Re: [gmx-users] g_sas problem

tangxuan wrote: Hi Mark, Thanks very much for your reply. I checked the structure of A and B at these three ps, and there is no much change in the structures. Then I calculated the reside area in A+B at these three specific time (1536,15937,15938), and it shows that there are a big diffrence in

Re: [gmx-users] g_sas problem

Hi Mark, Thanks very much for your reply. I checked the structure of A and B at these three ps, and there is no much change in the structures. Then I calculated the reside area in A+B at these three specific time (1536,15937,15938), and it shows that there are a big diffrence in size of area at ma

Re: [gmx-users] g_sas problem

tangxuan wrote: Yes, the default value of -pbc is 'yes'. I did not add it in my command, but i think pbc should has been considered. It seems there is no contact between the two subunits, but at some specific time the total ASA of interaction region is very high(shown below). time total S

Re: [gmx-users] g_sas problem

Yes, the default value of -pbc is 'yes'. I did not add it in my command, but i think pbc should has been considered. It seems there is no contact between the two subunits, but at some specific time the total ASA of interaction region is very high(shown below). time total SAS of interaction

Re: [gmx-users] g_sas problem

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 g

[gmx-users] g_sas problem

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 compu