[gmx-users] Re: g_sas of ligands

[Steven Neumann]

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?



On Fri, Sep 9, 2011 at 8:23 AM, Steven Neumann <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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