Dear Gromacs Users, I have GPCR-protein complex simulation and want to calculate buried surface area of the complex. I am using gmx sasa but facing problem in using the command especially the -output part.
I need to calculate SASA for unbound receptor,unbound ligand and of complex. I have made index file where complex is ofcourse group 1 Protein and receptor is group 24 and ligand is group 25 when I provide the following command I gt TOTAL SASA gmx sasa -f .xtc -s .tpr -o bound-sasa.xvg -tu ns -n .ndx -surface 'group "1"' but when I add the output part -output '"hydrophobic" group "1" and charge {-0.2 to 02}; "hydrophilic" group "1" and not charge {-0.2 to 0.2}; Error in user input: Selection '"hydrophilic" group "1" and not charge {-0.2 to 0.2}' never matches any atoms. Can anyone tell me how to get SASA for receptor, ligand and compex. Thanks Archana -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.