AMBER Archive (2006)

Subject: AMBER: Correction on Zinc parameters

From: Nitin Bhardwaj (nbhardwaj_at_gmail.com)
Date: Thu Jul 27 2006 - 11:38:00 CDT

Hi,
 I am sorry I am using amber 8.
Thanks
Nitin
On 27/07/06, Nitin Bhardwaj <nbhardwaj_at_gmail.com> wrote:
> Dear amber users,
> I have a zinc atom in my protein and so i am trying to create
> either a zinc.lib + zinc.frcmod file or a zinc.prepin file. I tried to
> create zinc.lib file following this mail from Ross:
>
> http://structbio.vanderbilt.edu/archives/amber-archive/2004/4188.php
>
> I am using amber 7 on SGI and when I say
>
> loadamberparm frcmod.zna
>
> it gives an error "syntax error"
>
> it runs fine when I say 'loadamberparams frcmod.zna'
>
> after this, when i load my protein with zinc, it still can not
> identify the zinc atom.
>
> I also tried to run this tutorial
> http://www.rosswalker.co.uk/tutorials/amber_workshop/Tutorial_four/
>
> again the problem is when i say 'desc ZNA'
> it does not give any unit name.. the field is blank..
>
> can anyone help?
>
>
> Also i had seen a mail on developing Ca2+ prepin file on the archive
> that i could not find now... where it was shown how do we create a
> prepin file for Calcium ...
> does anyone know when it was?
>
> thanks a lot in advance.
> Rgds,
> Nitin
> 

-- 
$B&-(BI+I$B'*(B
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