[gmx-users] Metal interactions with proteins
drrahulsuresh at gmail.com
Wed Nov 15 12:44:23 CET 2017
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.
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