[gmx-users] help on g_hbond -contact

[Tsjerk Wassenaar]

Hi Caterina,

g_hbond is, surprisingly, for h-bonds. If you want contacts, try g_mindist.

Cheers,

Tsjerk

On 2/26/07, Caterina Arcangeli <caterina.arcangeli at casaccia.enea.it> wrote:
> Dear all,
> I would like to compute the residue contacts within the protein. In
> particular I want to obtain the pair residues forming contacts with a
> distance cut-off of 0.4 nm.
> I used g_hbond -contact:
> g_hbond_d -f my_protein.trr -s my_protein.tpr -n my_protein.ndx -nomerge
> -contact -r 0.4
>
> However I obtained the following message:
> Fatal error:
> Donor 2419 does not have hydrogen -12344 (a = 2412)
>
> The same command without -contact produces fine results, i.e. the number
> of hbonds, without errors.
>
> I'm using GROMACS 3.3 version.
>
> Suggestions?
>
> Thanks to all.
>
>
>
> --
> Caterina Arcangeli
> ENEA, Computing and Modelling Unit (CAMO)
> Casaccia Research Center - Post Bag 026
> Via Anguillarese 301 - 00060 Roma
> phone +39 06.3048.6898
> fax   +39 06.3048.6860
> http://www.enea.it
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-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623