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

From: Dean Cuebas <deancuebas.missouristate.edu>
Date: Wed, 9 Sep 2009 20:12:00 +0100

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!

Dean

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
deancuebas.missouristate.edu, Ph 417-836-8567 FAX 417-836-5507
Dept. of Chemistry, Missouri State University
Springfield, Missouri 65897
> From: case <case.biomaps.rutgers.edu>
> Reply-To: AMBER Mailing List <amber.ambermd.org>
> Date: Wed, 9 Sep 2009 13:50:13 -0500
> To: AMBER Mailing List <amber.ambermd.org>
> 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 how....here 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.top  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
> 
> 
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Received on Mon Sep 14 2009 - 13:38:44 PDT