I have done my protein-ligand MD simulation and now I am going to calculate SASA for my protein-ligand complex with the spherical probe of 1.8 Å radius over the protein surface, but I have not found the right command.
Could anyone help me?
hey, you didn´t mention which gromacs version you are using. Anyway, the command is gmx sasa. You can have a look at the different options by typing gmx sasa -h (help). if you want to get a plot of SASA Vs simulation time for some specific residue you will have to use the -output flag and select the residue(s), atom(s) or whatever you have available inside your .ndx file.
Thanks for your assistance. By the way, I use GROMACS 2021.4 version.