Thank you very much Jason.
Sajeewa
On Thu, Oct 4, 2012 at 6:28 PM, Jason Swails <jason.swails.gmail.com> wrote:
> On Thu, Oct 4, 2012 at 6:20 PM, Sajeewa Pemasinghe <sajeewasp.gmail.com
> >wrote:
>
> > Hi all,
> >
> > I am running MD using generalized Born solvation model. While I was
> running
> > my minimization I go this error message.
> >
> >
> > Atom 109 has radius 0.800000000000000 outside of
> allowed
> > range
> > of 1.0 to 2.0 angstroms for igb=7. Regenerate prmtop file with bondi
> > radii.
> >
> > The atom number 109 is a gamma hydrogen of the amino acid serine. Could
> > anyone please tell me how to generate prmtop files using bondi radii as
> has
> > been suggested?
> >
>
> You need to use the command
> set default pbradii bondi
>
> in tleap. If you already have a topology file, you can set the radius set
> using ParmEd directly, without having to go through tleap again. Open up
> the prmtop in xparmed.py (you can run that command with no arguments and
> choose your prmtop, or ), choose "changeRadii", and select bondi.
>
> Note, I think that igb=8 is a significantly better GBn model, so that may
> be worth using instead (this uses the mbondi3 radius set, which can be set
> the same way).
>
> See this page for details about using parmed:
> http://jswails.wikidot.com/parmed#toc17
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
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Received on Thu Oct 04 2012 - 16:00:02 PDT
