Thank you very much for that.
Could you please tell me how to extract the radii from the prmtop file?
Yes, I found the VDW radius in the parameter files.
But when we tried to run MM_PBSA, it ended with the error: No radius found
for KA(the name for Ca2+ in my parameter file).
Should the parameter be provided by the prmtop file already?
If not, how to include the vdw radius for MM_PBSA calculations?
Thank you very much!
Zhihong
On Mon, Aug 30, 2010 at 11:20 AM, Jason Swails <jason.swails.gmail.com>wrote:
> Hello,
>
> This radii means nothing outside the context of an implicit solvent
> calculation, so you can consider this to be a dummy variable. The VDW
> radius is mixed up in the LENNARD_JONES_A/BCOEF arrays, and you have to
> apply the combining rules in reverse to extract the radii from the prmtop
> (but it should also be in the parameter files).
>
> This is a dummy variable because simulating explicit ions in implicit
> solvent is atypical, as salt effects are included implicitly as well
> through
> a debye-huckel parameter in GB solvents.
>
> Hope this helps,
> Jason
>
> On Mon, Aug 30, 2010 at 1:15 PM, zhihong ke <ebelleke.gmail.com> wrote:
>
> > Hello.
> >
> > In my system, there is a Ca2+ ion.
> > I have download its parameter from the
> > http://www.pharmacy.manchester.ac.uk/bryce/amber.
> > Then, I found the in the prmtop file, the modified Bondi radii for Ca2+
> and
> > Na+ is 1.500.
> > Why they share the same radii?
> > And is it right?
> >
> > Thank you very much!
> >
> > Zhihong
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-4032
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Mon Aug 30 2010 - 11:00:03 PDT
