AMBER Archive (2002)

Subject: Re: GB in amber6

From: CUI, Guanglei (cuigl_at_morita.chem.sunysb.edu)
Date: Fri Aug 16 2002 - 08:25:52 CDT

Sorry for the confusion I could've made.

On Thu, 15 Aug 2002, David Case wrote:

> On Thu, Aug 15, 2002, CUI, Guanglei wrote:
>
> > The current implementation of GB (gbparm = 1) requires hydrogen
> > atoms are immediately behind the heavy atoms they attach to. One
> > cure is to modify your pdb file then it should be fine.
>
> Well, amber6 is not really the "current implementation of GB". Even for
> amber6, the restriction referred to above is out of date (see bugfix.26 for
> Amber 6).
>
> Generally, though, I would suspect that trying to use antechamber files
> (which only were distributed beginning with amber7) inside amber6 GB would
> lead to many problems....among other things, I don't think GB in amber6
> knows about the lower case atom types used by antechamber.
>
> So, please use Amber7 GB with antechamber. If you are planning to use the
> surface area term, be sure to apply bugfix.7 for Amber 7.
>
> ....good luck...dac
>
> >
> > On Thu, 15 Aug 2002, Prabal Maiti wrote:
> >
> > > I am trying to use Generalized Born model for a system of DNA/polymer
> > > complex. For the polymer I have generated the FF using antechamber program
> > > of AMBER7. I have built the DNA/polymer complex using xleap in
> > > amber6.
> > > When I try to run a GB minimiztion in amber6 (using gbparm =
> > > 2) it exits saying
> > > >Using modified Bondi radii and Tinker screening parameters
> > > >Unable to find bonded partner for atom 5182
> > >
> > > 5182 happens to be of type hn.
> > >
> > > However, with gbparm = 1 it runs fine.
> > >
>
> 

-- 
Guanglei Cui
Dept. of Chemistry
SUNY at Stony Brook
Stony Brook, NY 11790