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

[Tsjerk Wassenaar]

Hi Jo,

>  > 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 semantically garbled. You comparing anything should
not influence the results (otherwise you're doing something terribly
wrong). If the question is whether the ligand has a (huge) effect on
the SASA, that's what the comparison is for. The meta-question whether
the (putative) influence on the SASA is due to an effect of the ligand
on the protein or an effect of the ligand in the SASA measurement
itself, can not be answered from here. It's for you to analyze.

Cheers,

Tsjerk

-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623