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
Received on Wed Oct 12 2011 - 11:00:03 PDT
