[gmx-users] regarding ligands in proteins

[Luke Czapla]

Greetings GROMACS user list:

  I am a graduate student working on setting up a simulation of a
glucose-binding protein.  The glucose is not covalently linked.  I have a
topology file for the glucose using the PRODRG server and a modified PDB
file for the protein without the glucose residue as well as the original
one with the glucose labeled GLC.
  Has anyone had experience with a system similar to this?  I'd like to
place the glucose inside the protein before energy minimization and I have
looked all through the documentation for genbox and pdb2gmx and found
nothing to do this.  Any help would be greatly appreciated!

cheers,
Luke Czapla