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,
-- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
