[gmx-users] Metal-Protein interactions

[Justin Lemkul]

On 12/5/17 2:10 PM, RAHUL SURESH wrote:
> 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.


grompp doesn't find such a bond, so whatever you did had no effect. 
Indeed a covalent linkage would preserve the binding mode, but depending 
on how you do it, you may need to add exclusions and/or pair 
interactions. It's not something that is simple to hack.

-Justin

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

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