[gmx-users] g_sas WARNING: could not find a Van der Waals radius

Mark Abraham mark.abraham at anu.edu.au
Sun Mar 30 03:24:49 CEST 2008

> Dear users,
> I am using g_sas to analyse simulations which contain an AMP molecule and
> Mg
> ion (in addition to amino acid ligands and an enzyme). When running g_sas
> I
> get the message: WARNING: could not find a Van der Waals radius for 2
> atoms.
> I presume these two atoms are the P and Mg. Is there any way of defining
> radii for these atoms?

Yes, the definitions are taken from $GMXLIB/vdwradii.dat. You could either
edit that, or possibly copy it to your working directory, edit there and
g_sas should pick up the local copy. This mechanism works for other such
files, so I'd guess it works here too.

> Also if I am comparing the SASA for the enzyme in
> three different simulations were only the ligand (for which all radii are
> defined) differs, would this have a huge effect on the results?

Your question is not clear to me.


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