RE: AMBER: metal atoms in Xleap

From: Ross Walker <>
Date: Thu, 19 Aug 2004 09:59:28 -0700

Dear Atilio,

> I am trying to model some DNA-transition metal interactions, but
> xleap is not recognizing the metal atom. So far I have chosen
> leaprc.gaff as a source and I used the command: mods = loadamberparams
>, to load a valid force field for the metal ion. But when I
> select the complex, xleap cannot assign the atom type nor the charge
> to the metal.

You need to create a separate unit for the metal atom. You will also need to
calculate RESP charges for this. What is the metal ion? Is it going to be
bonded to anything or just modelled as a charged ion?

Your best option is to create a pdb file with just your metal ion in. Pick a
suitable, unused residue type for it (e.g CUX). Then run Xleap, and do...

CUX = loadpdb CUX.pdb <or whatever you called it>

Xleap should report that it doesn't recognise the unit and add a new atom.
Then edit it:

Edit CUX

In the editor window highlight the atom (should be the only one) and then
select Edit->Edit selected atoms

In the box that comes up enter the charge of the ion, simply it's full
charge if you are just using it as a unit on its own. Ideally you should
change the surrounding residues as well and do a resp fit for the whole
metal ion system in order to see how it perturbs nearby charges. This is
probably a bit beyond what you are comfortable with doing at the moment so
until you have learnt how to create your units you should just skip the resp
charge stage and enter the ion's charge at this point.

Enter the element using standard element names. In type enter an atom type -
e.g CUX would do... It must be a unique atom type.

Then close the editor and save a library file for this unit.

Saveoff CUX.lib

At this point you can quit xleap, prepare your main pdb file (change the
ion's residue name to the one you used when creating the unit.)

Then when you are all ready fire up xleap with the force field you want.
Load the CUX library file

Loadoff CUX.lib -> this will tell xleap about this new unit.

If you type 'list' you should see the unit is now part of the unit list.

Then load your pdb file. Xleap should now recognise your ion.

At this point you need to decide if you are formally bonding the ion to
anything. If you are not you should just be able to do saveamberparm at this

If you want to bind it you will need to identify the atoms that are bound
and use the bond command. You are also going to need to create an frcmod
file with all of the missing force field parameters for your ion... See some
of the tutorials for this...

I hope this helps
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 Aug 20 2004 - 02:53:01 PDT
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