[gmx-users] Hydrogen bonding analysis
spoel at xray.bmc.uu.se
Sat Sep 14 15:00:23 CEST 2002
On Sat, 2002-09-14 at 14:19, Dr. Y. U. Sasidhar wrote:
> I am looking for following types of hydrogen bonding in a pentapeptide
> in water.
> 1. 5--->1 hydrogen bonding broken by an inserted water molecule
> h-bonding to 5 and 1.
> 2. 5--->1 hydrogen bonding & simultaneous h-bonding of 5 and 1 to a
> common water molecule.
> I need to know time step, identities of donor residue, acceptor residue,
> and water molecule whenever these hydrogen bonds are present. ( I need
> to generate pdb files to demonstrate such hydrogen bonds visually )
> I used g_hbond. It does give an xpm file which can be converted to an
> eps picture which is summary of hydrogen bonds as a function of time.
> While I could find what I wanted in 1 and 2 above with g_dist with -dist
> option I wonder if I am missing some way of using g_hbond itself. For
> example what is the utility of the index file generated by -hbn option
> of g_hbond ?
This allows you to rerun g_hbond and get information on specific
hydrogens bonds (i.e. distances).
> gmx-users mailing list
> gmx-users at gromacs.org
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
Dr. David van der Spoel, Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576, 75123 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://zorn.bmc.uu.se/~spoel
More information about the gromacs.org_gmx-users