Dear Carlos
Thanks for the patience, this got fixed... I was missing the default
pbradii set. Thanks Dr Case suggestion
Sincerely
Abhishek
On Wed, Oct 12, 2011 at 1:36 PM, Carlos Simmerling <
carlos.simmerling.gmail.com> wrote:
> as we said before, we'll need to know how you set the radii in the prmtop.
>
> On Wed, Oct 12, 2011 at 1:32 PM, Abhishek Singh <asingh7.ncsu.edu> wrote:
>
> > Dear Carlos
> >
> > Shown below are results from minimization out put. However, things run
> fine
> > with igb5
> >
> > I have tried *igb8 *
> >
> > Implicit solvent radii are modified Bondi radii
> > (mbondi)
> > Replacing prmtop screening parameters with GBn2 (igb=8) values
> > and got this error
> > .....
> > .......
> > Atom 114 has radius 0.800000000000000 outside of
> allowed
> > range
> > of 1.0 to 2.0 angstroms for igb=7. Regenerate prmtop file with bondi
> > radii.
> >
> > and using *igb=7*
> >
> > Implicit solvent radii are modified Bondi radii
> > (mbondi)
> > Replacing prmtop screening parameters with GBn (igb=7) values
> > and got this error
> > .....
> > .......
> > Atom 114 has radius 0.800000000000000 outside of
> allowed
> > range
> > of 1.0 to 2.0 angstroms for igb=7. Regenerate prmtop file with bondi
> > radii.
> >
> > Sincerely
> > Abhishek
> >
> >
> > On Wed, Oct 12, 2011 at 11:55 AM, Carlos Simmerling <
> > carlos.simmerling.gmail.com> wrote:
> >
> > > a couple things:
> > >
> > > - which radii set did you define when you built the prmtop? that's
> > > important.
> > > - I strongly suggest igb=8, it's igb=7 with optimized parameters. The
> > paper
> > > is in revision so not out yet, but we and others have found this model
> to
> > > be
> > > better.
> > >
> > > Jason- is there any web resource that describes your prmtop modifier
> > > program
> > > to use for this?
> > > carlos
> > >
> > >
> > > On Wed, Oct 12, 2011 at 11:15 AM, Abhishek Singh <asingh7.ncsu.edu>
> > wrote:
> > >
> > > > Dear All
> > > >
> > > > I am trying to simulate a protein using ff10 and igb7 model . In the
> > > > topology file it shows lower than acceptable born radii (0.8A) for
> > > tyrosine
> > > > hydrogen atoms that are attached to hydroxyl oxygen. Any views on
> that
> > ?
> > > >
> > > > Sincerely,
> > > > Abhishek
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> >
> >
> >
> > --
> > Sincerely,
> >
> > Abhishek Singh
> > Doctoral student
> > Material Science and Engineering
> > North Carolina State University
> > Raleigh, NC 27695-7907
> > Phone # 5179272418
> > _______________________________________________
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> >
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>
--
Sincerely,
Abhishek Singh
Doctoral student
Material Science and Engineering
North Carolina State University
Raleigh, NC 27695-7907
Phone # 5179272418
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Received on Wed Oct 12 2011 - 11:00:08 PDT
