AMBER: Adding/recognizing calcium atoms

From: Nitin Bhardwaj <>
Date: Wed, 7 Dec 2005 15:24:38 -0600

Dear Amber users,
  I had a problem with Xleap not identifying calcium atoms present in
my system. After loading leaprc.ff99 and leaprc.gaff, it gave an error
saying that the 2 calcium atoms are not in residue template. I guess
that's because for the two calcium atoms, they were marked as CA in
both atom and residue column. So I looked up in in parm99.dat to find
out how does xleap call it. They mark it as 'CO'. But when I say
'list' in xleap (after loading leaprc.ff99 and leaprc.gaff), there is
no residue as 'CO'. The closest one is 'CIO', which I guess is the
calcium atom.
So, my first questions is what is the difference between the two 'CO' and 'CIO'?

Next, I tried to add calcium using 'addIons' in xleap. I said:

addIons [unit] CIO 2.

It added two atoms which were 'CIO' in the resdue column and 'Na+' in
the atom column. And they only increased the charge by 2 meaning that
each of them had only +1 charge. So is CIO a calcium or a sodium atom?

What do I call my calcium atoms (both in atom and residue columns) so
that xleap can recognise them as Ca2+ ions?
How can I add 2 calcium atoms to my system?
Any help would be greatly apprecited.
Thanks a lot in advance.
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Received on Wed Dec 07 2005 - 21:53:01 PST
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