Dear Justin, Firstly thanks for your valuable information. Now, is there any error? Please see the following commands:
protein and ligand are merged by make_ndx g_sas -f run.xtc -s run.tpr -o area_protein.xvg -n protein_ligand.ndx Select a group for calculation of surface and a group for output *select a group: 1 (protein_ligand)* *select a group: 2 (protein)* *I have protein SASA.* g_sas -f run.xtc -s run.tpr -o area_ligand.xvg -n protein_ligand.ndx Select a group for calculation of surface and a group for output *select a group: 1 (protein_ligand)* *select a group: 2 (ligand) I have ligand SASA.* 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: 1 (protein_ligand)* *select a group: 2 (protein_ligand) I have protein_ligand SASA.* *(SASA between protein and ligand)=(protein)+(ligand)-(protein_ligand)* Thanks 2011/7/3 Justin A. Lemkul <jalem...@vt.edu> > > > ahmet yıldırım wrote: > >> Dear users, >> >> I want to compute SASA between protein and ligand. >> *1.)* >> protein and ligand are merged by make_ndx >> g_sas -f run.xtc -s run.tpr -o protein_ligand.xvg -n protein_ligand.ndx >> Select a group for calculation of surface and a group for output >> select a group: 1 (protein+ligand) >> select a group: 2 (ligand) >> is this correct? >> >> *2.)* >> or >> g_sas -f run.xtc -s run.tpr -o protein_protein.xvg >> Select a group for calculation of surface and a group for output >> select a group: 1 (protein) >> select a group: 2 (protein) >> I have protein SASA. >> >> g_sas -f run.xtc -s run.tpr -o ligand_ligand.xvg >> Select a group for calculation of surface and a group for output >> select a group: 1 (ligand) >> select a group: 2 (ligand) >> I have ligand SASA. >> >> protein and ligand are merged by make_ndx >> g_sas -f run.xtc -s run.tpr -o protein_ligand.xvg -n protein_ligand.ndx >> Select a group for calculation of surface and a group for output >> select a group: 1 (protein_ligand) >> select a group: 2 (protein_ligand) >> I have protein_ligand SASA. >> >> (SASA between protein and ligand)=(protein)+(ligand)-(**protein_ligand) >> >> I am confused. which of choices is correct? >> >> > Neither. Your equation is right, but your method of calculating each of > the quantities is not. The group for the surface calculation should always > be all non-solvent atoms (per the instructions in g_sas -h). The output > group can then be whatever you like, a subset of that surface. So you will > need three calculations (sort of like option #2), but in each case the > calculation group should always be the protein-ligand merged group. > > -Justin > > -- > ==============================**========== > > 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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==============================**========== > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<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 gmx-users-requ...@gromacs.org. > Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> > -- Ahmet YILDIRIM
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