[gmx-users] g_hbond (method)
David van der Spoel
spoel at xray.bmc.uu.se
Thu Jun 7 07:40:37 CEST 2007
Anil Kumar wrote:
> Dear all,
> I would like to know the actual cut-off angle used by gromacs package to
> calculate Hydrogen bond.
> since in User manual of version 3.2 and earlier, it was written
> á equal to or lesser than áHB = 60 degree
> While in User manual of version 3.3, it is mentioned as
> á equal to or lesser than áHB = 30 degree
> so,in actual whether program uses 30 degree or 60 degree in all versions
> of GROMACS packages. I hope and believe that it (GROMACS) uses 30 degree
> cut-off criteria for angle (standard and typical value).
> Thanks in Advance,
> With Regards,
The default was changed from 60 (used in older programs like DSSP IIRC)
to 30 degrees since most programs use that, and also because that is
what follows from experimental data. However you can of course change it
on the command line (g_hbond -h). The -da flag is out of order apparently.
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://folding.bmc.uu.se
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