Dear Justin, Thank you for the link! I know how to calculate it - that is what I am doing. Interface AREA = 0.5 (Protein SAS+ 30 Ligands SAS- Protein and 30Ligands SAS) This is relevant to the situation where ligands do not aggregate.
I my system 22 out of 30 ligands bind to my protein creating two clusters on the terminals of the protein. In this case they cover the area between them. What I think is that I have to substract the interface between them from this equation. Am I right? The question is - how to do this? g_cluster will help? Thank you. Jan Marzinek ________________________________________ From: [email protected] [[email protected]] on behalf of Justin A. Lemkul [[email protected]] Sent: Tuesday, July 05, 2011 12:45 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] SAS of ligands Marzinek, Jan wrote: > Dear Gromacs Users, > > > > My system has 30 ligands - they aggregate and and seperate during the > simulation time and stack to two sites of my protein (two clusters). I > want to calculate the interface area between ligands and protein so I > need to substract the interface between ligands due to the aggregations. > Do you know how to do this? > See the thread from just a few days ago about the same question: http://lists.gromacs.org/pipermail/gmx-users/2011-July/062707.html -Justin > > > Thank you in advance! > > > > Jan > -- ======================================== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ======================================== -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists-- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
