[gmx-users] g_sas problem

[David van der Spoel]

tangxuan wrote:
> Dear,all
> 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.
> A:
>          0     136.923     81.5686     218.491           0
>          1     136.149     87.5994     223.748           0
>          2     136.607     90.9957     227.603           0
> B:      
>          0     129.967     85.1524     215.119           0
>          1     140.375      86.953     227.328           0
>          2     138.37     90.9806      229.35           0
> A+B:      
>          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.

Hi Tang,

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