[gmx-users] SAS of ligands
j.marzinek10 at imperial.ac.uk
Tue Jul 5 14:25:21 CEST 2011
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?
From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] on behalf of Justin A. Lemkul [jalemkul at vt.edu]
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:
> Thank you in advance!
Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
gmx-users mailing list gmx-users at gromacs.org
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 gmx-users-request at gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
More information about the gromacs.org_gmx-users