[gmx-users] Metal-Protein interactions
drrahulsuresh at gmail.com
Tue Dec 5 10:16:35 CET 2017
The topology says the Copper ion is with +2 charge.
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
What can be done?
On Mon, Dec 4, 2017 at 7:51 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> On 12/4/17 6:53 AM, RAHUL SURESH wrote:
>> Dear Justin
>> I have manually added Cu ion to the protein structure. the total charge of
>> the system is -0.99999. How do I make sure that gromacs is considering Cu
>> in +2 state only?
> pdb2gmx writes a topology based on whatever you tell it. If you specified
> an ion with a +2 charge, that's what's used. Verify that in the pdb2gmx
> screen output (if it was a separate chain, it should say) or just look in
> your topology.
> 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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