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
<[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
_______________________________________________
gmx-users mailing list [email protected]
http://www.gromacs.org/mailman/listinfo/gmx-users
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
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
_______________________________________________
gmx-users mailing list [email protected]
http://www.gromacs.org/mailman/listinfo/gmx-users
Please don't post (un)subscribe requests to the list. Use the www
interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
_______________________________________________
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
[EMAIL PROTECTED] http://xray.bmc.uu.se/molbiophys
_______________________________________________
gmx-users mailing list [email protected]
http://www.gromacs.org/mailman/listinfo/gmx-users
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
