[gmx-users] salt bridge analysis
spoel at xray.bmc.uu.se
Tue Jun 14 22:04:41 CEST 2005
On Tue, 2005-06-14 at 14:37 -0400, Lei Zhou wrote:
> Dear gmx-users,
> I have one question about g_saltbr. What is the distance in the output
> file representing? Is that the minimum distance between two residues
> (so the corresponding atom pairs might be any atom in the residues) or
> just the charged atoms?
Actually this analysis is kind of tricky, isince it is based on charge
groups (ch 4 manual). For instance in the case of ARG these definitions
are not the same in every force field.
Anyway the distance reported is the shortest distance between any pair
of atoms from the groups.
> Thank you.
> Lei Zhou
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
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