AMBER Archive (2009)

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

From: Dean Cuebas (
Date: Wed Sep 09 2009 - 14:12:00 CDT

That is EXACTLY what I wanted...

Thanks so very much... now I can proceed.

(I just wasn't sure how to "merge" more than one molecule in tleap to create
the system)

Thanks again!


PS. Yes, it is obvious once you know how :-)

PPS. To anyone else that's new to this... I've very successfully used
Autodock to blindly dock cofactors to proteins when I only have the
coordinates of the protein. That has been my starting point for MD (I've
used gromacs before) and in fact, Autodock was able to correctly predict a
docking pose that I would have never predicted by homology to another
protein, but was confirmed when a much more homologous protein's structure
was eventually determined with the cofactor bound in this unusual pose.

Dr. Dean Cuebas, Associate Prof of Chemistry, Ph 417-836-8567 FAX 417-836-5507
Dept. of Chemistry, Missouri State University
Springfield, Missouri 65897

> From: case <> > Reply-To: AMBER Mailing List <> > Date: Wed, 9 Sep 2009 13:50:13 -0500 > To: AMBER Mailing List <> > Subject: Re: [AMBER] Any tutorial on the proper way to merge a ligand and > protein? > > 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 > ligand.) > > ...solvate, etc. > saveAmberParm complex complex.crd > quit > > 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 > > > _______________________________________________ > AMBER mailing list > >

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