Re: [AMBER] Counter Ions in X-Ray structure.

From: Keiran Corbett <>
Date: Thu, 27 Sep 2018 15:08:27 +0100

Thank you for the reply.

It is a pdb file I have prepped in MOE
I use tip3p for my sourced file.

Building topology.
Building atom parameters.
For atom: .R<MG 259>.A<MG 1> Could not find vdW (or other) parameters for
type: Mg2+

I get this error in tleap and this is what I typed
(It is a slightly older version of AMBER but that can't be changed at this
source leaprc.gaff
source leaprc.ff14SB
source leaprc.tip3p
gaff=loadamberparams gaff.dat
LIG=loadmol2 3HVHL.mol2
loadamberparams 3HVHL.frcmod
saveoff LIG 3HVHL.lib
loadoff 3HVHL.lib
complex=loadpdb 3HVH.pdb
solvatebox complex TIP3PBOX 8.0
loadamberparams frcmod.ionsjc_tip3p
addIons2 complex Na+ 0
addIons2 complex Cl- 0
saveamberparm complex 3HVH.prmtop 3HVH.crd

On Thu, 27 Sep 2018 at 13:53, David Case <> wrote:

> On Thu, Sep 27, 2018, Keiran Corbett wrote:
> > I have counter ions i.e. Mg2+ in the binding site of my protein-ligand
> > strucuture determined by X-ray crystallography.
> > I wondered what people thought was the best way to deal with this as
> > doesn't recognise these kind of counter ions.
> Amber should recognize these MG ions, assuming that you have sourced a
> leaprc.water.xxxx file in your tleap input. If you are seeing problems, we
> would need to know details: esp. is this a "standard" pdb file from the PDB
> website? Or might it be a file with non-standard atom or residue names?
> ....dac
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Received on Thu Sep 27 2018 - 07:30:03 PDT
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