AMBER Archive (2002)

Subject: Re: GB in amber6

From: CUI, Guanglei (cuigl_at_morita.chem.sunysb.edu)
Date: Thu Aug 15 2002 - 21:33:27 CDT

Hi, Prabal,
    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.

    Cheers,

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.
>
> Any suggestions?
>
> Prabal
>
>
>
> 

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