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