AMBER Archive (2007)

Subject: RE: AMBER: calcium parameters

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Mon Sep 24 2007 - 11:04:08 CDT


Dear Mattia,
 
Calcium has the atom type C0
 
See line 18 of $AMBERHOME/dat/leap/parm/parm99.dat
 
C0 40.08 calcium

This confusing atom type assignment is because CA is used for aromatic
carbons.
 
The second issue is that for some reason there is not calcium residue
defined. So you will need to build this yourself. This is fairly easy to do
in xleap. Firstly start xleap and load the frcmod.ff99SB file. Then pick the
residue name you want to use for the calcium ions in your pdb file. I
suggest Ca2. Then
 
edit Ca2
 
select draw and then other elements and then Calcium.
 
Then draw a single calcium ion in the leap edit window.
 
Then choose "select", rubber band the calcium ion you just created to
highlight it.
 
Then Edit->Edit selected atoms.
 
Specify the name as Ca, the type as C0, and the charge as +2.
 
Then Table->Save and Quit.
 
you can then save yourself a library file for use later.
 
saveoff Ca2 Ca2.lib
 
Then edit your pdb file to make sure all the calcium ions belong to residue
name Ca2 and that they have atom names of Ca. You may also want to add TER
cards between each ion.
 
Then you can load xleap again from scratch.
 
source leaprc.ff99SB
loadoff Ca2.lib
foo = loadpdb foo.pdb
 
And this time it should recognize the calcium ions.
 
Good luck,
 
Ross
 
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From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of
Mattia Mori - CERM
Sent: Monday, September 24, 2007 08:25
To: amber_at_scripps.edu
Subject: AMBER: calcium parameters

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

-- 

**-**-**-**-**-**-**-**-**-**-**-**-**

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

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