On Sun, Jun 24, 2012 at 8:40 PM, Daniel Aioanei <[email protected]> wrote:
> Dear Richard,
>
[Bob]
>
> Let me see if I got it right. What I need is "set solventProbe 1.4;
> isosurface sasurface", which is also equivalent to "isosurface
> sasurface 1.4". But while that works for larger molecules, it doesn't
> work for the water molecule.
>
> I think I said that wrong. For water you need
isosurface vdw +1.4
that's different from
isosurface vdw 1.4 # 1.4 ang each
> You mentioned in a previous reply that "That's a bug when the number
> of vertices is 0. That's fixed, but for now just don't do that." I
> just updated jmol to the latest svn version (rev. 17329) and for water
> "sasurface 1.4; show isosurface" doesn't freeze the GUI any longer,
> but the surface is still not there. Are there any plans to make
> sasurface work for very small molecules in the near future?
>
>
no. It is very important that sasurface not work for solvent. Use VDW +1.4
> As for PQR, I'm using the GAFF force field, and I'm not getting any
> zero radii so far. But how can I load the pqr file? I tried "load
> 'pqr::drgfin_GMX.pqr'", but the molecule just disappears when I do
> that.
>
>
?? send me the file, please.
> Thanks,
> Daniel
>
>
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--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Chemistry Department
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
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