[gmx-users] constraints between protein ligand - metal chelation
francesco oteri
francesco.oteri at gmail.com
Mon May 21 18:01:43 CEST 2012
You are right Peter
2012/5/21 Peter C. Lai <pcl at uab.edu>
> This approach still requires the system to be parameterized as a single
> moleculetype, doesn't it?
>
> On 2012-05-20 04:42:26PM +0200, francesco oteri wrote:
> > Hi,
> > if you are able to define atom couples able to mantein the structure of
> > your complex,
> > you can insert in .top file a set of bond using function 6 (see table at
> > pag 125 of the user manual).
> > For example, let atom 1 and 100 are at distance 0.6nm, you can insert in
> > .top a row like
> >
> > 1 100 6 0.6 1000
> >
> > you impose a bond between the two atoms having as eauilibrium distance
> > 0.6nm and
> > force strenght 1000J.
> >
> > Function 6 doesn't implie the generation of angles and dihedrals so it is
> > the right choice
> > to impose distance restraints
> >
> >
> > Francesco
> > 2012/5/20 R.S.K.Vijayan <biovijayan at gmail.com>
> >
> > > 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
> > >> (205) 690-0808 |
> > >> ==================================================================
> > >>
> > >> --
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> > >
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> >
> >
> >
> > --
> > Cordiali saluti, Dr.Oteri Francesco
>
> > --
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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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--
Cordiali saluti, Dr.Oteri Francesco
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