AMBER Archive (2002)

Subject: Re: GB simulation

From: CUI, Guanglei (cuigl_at_morita.chem.sunysb.edu)
Date: Mon Mar 04 2002 - 09:41:53 CST

In the GB code of AMBER6, the hydrogen atoms must follow the heavy atoms
they are bonded to. Otherwise, you'll see this message.

On Mon, 4 Mar 2002, Giulio Rastelli wrote:

> Dear all, I got the following error message for a sander simulation
> employing the generalized Born model:
> Using modified Bondi radii and Tinker screening parameters
>
> Unable to find bonded partner for atom 43
>
> Atom 43 in an HC hydrogen attached to a CT, nothing strange. SImulations
> are ok without GB.
> Any ideas?
> Thank you very much for you help
> Giulio
>
> Giulio Rastelli
> Dipartimento di Scienze Farmaceutiche
> Universita di Modena e Reggio Emilia
> Via Campi 183
> 41100 Modena - ITALY
> -------------------------------------
> tel 0039-059-2055145
> fax 0039-059-2055131
> -------------------------------------
>
> 

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