Re: [AMBER] Complex MD with protein ligand covalent bond

From: David A Case <>
Date: Mon, 20 Oct 2014 08:10:28 -0400

On Mon, Oct 20, 2014, Bikash Ranjan Sahoo wrote:

> I am Bikash from Osaka Univ. Japan. I am trying
> to MD in Amber for a protein-ligand complex. The ligand is covalently
> attached to two adjacent residues and are unnatural amino acids. How can I
> perform MD for this complex retaining the covalent bonds between protein
> and ligands. Removing the ligand is creating gap in the protein. Hoping a
> positive response.

We don't (yet) have a standard tutorial on creating libraries and force
fields for non-standard amino acids (which sounds like your situation).
But there is a fairly detailed example here:

...hope this helps....dac

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Received on Mon Oct 20 2014 - 05:30:02 PDT
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