Thank you Justin! ________________________________________ From: [email protected] [[email protected]] on behalf of Justin A. Lemkul [[email protected]] Sent: Tuesday, July 05, 2011 1:30 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] SAS of ligands
Marzinek, Jan wrote: > 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? > Yes, you do have to account for ligand-ligand interactions and buried surfaces, and I suspect that doing so won't be trivial. Probably lots of iterations of g_sas will be required to cover all the necessary permutations of different interfaces. g_cluster may help, but if you already know that the clusters form it's just a matter of determining which molecules (by residue number) are involved in each cluster so you can make appropriate index groups. -Justin > 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 -- ======================================== 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
