[gmx-users] g_analyze

David van der Spoel spoel at xray.bmc.uu.se
Sat Mar 29 16:24:14 CET 2008

A Heddell wrote:
> Hi,
> I am trying to analyse the number of hydrogen bonds between two sets of
> residues in four different structures.  I have run g_hbond for the two sets
> on each structure and now I wish to work out the average and standard
> deviation of the number of hydrogen bonds between these two sets for each
> structure.  I am using g_analyze for this, but it gives me out two sets of
> values: SS1 and SS2.  What are each of these, as I thought the value I was
> looking for was a single value of the hydrogen bonds between my two sets of
> residues?  Am I missing something obvious or should I be doing something
> different?
The second set is the number of contacts: within hb distance but not a 
hb. You want to look at SS1 only.

> Many thanks in advance,
> Anna
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David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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