AMBER Archive (2009)
Subject: Re: [AMBER] Any tutorial on the proper way to merge a ligand and protein?
From: Dean Cuebas (deancuebas_at_missouristate.edu)
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
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_at_missouristate.edu, Ph 417-836-8567 FAX 417-836-5507
Dept. of Chemistry, Missouri State University
Springfield, Missouri 65897
> From: case <case_at_biomaps.rutgers.edu>
> Reply-To: AMBER Mailing List <amber_at_ambermd.org>
> Date: Wed, 9 Sep 2009 13:50:13 -0500
> To: AMBER Mailing List <amber_at_ambermd.org>
> Subject: Re: [AMBER] Any tutorial on the proper way to merge a ligand and
> 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
> ...solvate, etc.
> saveAmberParm complex complex.top 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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