[gmx-users] Metal interactions with proteins

[RAHUL SURESH]

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?

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

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

Thank you

>
> Charges in this file are never used for anything. The column is a relic of
> an ancient idea for building molecules.
>
> -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
>
> ==================================================
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support
> /Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>



-- 
*Regards,*
*Rahul Suresh*
*Research Scholar*
*Bharathiar University*
*Coimbatore*