AMBER Archive (2006)

Subject: AMBER: Zinc parameters

From: Nitin Bhardwaj (nbhardwaj_at_gmail.com)
Date: Thu Jul 27 2006 - 11:35:57 CDT

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
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