[gmx-users] Masses and atomic radii for SASA

[Marlon Sidore]

Hello,

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
France


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.
>
> Thanks
> Anthony
>
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>