[AMBER] Compute SASA through molsurf

From: Francesco Gentile <fgentile.ualberta.ca>
Date: Wed, 13 Jul 2016 16:02:21 -0600

Dear Amber users,
I want to compare the SASA of a 84 residues protein domain in three
different cases:

1) alone
2) dimerized with another protein domain
3) bound to a ligand but not dimerized

Please note that I have three different trajectories I have ran for these
three cases. Looking through the documentation and previous posts I
understood that what I should do is separately calculate the SAS with
molsurf on the three trajectories using

molsurf :1-84 out SASA.dat

and then compare these values (the protein is supposed to have a much
bigger exposed area when not in dimer and the ligand would ideally bring
the exposed area closer to the dimeric form).

However I found this in the manual of Amber14:

"Remarks regarding the usage of molsurf:

The correct way to evaluate the SASA is to augment the radii of all atoms
by the probe radius (usually 1.4 Å) and then run molsurf with a probe of
radius of zero. This is also the implemen- tation in ffgbsa here. The atom
radii values are given in the following table:

Note: In some rare cases molsurf fails to give back a valid surface area.
Scripts calling ffgbsa must be prepared to capture this. The pymdpbsa procedure
described later catches such instances and excludes value sets in which the
error occurs from the statistical analysis (cf. end of section"

I don't understand well what does it mean, if I need to change all the
radii in the prmtop file (add 1.4 to each radius) and then use

molsurf '1-84' probe 0 out SASA.dat

or if molsurf already does it automatically. Thanks in advance for your
help, cheers
Francesco Gentile
PhD Student, Biophysics
CCIS 3-215, Department of Physics
7-112, Li Ka Shing Centre for Health Research Innovation
University of Alberta, Edmonton, AB T6G 2E1
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Received on Wed Jul 13 2016 - 15:30:02 PDT
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