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

[Peter C. Lai]

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			|
==================================================================