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

[francesco oteri]

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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