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. Thank you, Tang Jiaowei _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php