Re: [AMBER] this a very green neophyte's question.

From: David A Case <>
Date: Sat, 2 Aug 2014 08:27:46 -0400

On Fri, Aug 01, 2014, J.W. Halley wrote:
> Actually I noticed that an oxygen was missing in the sense that the
> stoichiometric formula for RET in the pdb file says that there should
> be 20 carbons and 1 O but I searched the file repeatedly and couldn't find
> an O associated with any of the RET residues.

PDB files often have missing atoms. But your should also check the residue
that the RET is connected to. Easiest thing is to use a visualization program
to see where things are. You may need to place the missing atom by hand.

As before, I suggest treating the retinal-Schiff base as a modified
amino acid, and using R.E.D. or the web page below as a template for how
to create such an entity:


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Received on Sat Aug 02 2014 - 06:00:02 PDT
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