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? Thanks in advance -- Ahmet YILDIRIM
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