Re: AMBER: Protein ions?

From: Stefano Federico Massimiliano Pieraccini (Stefano.Pieraccini) <>
Date: Thu, 02 Jun 2005 16:57:02 +0200

Dear Anthony,

Sodium and calcium are included in parm99, so you have the parameters,
but a prep file for calcium is not included in the .in files, so you
have to create your own and load it in leap with the
command "loadamberprep file_name.prep". A prep file with a single ion
is very simple and should look like this one we used to solve a
similar problem

0 0 2

Calcium Ion
1 DUMM DU M 0 -1 -2 0.0000 0.0000 0.0000 0.000
2 DUMM DU M 1 0 -1 1.0000 0.0000 0.0000 0.000
3 DUMM DU M 2 1 0 1.0000 90.0000 0.0000 0.000
4 Ca+ C0 M 3 2 1 1.0000 90.0000 180.0000 2.000


The first three atoms are dummy atoms, and then there is rhe calcium
ion with its atom type (taken from parm99), the internal coordinates
with respect to the dummy atoms and the charge (2.000). Ca+ was the
atom name of calcium in our PDB file, you can change it either in your
pdb or in the prep file, but they must be the same. CAL is the residue
name (CAL residue is formed only by atom Ca+ ), and this name must be
the same in your PDB and prep file. The identity of names is needed to
allow leap to recognize who is who in the different files.

Best Regards

Stefano Pieraccini

----- Original Message -----
From: Anthony Cruz <>
Date: Thursday, June 2, 2005 4:12 pm
Subject: AMBER: Protein ions?

> Hi users:
> I try to make a simulation of a protein that have 2 calcium and 1
> sodium. But
> leap don't recognize this atoms. I search the parm99.dat and the
> sodium and
> the calcium is included. How I could change my pdb for leap to
> recognize it?
> Kind Regards
> Anthony Cruz
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Received on Thu Jun 02 2005 - 16:53:00 PDT
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