[gmx-users] bond

Berk Hess gmx3 at hotmail.com
Thu Mar 7 17:26:16 CET 2002

As I stated in the mail "ligand docking", pdb2gmx can do the
molecule_type merging for you, if you have an rtp entry for
the ligand. Using pdb2gmx -merge you can choose to merge
molecules into one molecule_type entry and pdb2gmx will
do the renumebering for you.
Also do not use a normal bond (bond type 1 or 2), since this
will generate exclusions, which you don't want when the ligand
is not chemically bonded to the protein, use bonds type 6 (see
the manual).


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