[gmx-users] Metal-Protein interactions

[Justin Lemkul]

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).

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

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