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
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Sincerely,
>
> Abhishek Singh
> Doctoral student
> Material Science and Engineering
> North Carolina State University
> Raleigh, NC 27695-7907
> Phone # 5179272418
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Oct 12 2011 - 11:00:04 PDT
