[gmx-users] MD simulations of Tyrosinase using GROMACS

naresh_sssihl knnaresh at sssihl.edu.in
Fri Sep 13 19:03:42 CEST 2013

Dear GMX users,

I am trying to carry out MD simulations with tyrosinase protein. Tyrosinase
is a tyoe-3 copper protein. In its oxygen binding active site, the protein
has two copper atoms that bind to two oxygen atoms in a peroxo
configuration. Each copper is co-ordinated by three histidine residues.

While I am trying to generate a topology file for the protein I always get
an error message showing CU is not recognized by any force field. This
pretty clear that Copper is not parameterized by any of the force fields. 

Could any one hep me in this regard by including Copper parameters into the
force field and also defining the bonds between Copper - Oxygen and Copper

If any one has carried out MDS in similar lines please help me in this

Thanking you.

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