[gmx-users] g_sas -or -oa

David van der Spoel spoel at xray.bmc.uu.se
Thu Apr 1 08:52:01 CEST 2004

On Thu, 2004-04-01 at 02:56, Linda wrote:
> Hi, all,
>    I use g_sas to analyze the sasa. I browse the mailing list and found someboday said the -or and -oa option generate incorrect residue or atom areas. Now I use gromacs3.1.4 and do not know if that has been fixed? If not, how to solve this problem?
upgrade to the latest version. 

> BTW, I do not understand the meaning of connelly.pdb. Can somebody explain it for me or introduce some reference paper to me? thanks in advance.
the connelly surface, made up by the dots in the file, is the surface as
seen by water. i.e., water can not come closer than that surface (if you
generate it with the correct water size, 0.14 nm roughly)

> Cheers,
> Linda
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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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