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

From: David A Case <>
Date: Wed, 30 Jul 2014 21:18:55 -0400

On Wed, Jul 30, 2014, J.W. Halley wrote:

> test5 = loadPdb protonpumprhodospinAR23AM6.pdb
> Unknown residue: RET number: 896 type: Terminal/beginning
> Unknown residue: CLR number: 897 type: Nonterminal

Amber's standard libraries don't know anything about retinal or CLR (not sure
what that is supposed to be.) It's by no means a simple task to model a
rhodopsin-like system because the user needs to create libraries that define
these non-standard residues.

The basic approach is outlined in tutorial B4, but that is a rather different
problem than having a covalently bound external component. Your best approach
is to use the Google, say with a search phrase like "rhodopsin amber molecular
dynamics" (or "bacteriorhodopsin..." -- not sure what your system really is.)
Either of those strings will show papers that have attacked similar problems,
and give you both an idea of how hard this might be, and how other people have
modeled similar systems.

....hope this helps....dac

[Aside to Rutgers folks: we *really* need to finish off the GFP tutorial,
which would help people with covalently bound chromophores see how to

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Received on Wed Jul 30 2014 - 18:30:03 PDT
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