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amber6, the restriction referred to above is out of date (see bugfix.26 for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.
> >
--
==================================================================
David A. Case | e-mail: case_at_scripps.edu
Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896
The Scripps Research Institute | phone: +1-858-784-9768
10550 N. Torrey Pines Rd. | home page:
La Jolla CA 92037 USA | http://www.scripps.edu/case
==================================================================
Received on Thu Aug 15 2002 - 22:23:23 PDT
