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

From: David A Case <>
Date: Fri, 1 Aug 2014 09:40:31 -0400

On Thu, Jul 31, 2014, J.W. Halley wrote:
> Thanks, but a question about a detail. Are, for example, the following
> lines enough for RET or does the pdb file need some more structure?

This is a much harder problem than you may think. Retinal is covalently
linked to the protein, so you really have to think of it more as a modified
residue than as a conventional ligand. [This is the reason I'm hoping we can
finish the GFP tutorial soon, since that also involves a covalently bound

You need to plan to spend some time on this, and to become familiar with
simpler calculations before going after your real target. Among many other
things, you need to add all hydrogens to your RET and CLR pdb files. Also,
since other groups have carried out Amber simulations on similar systems,
carefully reading how they did this, and asking them for (say) advice and/or
the input files they used is likely to be more productive than more generic
questions to the Amber reflector.

...good luck...dac

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Received on Fri Aug 01 2014 - 07:00:02 PDT
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