[gmx-users] g_sas and -qmax
spoel at xray.bmc.uu.se
Sun Apr 4 17:44:00 CEST 2004
On Sun, 2004-04-04 at 16:28, Michael Brunsteiner wrote:
> dear all,
> I would like to calculate solvent accessible surface areas
> in my system. I find that the g_sas program that comes
> with gromacs has an argument qmax for giving a threshold
> above which an atom is to be considered as hydrophilic.
> I wonder if the default value for this number (0.2 e) is
> 1) an educated guess
> 2) derived from experimental data, or
> 3) derived theoretically ?
> I'd be also grateful if somebody could point me to
> literature discussing this topic.
Evrything called hydrophilic has a larger charge in both OPLS and GROMOS
force fields. With this value aromatic as well as CH3 groups in OPLS are
still considered hydrophobic (C in CH3 has -0.18e).
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David van der Spoel, PhD, Assist. 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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