Hi Caterina,
g_hbond is, surprisingly, for h-bonds. If you want contacts, try g_mindist.
Cheers,
Tsjerk
On 2/26/07, Caterina Arcangeli <[EMAIL PROTECTED]> 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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