Hey, The protein-buried hydrophobic area will only be considered if you use a combined group comprising ligands and protein to calculate the surface (and ligands only for output). If you use ligand only as group for calculation and for output, you'll only get the area buried between ligands.
Hope it helps, Tsjerk On Fri, Sep 9, 2011 at 3:03 PM, Justin A. Lemkul <[email protected]> wrote: > > > 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 <[email protected] >> <mailto:[email protected]>> 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, >> > > -- > ======================================== > > 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 > > ======================================== > -- > 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 > -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- 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
