AMBER Archive (2008)

Subject: RE: AMBER: Ca ions not recognized

From: Peterson, Matthew W. (mpeterson_at_mitre.org)
Date: Tue Sep 30 2008 - 09:08:16 CDT

You can create a .lib file describing a calcium ion in xleap.

http://archive.ambermd.org/200709/0211.html

This method worked for me.

Matt

-----Original Message-----
From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On
Behalf Of Cristina Sisu
Sent: Tuesday, September 30, 2008 10:00 AM
To: amber_at_scripps.edu
Subject: AMBER: Ca ions not recognized

Hi all,

I have a problem with the calcium ions. I've looked already in the
amber
archives but nothing that I try seems to work. I am working on
calmodulin and in the PDB file I have some calcium ions. When I try to
edit my file with leap, it does not recognize them. I changed them from
CA to C0, but still no improvement. I looked in the param99.dat library
and I found C0 for calcium, but I did not find any remark for it in
ions94.lib. What can I do next?

Thanks
Cristina
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