[gmx-users] help on g_hbond -contact

[Caterina Arcangeli]

Thanks to Tsjerk and Erik for their prompt replies. I've looked at
g_saltbr and it seems to be appropriate for my requirements.


Caterina




Erik Marklund wrote:
> 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
>> F: +31-30-2537623
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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
> 
> 
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