[gmx-users] constraints between protein ligand - metal chelation
Peter C. Lai
pcl at uab.edu
Sun May 20 04:23:09 CEST 2012
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
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
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Peter C. Lai | University of Alabama-Birmingham
Programmer/Analyst | KAUL 752A
Genetics, Div. of Research | 705 South 20th Street
pcl at uab.edu | Birmingham AL 35294-4461
(205) 690-0808 |
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