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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