Dear Gromacs,
There seems to be very little explanation on the "-surface" and "-output" options of "gmx sasa": -surface: This should always consist of all non-solvent atoms in the system. The area of this group is always calculated -output: can specify additional selections, which should be subsets of the calculation group. Can I understand in this way: 1. The "-surface" will calculate the surface area of the suppiled group. Regardless the group is inside or outside of the protein, the "sasa" will always assume the group to be fully solvent-exposed. So actually, it is not "Solvent Accessible Surface Area" of the group; it is "taking the group out from the protein, and put it in solvent, then calculate its surface". 2. When all the residues are supplied to the "-output" option, I have tested that the sum of "-output" equals to the "-surface": gmx sasa -s protein.pdb -o area.xvg -tu ns -surface 'group 1' -output 'resnr 1; resnr 2; resnr 3; ...; resnr n' This is good. However, I saw many residues having area of 0 even though they locate on the very outer surface. I think the explanation could be, their side-chains are totally shielded by their neighbouring side-chains. Is that correct? (I just feel SASA value of 0 is almost impossible) Thank you! Yours sincerely Cheng -- 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.
