[gmx-users] SAS of ligands

Marzinek, Jan j.marzinek10 at imperial.ac.uk
Tue Jul 5 14:25:21 CEST 2011

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: 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!
> Jan


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080

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