>> Gromacs Users mailing list
>>> 
>>> * Please search the archive at
>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>>> posting!
>>> 
>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>> 
>>> * For (un)subscribe requests visit
>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>> send a mail to gmx-users-request at gromacs.org.
>>> 
>> 
>> 
>> 
>> --
>> Yours Sincerely,
>> --------------------------
>> SUBHOMOI BORKOTOKY,
>> Centre for Bioinformatics
>> Pondicherry University
>> Pondicherry,INDIA.
>> 
>> Alternate Email: subhomoi at mails.bicpu.edu.in
>> --
>> Gromacs Users mailing list
>> 
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
>> 
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> 
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-request at gromacs.org.
>> 
> -- 
> Gromacs Users mailing list
> 
> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
> 
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> 
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.