Charles, all:
Do you know how to increase the van der Waals radius of a specific atom in a
molecule without creating a new atom type or changing the radius in the
parameter file?
The reason I ask is I am doing structural studies on peptides that have
N-methyl residues. At this point I do not w
Hello Keith--
>
> Do you know how to increase the van der Waals radius of a specific atom in a
> molecule without creating a new atom type or changing the radius in the
> parameter file?
Yes- using atom-based parameters.
(e.g. http://nmr.cit.nih.gov/xplor-nih/doc/current/xplor/node56.html)
Hi Charles,
Thanks a lot - this works fine.
I used:
parameter
nonbond (resid X and name HN) 0.0498 4. 0.0498 4.000
end
If I am correct, setting sigma to 4.000 should correspond to a radius of ~1.30
angstroms, which is close enough for this application.
Best regards,
Keith
Keith
Hi Keith--
> I used:
>
> parameter
> nonbond (resid X and name HN) 0.0498 4. 0.0498 4.000
> end
>
> If I am correct, setting sigma to 4.000 should correspond to a
> radius of ~1.30 angstroms, which is close enough for this
> application.
>
Rvdw = sigma 2^(1/6) / 2
so, to get a radi
