[gmx-users] about g_sas analysis

[supti mukherjee]

Dear gromacs users,
I have some doubts regarding the options to be selected in g_sas program.
g_sas asks for two groups, first one for calculation and second one for
output. As I have understood from the manual that first group should contain
all non solvent groups and second one the whole or part of these groups. Now
my doubt is that in a system of protein+ligand, when I am selecting both the
protein and ligand in option 1 ( in the calculation group) it automatically
is sending the second selected group to second option ( that is in the
output group). Is the solvent accessible area  given in terms of the output
group in the xvg file?
 I want to calculate solvent accessibility of the ligand which is surrounded
by the protein. Selecting what option can mimic that situation most closely?

Regards
Supti
NIMHANS, BANGALORE
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