[gmx-users] Metal-Protein interactions

Justin Lemkul jalemkul at vt.edu
Wed Dec 6 01:21:56 CET 2017

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

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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