[gmx-users] Regarding calculation of Hydrogen-Bond

[Justin Lemkul]

On 3/14/18 11:57 PM, Dilip H N wrote:
> 1) I tried with the Nitrogen atom of glycine and the oxygen atom of water
> also using the command
>
> gmx hbond -f nptmd.trr -s nptmd.tpr -n NgOw.ndx -num abc.xvg
>
> but still, i am getting the same error as:-
> Specify 2 groups to analyze:
> Group     0 (              N) has     1 elements
> Group     1 (             OW) has   511 elements
> Select a group: 0
> Selected 0: 'N'
> Select a group: 1
> Selected 1: 'OW'
> Checking for overlap in atoms between N and OW
> Calculating hydrogen bonds between N (1 atoms) and OW (511 atoms)
> Found 0 donors and 512 acceptors
> No Donors found
> -------------------------------------------------------
> Program:     gmx hbond, version 2016.2
> Source file: src/gromacs/gmxana/gmx_hbond.cpp (line 2732)
> Fatal error:
> Nothing to be done
>
> 2) I tried to find out the distance between Calpha(Ca) and Ow from the
> command
> gmx hbond -f nptmd.trr -s nptmd.tpr -n NgOw.ndx -dist abc.xvg
>
> but still, i am getting the same error as above one.
>
> Any suggestions...

Neither of your groups has any H atoms. gmx hbond can't calculate 
hydrogen bonds without them.

-Justin

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Justin A. Lemkul, Ph.D.
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Virginia Tech Department of Biochemistry

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