On Mon, Mar 9, 2020 at 2:47 PM ZHANG Cheng <272699...@qq.com> wrote: > 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) > > To calculate the surface a radii of 0.14 nm is used for the solvent probe, and also a radii is associated to each atom belonging the surface (for the values of the radii see the reference Eisenhaber F, Lijnzaad P, Argos P, Sander C, & Scharf M (1995) J. Comput. Chem. 16, 273-284). Thus it could be that atoms are shielded by other atoms volume or not accessible to the water bead.
Best regards Alessandra > > 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. > -- 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.
