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?
>
No, and there's no available version really except for the one in the git
repo. I think there's an old version of my ChangeParmRadii.py script
floating around in the mailing list archives with instructions for getting
it working, but that's about the only way I know of for getting the igb=8
mbondi3 radii.
We can post a standalone version on the Amber website that would work along
with a PDF taken from a cutout of the AmberTools manual pertaining to parmed
as an instruction manual, or we could run some kind of web-server thing
(like what the GLYCAM folks have?) to build an mbondi3 prmtop from a
supplied topology file. Or we could say stick with mbondi2 until AmberTools
1.next comes out.
Whatever people think is best I'll do (but not-it for the web server thing,
if that's the direction we decide to go in -- too much of a time commitment
to learn how to do it for what's on my plate right now :).
Thanks!
Jason
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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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Wed Oct 12 2011 - 11:00:05 PDT
