[gmx-users] help on g_hbond -contact

[Erik Marklund]

Well... g_hbond works, surprisingly, for non-hydrogen bonds with the - 
contact flag. However, that part of the g_hbond code was not really  
functional in gromacs 3.3. I suggest doing what Tsjerk suggested, or  
trying g_hbond -contact with a newer version of gromacs. g_saltbr may  
also provide useful insight about intermolecular contacts.

/Erik

26 feb 2007 kl. 20.09 skrev 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
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_______________________________________________
Erik Marklund, PhD student
Laboratory of Molecular Biophysics,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,	75124 Uppsala, Sweden
phone:	+46 18 471 4537		fax: +46 18 511 755
erikm at xray.bmc.uu.se	http://xray.bmc.uu.se/molbiophys