[gmx-users] Masses and atomic radii for SASA

Marlon Sidore marlon.sidore at gmail.com
Mon Jul 25 11:42:57 CEST 2016


You need to add the radii of your unique atoms in the vdwradii.dat file,
which gmx sasa reads.

Marlon Sidore

PhD Student
Laboratoire d'Ingénierie des Systèmes Macromoléculaire (LISM)
CNRS - UMR7255
31, Chemin Joseph Aiguier
13402 cedex 20 Marseille

2016-07-25 8:05 GMT+02:00 Nash, Anthony <a.nash at ucl.ac.uk>:

> 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.
> 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
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