Re: [AMBER] Protein-Ligand Energy Minimization

From: Carlos Simmerling <>
Date: Thu, 30 Nov 2017 15:10:42 -0500

this is a tough challenge; in addition to the tutorials that Dan suggested
I would also suggest reading some of the literature on trying to predict
ligand binding to model structures for proteins. It's hard enough to
predict binding affinity with MD when the structure is known...

this might be a good start:
Modeling complexes of modeled proteins
Ivan Anishchenko, Petras J. Kundrotas, Ilya A. Vakser
DOI: 10.1002/prot.25183

and maybe this older one

Are predicted protein structures of any value for binding site prediction
and virtual ligand screening?
Jeffrey Skolnick, Hongyi Zhou, Mu Gao

On Thu, Nov 30, 2017 at 3:02 PM, Daniel Roe <> wrote:

> On Wed, Nov 29, 2017 at 1:14 PM, Kadir Tung
> <> wrote:
> >
> > I am a new user of AmberTools, and a novice Linux user. I am currently
> engaged in a project in which I take a protein sequence, run it through a
> folding prediction software, and get out a pdb structure file. I am
> attempting to see which of my proteins will bind to a certain ligand. I
> have a collaborator who adds the ligand to the pdb file and measures the
> binding free energy, but so far, we have not gotten good energy values
> except with a known protein downloaded from the Protein Database. Our
> hypothesis is that our structures are rigid, so I would like to attempt
> taking the files my collaborator has produced and running them through
> Amber to carry out an energy minimization to remove collisions to see if we
> can get lower energy values from our predicted proteins. Looking around, i
> was told that I could use Amber to perform energy minimizations, so I
> downloaded it and installed it in my Ubuntu VM.
> >
> >
> > My question then, being a novice Linux user and beginner Amber user, is
> what is the simplest way that I can put a pdb file through Amber, have it
> minimized, and have it return a pdb file that I can then send back to my
> collaborator?
> You may find the introductory tutorials helpful:
> -Dan
> --
> -------------------------
> Daniel R. Roe
> Laboratory of Computational Biology
> National Institutes of Health, NHLBI
> 5635 Fishers Ln, Rm T900
> Rockville MD, 20852
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Received on Thu Nov 30 2017 - 12:30:04 PST
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