[gmx-users] about g_sas analysis

Milan Melichercik melichercik at nh.usbe.cas.cz
Thu Mar 18 09:07:16 CET 2010

supti mukherjee wrote:
> 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
You need to create new group which contains atoms from both protein and 
ligand (make_ndx or by hand) and input number of this new group - the 
most of the programs reads only one group per input (the rest write 
something about selecting two groups...). Therefore the second number is 
read for the second input (as the group for output).
About the rest of you question - I don't feel fully qualified to answer 
it and I hope, somebody will.


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