[gmx-users] g_sas problem
David van der Spoel
spoel at xray.bmc.uu.se
Tue Oct 30 14:57:14 CET 2007
> When I calculate the accessible surface area(ASA) of interaction region
> between two subunits A and B in my protein. First I calculated the ASA
> of A and B by "g_sas -f .xtc -s .tpr -n index.ndx -o .xvg -n index.ndx"
> respectively. After that, I combined A and B as the one group, then I
> computed SAS of group A+B in the same way above. When I calculated the
> hydrophobic SAS of interaction region between A and B by formula
> (SAS=SAS(A)+SAS(B)-SAS(A+B)), at some specific time this result is
> negative(the third ps in the result below). But in my opinion, this area
> should be positive. What is wrong? I can show you the result of the
> first 3 ps.
> 0 136.923 81.5686 218.491 0
> 1 136.149 87.5994 223.748 0
> 2 136.607 90.9957 227.603 0
> 0 129.967 85.1524 215.119 0
> 1 140.375 86.953 227.328 0
> 2 138.37 90.9806 229.35 0
> 0 264.215 169.394 433.608 0
> 1 274.129 176.945 451.074 0
> 2 276.924 180.027 456.951 0
> Look forward to your explanation.
I think this is actually a roundoff problem. It looks like your proteins
make no contact at all. Did you use the -pbc flag (it may be default though)
> Thank you,
> Tang Jiaowei
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David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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