dear justin I did the following steps. Is it true or not?
protein and ligand are merged by make_ndx in protein-ligand complex simulation. I've used the following command: "g_sas -f run.xtc -s run.tpr -o area_protein_ligand.xvg -n protein_ligand.ndx" Select a group for calculation of surface and a group for output select a group: protein_ligand select a group: protein_ligand I have SASA in bound state. SASA in ligand -water simulation is calculated by Previous command but select a group: ligand select a group: ligand I have SASA in free state. ∆SASA is the difference between these two stages. Please tell me your opinion about these steps Thank you for your guidance. On Monday, August 25, 2014 6:40 PM, Mahboobeh Eslami <[email protected]> wrote: dear justin Thank you for your guidance. I've done it. When I use the g_sas command, and asked me the following question: "Select a group for calculation of surface and a group for output" I do not know what groups should be selected. Sincerely. On Monday, August 25, 2014 5:39 PM, Justin Lemkul <[email protected]> wrote: On 8/25/14, 5:23 AM, Mahboobeh Eslami wrote: > i want to calculate free energy by LIE method. > I need to calculate the∆SASA. i need to calculate SASA in protein-ligand > complex simulation and SASA in ligand -water simulation. > Please guide me how I calculate it. Run two simulations (complex and ligand in solution) and use g_sas/gmx sasa. -Justin -- ================================================== Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 [email protected] | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul ================================================== -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to [email protected].
