[gmx-users] SAS of ligands

[Marzinek, Jan]

Thank you Justin! 
________________________________________
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 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:
> 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:
>
> 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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