AMBER Archive (2009)

Subject: Re: [AMBER] Any tutorial on the proper way to merge a ligand and protein?

From: case (
Date: Wed Sep 09 2009 - 13:50:13 CDT

On Wed, Sep 09, 2009, Dean Cuebas wrote:
> One of the tutorials at the ambermd site shows the preparation of a ligand
> and it's solvation, but does not show how to properly setup a system when
> the coordinates of the ligand and protein are known.

It seems obvious after you know is a typical tleap workflow:

source leaprc.ff99SB (for the protein part)
source leaprc.gaff (for the ligand part)
loadMol2 ligand.mol2 (where ligand.mol2 is created by antechamber) OR
loadAmberPrep ligand.prepi (where ligand.prepi is created by antechamber)
loadAmberParams frcmod (to get ligand-specific parameters, if any, created
                           by parmchk)

complex = loadPDB complex.pdb (where complex.pdb has consistent coordinates
                               of both the protein and the ligand, with the
                               ligand residue and atom names the same as in
                               the mol2 or prepi files loaded above. You
                               should have a TER card separating protein and

...solvate, etc.
saveAmberParm complex complex.crd

Note that Amber does not create the complex.pdb file -- you get that from
a docking program, or from the PDB, or from wherever. LEaP will use whatever
coordinates are in that file, so check things visually before proceeding.

[Note: things are rather more complicated if there is a covalent bond between
the protein and the ligand.]

...hope this helps...dac

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