[gmx-users] regarding ligands in proteins

Luke Czapla czapla at rutchem.rutgers.edu
Sun Oct 7 21:46:17 CEST 2001

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!

Luke Czapla

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