[gmx-users] Covalent bonds between topology files

[wjallen at vt.edu]

Hello fellow gromacs users,

I am working with a protein that has an FAD cofactor that is covalently bound to
a specific residue.  I am trying to model the protein in a style similar to Dr.
John E. Kerrigan's drug tutorial.  I used pdb2gmx to create topology and
coordinate files for the protein, and the Dundee PRODRG server to create a
topology and coordinates (.gro) for the FAD molecule.  I physically combined
the coordinate files, and I included the topology of the FAD molecule in the
header of the protein topology file:

; Include chain topologies
#include "protein.itp"
#include "FAD.itp"

and I included the FAD molecule at the end of the file:

[ molecules ]
; Compound        #mols
Protein             1
FAD                 1

Everything has been working well, the whole structure can be minimized and
processed so I know I have not made any errors yet.  But, this is where I am
stuck.  I need to covalently bind an atom in the FAD molecule to a residue in
the protein chain before I start minimizing anything.  Any suggestions on how
to approach this would be greatly appreciated!

Cheers,
W. Allen