AMBER Archive (2004)

Subject: Re: AMBER: how to check metal ion bonding ?

From: Oliver Hucke (ohucke_at_u.washington.edu)
Date: Tue Apr 13 2004 - 15:28:09 CDT

Hi Venkat,

why don't you use the the "edit [unit]" command within xleap? This
brings up a graphics interface showing you the specified unit (see leap
section in the manual).
It might be a good idea to use a small test system containing only the
zinc and the ligand amino acids for this purpose.

Oliver

Venkata S Koppuravuri wrote:
> Hi Amber Users,
>
> I am trying to add Zinc to Cystine. I have followed the same procedure as
> in Plastocyanin tutorial in the manual. Leap went fine without any error
> messages. Before I start with minimization I want to make sure that all
> the bonds with the Zinc are properly formed.
>
> I have tried using Xleap, Sybyl, spdbv programs but the zinc ion and its
> bonds were not shown.
>
> Can someone suggest me a visualization program that I could use to check
> the Zinc bonds.
>
> Regards,
> -Venkat
>
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-- 
_______________________________________________________________

Oliver Hucke, Dr.
                               Health Sciences Building - K418C
University of Washington      1959 NE Pacific St.
Dept. of Biochemistry         phone: (206) 685 7046
Box 357742                    fax  : (206) 685 7002
Seattle, WA 98195-7742        email: ohucke_at_u.washington.edu
_______________________________________________________________

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