[gmx-users] Metal-Protein interactions

[RAHUL SURESH]

On Tue, 5 Dec 2017 at 6:02 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 12/5/17 4:16 AM, RAHUL SURESH wrote:
> > Dear Justin
> >
> > The topology says the Copper ion is with +2 charge.
> > Thank you
> >
> > Here for the command *"gmx grompp -f em.mdp -c solv.gro -p cu.top -o
> > ions.tpr" *I get two notes. Note one descripbe the non-zero charge of the
> > system and note 2 states as,
> >
> >
> >
> >
> > *Removing all charge groups because cutoff-scheme=VerletAtom 1 'Cu' in
> > moleculetype 'Protein' is not bound by a potential or constraint to any
> > other atom in the same moleculetype.*
> >
> >
> >
> >
> >
> >
> > *NOTE 2 [file cu.top, line 5941]:  In moleculetype 'Protein' 1 atoms are
> > not bound by a potential or  constraint to any other atom in the same
> > moleculetype. Although  technically this might not cause issues in a
> > simulation, this often means  that the user forgot to add a
> > bond/potential/constraint or put multiple  molecules in the same
> > moleculetype definition by mistake.*
> >
> >
> >
> > The PDB is constructed by manually forming bond between His and Cu ion
> with
> > bond length 1.64. During the first minimization itself the ion moves at a
> > distance 2.64A
> >
> > What can be done?
>
> The "bond" you may see when visualizing a PDB file is meaningless. The
> only bonds that actually exist are those that are in the topology, of
> which there are clearly none in this system. If you need to preserve the
> binding pose, you need to parametrize bonded interactions (which I
> thought you said before you were going to do).


Dear Justin

Yeah I have to reparametarize. Before that I think I must carry out the QM
work. I will try to optimise Cu ion with His and add the parameters to the
file.

I thought manually adding the covalent bond would retain the bond
throughout the simulation. Miscalculated.





>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
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> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
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>
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-- 
*Regards,*
*Rahul Suresh*
*Research Scholar*
*Bharathiar University*
*Coimbatore*