[gmx-users] constraints between protein ligand - metal chelation

[Peter C. Lai]

Is there a particular reason why the ligand has been parameterized as a
separate moleculetype from the protein in your case? I prefer to treat
coordination bonds as "real bonds" instead of relying on electrostatic
interactions anyway, since it is the only way to conservatively ensure the
coordination geometry is preserved (like for Zn, where QM predicts a
tetrahedral geometry but Zn free ions will result in an octahedral geometry).
In any case, even if you stick with freeion Zn, you can paramaterize the
complex as a single moleculetype and use distance restraints there, can't 
you?


On 2012-05-19 09:42:25PM -0400, R.S.K.Vijayan wrote:
> Dear Gromacs users
> 
> I was wondering if there exists any technique that sets
> distance restraint between specified ligand (atoms) and the protein(atoms)
> in Gromacs.  I am simulating a system which contains metal ions coordinated
> to the Ligand. I looked in to the mailing list and Gromacs manual and
> figured out that  *genrster*  can be employed, to
> set distance, position and dihedral restraints. Unfortunately i also
> stumbled on the fact  that restraints between systems is not possible.
> 
> Since force fields are not good at handling chelation  between metal atoms,
> i find that the metals drifting away from the coordinated  ligand atoms
> during the course of simulation, hence i introduced position constraints
> for the metal and ended up realizing  that the coordination distance
> between the ligand and the metal exceeds the permissible range and the
> angles between the chelating atoms gets distorted  and some coordinating
> residues like Histidine and Aspartic  acid also moves away from the metal.
> 
> Hence, i was wondering if l anyone knows of any method (apart from
> QM/MM) that can help to set distance restraints between the protein (metal
> ion ) and the  ligand, also any suggestion that could help in handling
> ligand metal chelation is welcomed.
>     Thanking in advance
> 
> 
> Regards
> 
> Vijayan.R

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Peter C. Lai			| University of Alabama-Birmingham
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