Re: [AMBER] parameters for metal site

From: FyD <>
Date: Thu, 17 Mar 2011 15:03:21 +0100


> In my crystal structure, I have a tetrahedral coordinated metal site
> and I would like to observe the changes going to the trigonal state. I
> have optimized the complex with QM and get the charges using
> Kollman-Mertz schema as described earlier.

The radius in MEP computation for your metallic center was not defined
by Singh & Kollman...

How is it treated by the QM code you use?


> I use the tutorial from
> Ross and build the new residues - thanks to FyD here on the list - I
> have made the residues equivalent the three that coordinates the metal
> - so I have kept the water molecule which is the fourth coordinating
> in the tetrahedral complex and I have kept it in the trigonal to get
> some charge transfer of the metal site - I think by removed it the
> trigonal structure might be too strongly with respect to binding as
> well as charges.

Did you optimize the tetrahedral complex by QM? or did you manually
'arrange' the molecular system by adding a water molecule?

Did you optimize the trigonal complex by QM as well?

Did you compute RESP or ESP charges?

I would use R.E.D. Server development to generate various sets of
charges values, and compare them to these you already derived. With
the statistics module of R.E.D. Server you can now compare RESP, ESP
and Mulliken charges...

> I have parametrized the amino acids ligand as histidine with a new
> residue type and the only atom type changes is the coordinating
> nitrogen atom - charges have been added in the new lib file.


> I build
> the metal with the water molecule where I have taken the parameters
> from TIP3P - the types are the same but the charges are different
> which is reasonable in my case.

Did you try not using parameters from TIP3P?
My understanding is that TIP3P is for a solvent...

> Then I do a minimization of the
> complex and the hydrogens go to the negative charges nitrogens on the
> histidine residue - so the oxygen of the water has a vdw=1.7682 and
> 0.1512 and the metal it is 1.74 and 1.14 so the repulsion part so be
> rather strong going below 1.5 A but in the minimized complex the
> distance is 0.99 between the newly parametrized water and metal and
> the hydrogens have a distance between the nitrogens of 0.98 A - so
> somehow the vdw does really work for my parameters or libs - I do not
> know how to solve this any suggestions or comments appreciated

In the order, I would (i) get various set of charges for your two
entire complexes optimized by QM, (ii) try to have some ideas for the
vdW parameters for this water molecule & for the metal, and (iii) (i)
check the minimization input used.

regards, Francois

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Received on Thu Mar 17 2011 - 07:30:03 PDT
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