[gmx-users] constraints between protein ligand - metal chelation
R.S.K.Vijayan
biovijayan at gmail.com
Mon May 21 18:20:26 CEST 2012
Many thanks for your response
On Mon, May 21, 2012 at 12:01 PM, francesco oteri <francesco.oteri at gmail.com
> wrote:
> 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 |
>> ==================================================================
>>
>> --
>> gmx-users mailing list gmx-users at gromacs.org
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>
>
>
> --
> Cordiali saluti, Dr.Oteri Francesco
>
> --
> gmx-users mailing list gmx-users at gromacs.org
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