Re: [AMBER] Protein-Ligand Energy Minimization

From: Daniel Roe <>
Date: Thu, 30 Nov 2017 15:02:59 -0500

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:


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 - 12:30:03 PST
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