AMBER Archive (2000)

Subject: Re: Adding metal parameter

From: Michael Cooney (mike_at_bmbiris.bmb.uga.edu)
Date: Tue Oct 24 2000 - 13:37:55 CDT

Dear Dr. Nam,
I'm not quite sure what files Moilview requires to read in and display
metal ions--this may just be a nomenclature problem. You may be able to
find more information at
http://morita.chem.sunysb.edu/carlos/moil-view.html
(Dr. Carlos Simmerling at Stony Brook is a developer of Moil-view.)
Other graphics programs that seem to handle Zn and Ca fairly well are
Insight, Sybyl and Rasmol. It may help to check the name that xleap gave
to the Zn and Ca ions in the output pdb files (made by carnal or pdbgen).
Good luck!
Sincerely,
Michael G. Cooney
Department of Biochemistry and Molecular Biology
The University of Georgia
Athens, GA 30602

On Mon, 23 Oct 2000 kiyean.nam_at_pharma.Novartis.com wrote:

> Hi All,
> I am pretty new to AMBER. I tried to include Zn and Ca ions in the MD
> simulation. So, I appended parameters for these ions to the copy of
> parm94.dat and ion94.lib in my local directory and loaded them by xleap.
> Leap did not complain about new ions, everything seemed fine. After I saved
> coordinate and topology files, I checked the files by reading into
> Moilview. But Moilview reported error in the file and displayed no
> connection between atoms.
>
> Have I done something wrong? Is there any recommanded way to add new atom
> type and parameter ?
>
> Any suggestion will be very helpful for me.
>
> Thanks.
>
> Kiyean Nam
> UMDNJ/Novartis Predoctoral Program
> kiyean.nam_at_pharma.novartis.com
>