On Fri, Jul 15, 2016, windy wrote:
>
> I want to calculate the hydrophobic surface which exposed to the
> solvent of a protein and using the surf or the molsurf command in
> cpptraj. The command is here:
>
> surf :ALA,VAL,LEU,ILE,PRO,PHE,TRP,MET out XXX.out
>
> However, I wonder that is the surf or the molsurf calculate the
> surface exposed to the solvent of a protein, or the command just
> culculate the area of each residue surface and then sum up？
"surf" and "molsurf" do very different things. In the molsurf section of
the manual, note this sentence:
"Also note that this routine only calculate absolute surface areas, i.e. it
cannot be used to get the contribution of a subset of atoms to overall surface
area; if such functionality is needed try the surf command"
[We should rewrite this: the notion of "absolute sufrace area" is not very
clear here.]
Molsurf extracts the atoms in the mask and calculates the surface area of
those extracted atoms, completely ignoring any other atoms that might be
present in your solute.
Surf computes the summed contributions of the atoms in your mask to the total
surface area of the solute. For your application (getting the hydrophobic
surface area), "surf" is what you want. Note, however, that your mask
includes the backbone atoms of the amino acids, which are polar.
...dac
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sun Jul 17 2016 - 04:30:03 PDT
