[gmx-users] help on g_hbond -contact

Caterina Arcangeli caterina.arcangeli at casaccia.enea.it
Mon Feb 26 15:43:18 CET 2007

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.


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

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