Hi,
Note that the recipe below has been codified in the context
of a much more general approach in the DOCK Amber Score preparation
scripts. For details see
http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#AmberScorePreparationScripts
http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#AMBERScore
http://dock.compbio.ucsf.edu/DOCK_6/tutorials/amber_score/amber_score.htm
Although these amberize preparation scripts are nontrivial Bourne
shell reading, the usage section and the tleap input section should
be easy to follow by anyone familiar with Amber. These scripts are in
dock6/src/accessories
UCSF DOCK 6.3 was released this summer. It is free for academics.
http://dock.compbio.ucsf.edu/DOCK_6/index.htm
Scott
On Wed, Sep 09, 2009 at 02:12:00PM -0500, Dean Cuebas wrote:
>
> 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)
>
> 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.
> --
>
> > From: case <case.biomaps.rutgers.edu>
> > 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.]
> >
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Received on Fri Oct 16 2009 - 13:00:03 PDT
