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

From: Matias Machado <>
Date: Thu, 27 Sep 2018 14:25:17 -0300 (UYT)

sorry about the typo... I mean "frcmod.ionslrcm_hfe_tip3p" not "frcmod.ions1lsm_hfe_tip3p"


----- Mensaje original -----
De: "Matias Machado" <>
Para: "AMBER Mailing List" <>
Enviados: Jueves, 27 de Septiembre 2018 13:24:24
Asunto: Re: [AMBER] Counter Ions in X-Ray structure.

Dear Keiran,

I guess you are using AMBER 14 or so... as far as I know, at that version a transition began to improve the transferability and readability of the force fields, so several leaprc files were simplified to identify self-contained models... many years back one leaprc file was supposed to load protein, DNA, water and ions models... which was a nightmare! people used to confuse parm99SB (for proteins) with parmbsc0 (for DNA) and so on... these issues are better treated in newer AMBER versions...

Notice for example that sourcing to "leaprc.tip3p" is redundant (if you are using TIP3P)... because "leaprc.ff14SB" also loads the same solvent parameters by default.

Any way... both "leaprc.ff14SB" and "leaprc.tip3p" load the residue libraries for MG, however non of them load the parameters to handle it (atom type Mg2+) because there are many flavours to choose... so you have to load the corresponding frcmod file yourself...

The only issue you have is choosing the proper parameter set, because (1) there are several option available at $AMBERHOME/dat/leap/parm and (2) MG is not a trivial ion, so their parameters may be different in solution or at a binding site and even more, with a simple 12-6 LJ potential is not possible to fit all its experimental properties at once (i.e coordination number and binding energy)... so you'll probable have to choose between these sets:

frcmod.ions1lsm_hfe_tip3p # Parameters fit to reproduce Hydration free energies (HFE)
frcmod.ionslrcm_iod # Parameters fit to reproduce the ion-oxygen distance in the first solvation shell (IOD)
frcmod.ionslrcm_cm_tip3p # Compromised (CM) parameters to "best" fit both coordination and energetics

You better read this paper:
Li, Roberts, Chakravorty and Merz (JCTC 2013, 9, 2733-2748)



Researcher at Biomolecular Simulations Lab.
Institut Pasteur de Montevideo | Uruguay

----- Mensaje original -----
De: "Keiran Corbett" <>
Para: "david case" <>,
Enviados: Jueves, 27 de Septiembre 2018 11:08:27
Asunto: Re: [AMBER] Counter Ions in X-Ray structure.

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
> _______________________________________________
> AMBER mailing list
AMBER mailing list

AMBER mailing list
Received on Thu Sep 27 2018 - 10:30:04 PDT
Custom Search