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.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf Of
Mattia Mori - CERM
Sent: Monday, September 24, 2007 08:25
To: amber.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
www.cerm.unifi.it
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Received on Mon Sep 24 2007 - 17:45:31 PDT
