Re: [AMBER] parameters for metal site

From: FyD <>
Date: Thu, 17 Mar 2011 19:30:37 +0100


>> The radius in MEP computation for your metallic center was not defined
>> by Singh & Kollman...
> No the radius for the atoms were taken from


> and used for the RESP calculation.

RESP charges, Yes, it should work in some circumstances. I would first
start with ESP charges.

> Yes both states were optimized with QM and the basis set should be
> fine for copper which is the metal ion in my case. After optimization,
> I computed the hessian and from that the force constants.

So why the position of this water molecule versus the 3 other ligands
looks so weired?

> Also ESP and mulliken were calculated.

These charge values have to be correctly equivalenced as well.

>> Did you try not using parameters from TIP3P?
>> My understanding is that TIP3P is for a solvent...
> No - I have not (yet) but I still do not understand how the vdw radius
> defined in Amber is neglected during the minimization.

I think (I might be wrong) this has nothing to do with Amber; this is
about the TIP3P water model itself; see the TIP3P article.

> I could add a
> vdw term for the hydrogen and see if this helps. I have been able to
> parametrize a couple of tetrahedral complexes with TIP3P and I have
> not experienced any problems there - not during minimization nor MD
> simulation.

I might be wrong, but using this TIP3P water model in a metallic
complex seems a strange idea ;-) I am sure people in the list have
comments here.

regards, Francois

AMBER mailing list
Received on Thu Mar 17 2011 - 12:00:02 PDT
Custom Search