[gmx-users] Masses and atomic radii for SASA

[Nash, Anthony]

Hi all,

I am a little concerned by the warning given (by default) when I use gmx_d
sasa Š


WARNING: Masses and atomic (Van der Waals) radii will be guessed
         based on residue and atom names, since they could not be
         definitively assigned from the information in your input
         files. These guessed numbers might deviate from the mass
         and radius of the atom type. Please check the output
         files if necessary.


NOTE: From version 5.0 gmx_d uses the Van der Waals radii
from the source below. This means the results may be different
compared to previous GROMACS versions.


++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
A. Bondi
van der Waals Volumes and Radii
J. Phys. Chem. 68 (1964) pp. 441-451



How does the algorithm factor for complete bespoke atom names and atom
types in the topology? I have a post-translationally modified protein, the
particular unique area of interest does not come as standard in Gromacs so
I had to derive it from QM calculations. I now have it in my Amberffsb99
topology, but the definition is unique (atom names, atom types, residue
name etc.) Also, the warning says ³Please check the output files if
necessary.² Which ones beside the standard -o -oa and -or?

I am concerned, given the warning, that gmx_d sasa could be ignoring that
region of my protein.

Thanks
Anthony