[gmx-users] Metal interactions with proteins

Justin Lemkul jalemkul at vt.edu
Thu Nov 16 14:03:36 CET 2017

On 11/16/17 4:12 AM, RAHUL SURESH wrote:
> On Wed, Nov 15, 2017 at 6:58 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>> On 11/15/17 6:44 AM, RAHUL SURESH wrote:
>>> Hello users
>>> I am performing Metal-protein interactions with Charmm36ff using gromacs.
>>> The metals under study are Cu and Ag in +2 state. Is it sufficient to add
>>> the topology,i.e the necessary parameters (LJ-potentials) in nonbonded.itp
>>> and ions.itp alone?
>> Yes (unless you want pdb2gmx to deal with them, in which case they need to
>> be defined in atomtypes.atp, as well). Whether or not those parameters are
>> a suitable model of reality is another matter (no classical MD force field
>> treats transition metals particularly well).
> Thank you for the clarification. I will add it in atomtypes too.
>> In case of nonbonded.itp file, i find charge for most atom types are
>>> mentioned to be 0.000 and in the line
>>> *" ; Updated Mg2+ parameters by Allner et al. (DOI: 10.1021/ct3000734)MGA
>>> 12      24.305000    0.000  A   0.277000    0.01234280 " *the charge for
>>> this ion is also mentioned to be 0.000 and atom type is refered as MG*A.
>>> *What
>>> does this MGA refers to and why is the charge 0 for this ions.
>> MGA is the atom type for Mg2+ with the parameters by Allner et al. in the
>> linked paper. We have to distinguish between that Mg2+ type and the
>> official, "standard" Mg2+ CHARMM36 ion type.
> By default do charmm36 have every metal ions?

If you don't see it in the provided files, it's not there.

> In case I have to add the topology for Cu2+ and Ag2+, how can I name the
> atom type?

However you like.

> Should the charge be 0.000? In such case when we mention the charge to be
> zero, won't it denote just the atom instead resembling the ion?

Again, the charge in ffnonbonded.itp is completely irrelevant. The 
actual charge is read either from an .rtp entry (if processed by 
pdb2gmx) or ions.itp (if added e.g. by genion).

> I crosschecked with that of oplsaaff.. There in the nonbonded terms, every
> atom is given some partial charges.

...which are never used. It's confusing, I know. We should probably do a 
big cleanup of ffnonbonded.itp and remove unused columns.



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

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