[gmx-users] Masses and atomic radii for SASA
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.
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.
> ++++ 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.
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