[gmx-users] Covalent bonds between topology files

[Mark Abraham]

wjallen at vt.edu wrote:
> 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!

All atoms involved in bonded interactions must be defined within the 
same [ molecule ] segment. Thus you will need to go back and generate a 
[ molecule ] segment that has this, and the atoms numbered correctly (so 
you can't just concatenate).

Mark