RE: AMBER: how to prepare Zn.lib

From: Ross Walker <>
Date: Fri, 10 Dec 2004 10:29:24 -0800

Dear Yon,

> I want to simulate one protein with Zn2+ and Ca2+ ions.
> Althogh there are Zn and Ca parameter in Amber7.0 but when
> Xleap read protein_Zn_Ca.pdb, Xleap still cann't recoginise
> those kinds of atoms. So I must prepare Zn and Ca parameter
> seperately with protein.

Note Zn2+ currently exists in parm99.dat so you should just be able to use
the atom type "Zn" in your main system pdb file. Anyway, below I detail how
to create your own ion for zinc since the process is sufficiently general
that you can use it for any ion.

Try the following:

Create a pdb file with a single Zinc atom in it. The coordinates don't
matter as we will simply use it as a template to create the atom type we
need. We will call this atom type ZNA to avoid confusion with any other
atoms types that might be present. I prefer to use 3 letter atom types since
it gives less chance of a clash with other atom types. Note, you probably
want to use CAA for your calcium.

ATOM 1239 Zn Zn 1 1.069 -8.424 1.759 1.00 10.99

Open xleap

>xleap -s -f $AMBERHOME/dat/leap/cmd/leaprc.ff99

Load the zinc pdb file

ZNA = loadpdb zinc.pdb

Edit ZNA

Select the zinc atom in the window and select edit selected atoms:

>Zn ZNA 2.000 Zn

Since we won't be creating any bonds to this atom this is more or less all
we need to do, at least in xleap. We still need an frcmod file defining the
mass and vdw parameters for this atom.

Close the editor and edit window. Save a library file of the zinc atom.

>saveoff ZNA ZNA.lib

Now quit xleap.

Now create (in your favourite editor an frcmod file for zinc 2+). We shall
call it frcmod.zna so we know what it is:

>vi frcmod.zna

In the file add the following (Note: I got these parameters from parm99.dat,
if you have your own element for which parameters do not exist you would
need to guess or calculate the nonbond parameters:

This frcmod file is for ZNA (zinc 2+ ion).
ZNA 65.4

ZNA 1.10 0.0125

Save this as frcmod.zna and then put both this file and the zna.lib file
somewhere safe. This is your generic zinc ion.

Now, for a protein containing Zn2+ you would edit the PDB and change the
residue name for the zinc atom to ZNA.

Then open xleap:

Load the ZNA lib file (and any other lib files you may need)

>loadoff ZNA.lib

Then load the ZNA parameter file, and any other parameter files you may

>loadamberparm frcmod.zna

Then finally load your protein pdb. The ZNA residue should now be

>PROT = loadpdb myprotein.pdb

Solvate, neutralise etc etc..

>saveamberparm PROT myprotein.prmtop myprotein.inpcrd

And there you go. So for any protein with Zn2+ ions you would just change
the residue name to ZNA, load your lib file and frcmod file and then load
the protein pdb.

I hope this makes sense.

All the best

|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel:- +1 858 784 8889 | EMail:- |
| | PGP Key available on request |

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Received on Fri Dec 10 2004 - 18:53:00 PST
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