[gmx-users] Metal interactions with proteins

[RAHUL SURESH]

That’s good enough  to perform the simulation. Thank you Justin.



On Thu, 16 Nov 2017 at 6:33 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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
>
> --
> ==================================================
>
> 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
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==================================================
>
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-- 
*Regards,*
*Rahul Suresh*
*Research Scholar*
*Bharathiar University*
*Coimbatore*