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

[R.S.K.Vijayan]

Many  thanks for your response. No special reasons for parametrizing the
ligand and the protein as a separate system. I dont think that the ligand
and protein can be parametrized as a single system, but will definitely try
doing it as a single system and see if it works.
Regards
Vijayan.R

On Sat, May 19, 2012 at 10:23 PM, Peter C. Lai <pcl at uab.edu> wrote:

> 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
> Programmer/Analyst              | KAUL 752A
> Genetics, Div. of Research      | 705 South 20th Street
> pcl at uab.edu                     | Birmingham AL 35294-4461
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