[gmx-users] Re: g_sas of ligands

[Justin A. Lemkul]

Steven Neumann wrote:
> Was my question not clear or noone can help me? I am wondering whether 
> calculations of ligand hydrophobic SAS (decrease during the 
> simualtion) can be result of binding to protein? 
>  
> 

Presumably it's due to both aggregation and binding to the protein, if, in fact 
both phenomena occur.  The extent of each effect will vary with time and you may 
have to analyze each ligand separately (i.e. do 30 calculations) to gather the 
detail you need.  In the absence of seeing the commands used to calculate the 
quantities you did, it's hard to comment further on any of the other points.

-Justin

>  
> On Fri, Sep 9, 2011 at 8:23 AM, Steven Neumann <s.neumann08 at gmail.com 
> <mailto:s.neumann08 at gmail.com>> wrote:
> 
>     Dear Gromacs Users,
>      
>     I am calculating SAS using g_sas of ligands in my system: protein,
>     30 ligands in water. The hydrophobic SAS of ligands decrease and
>     reach stable value. Hydrophilic remains stable over the simulation
>     time. I am wondering whether it  (the decrease o hydrophobic) is
>     because of binding to protein or aggregations of my small molecules
>     (They do aggregate) or both? I mean: how is it caculated? Is binding
>     to protein included in the decrease of the hydrophobic SAS of
>     lignads or it is impossible and  aggregation will be the one thing?
>      
>     Thank you, 
> 
> 

-- 
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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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