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
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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
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