[gmx-users] Metal interactions with proteins

[RAHUL SURESH]

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?

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.

Thanks in advance












To add the topology,i.e the necessary parameters (LJ-potentials) where all
should I add the  in the forcefield.

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