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.neuman...@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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