[ghemical-devel] Tripos 5.2

[Donald Ephraim Curtis]

Well, after posting it appears that the tripos info is coming from the
$prefix/share/libghemical/*/param_mm/tripos52 directory.  But, i
couldn't find any information on what needs to be added to add Si
parameters or can get more accurate optimizations.  Is this actually
what i'm looking for as far as setting the correct force field information?

-Donald

(Wed, Jul 26, 2006 at 02:25:23PM -0400) Geoffrey Hutchison <geoff at geoffhutchison.net>:
> 
> On Jul 21, 2006, at 11:20 AM, Donald Ephraim Curtis wrote:
> 
> >Is there a elegant way to add silicon parameters for the Tripos  
> >engine?
> >I know there are a few other atoms that are just using  
> >"approximations"
> >basically Hydrogen values.
> 
> Actually, what would be really nice is if the ghemical engine would  
> substitute parameters from neighbors in the periodic table instead.  
> So if I simulate Si and no parameters exist, it uses carbon but with  
> a larger vdW radius. Same thing for Se using S parameters, etc.
> 
> A quick search turned up some interesting links:
> 
> Validation of the general purpose tripos 5.2 force field
> http://dx.doi.org/10.1002/jcc.540100804
> 
> GAFF - a General Amber Force Field
> http://amber.scripps.edu/antechamber/gaff.html
> 
> Cheers,
> -Geoff
> 
> P.S. I can send a PDF of the first article to anyone -- AFAIK, it has  
> the only set of published Tripos parameters.