AMBER Archive (2007)

Subject: AMBER: calcium parameters

From: Mattia Mori - CERM (mori_at_cerm.unifi.it)
Date: Mon Sep 24 2007 - 10:25:20 CDT

Dear Amber users,
I'm new about amber.
I'm using amber 8 and I would like to simulate the behaviour of a calcium binding protein during relaxation.
when I load pdb in tleap, I get this error message:
 

Creating new UNIT for residue:  sequence: 183
Created a new atom named: CA within residue: .R< 183>
Creating new UNIT for residue:  sequence: 184
Created a new atom named: CA within residue: .R< 184>
Creating new UNIT for residue:  sequence: 185
Created a new atom named: CA within residue: .R< 185>
Creating new UNIT for residue:  sequence: 186
Created a new atom named: CA within residue: .R< 186>
I'm using ff99 force field. when I check my unit the response is FATAL the atom does not have a type.

How can I assign the atom type for calcium?

Thank in advance for the help,

best regards

Mattia 
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**-**-**-**-**-**-**-**-**-**-**-**-**
 
Mattia Mori, PhD Student
CERM - Centro di Risonanze Magnetiche
via L. Sacconi 6,,
50019 Sesto Fiorentino, FI
fax (+39) 055 4573914
tel (+39) 055 4573912
www.cerm.unifi.it
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