[gmx-users] Metal-Protein interactions
jalemkul at vt.edu
Tue Dec 5 13:32:10 CET 2017
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 A. Lemkul, Ph.D.
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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