[gmx-users] H2O close to N-terms

[Erik Marklund]

On Tue, 2006-06-20 at 11:31 +1000, Mark Abraham wrote:
> rodrid3 at rpi.edu wrote:
> > 
> >   Someone has written a script to calculate how may times H2O molecules
> > get really close or bind to the N-terminals of a protein?(it's outer
> > part, not the core) Or maybe someone nows how to calculate the N-terms
> > interactions with the solvent? Anything related to this would help. 
> 
> See g_mindist in the manual.
> 

Or try cvs-version of g_hbond. It has recently been bug fixed in a
number of ways and should be able to give you plentiful information
about contacts (use -contact flag) and obviously hydrogen bonding
(without the -contact option). Depending on the specific information
about the interactions you are interested in there are numerous options
for g_hbond that may be of interest.

/Erik

> Mark
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-- 
Erik Marklund, PhD Student, Molecular Biopcysics group,
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
erikm at xray.bmc.uu.se