RE: AMBER: Molecular dynamic

From: Andy Purkiss <>
Date: Tue, 13 Jul 2004 10:21:02 +0100

On Mon, 2004-07-12 at 19:12, Ross Walker wrote:
> Dear Bo,

> > The template for the modeling contains 3
> > 'MSE' and 1 'TAR'. MSE refers Selenomethionine, and TAR refers to
> > tartaric acid. I don't know how these molecules got into the crystal
> structure. And the
> > auther did not mention anything about these unuausl molecules
> > with their crystal structure.
> Hmmm, this could be something to do with inhibiting the system to stop it
> reacting, or also as a way of encouraging crystallisation. Note such
> residues may well have an effect on the crystal structure and make it
> unrepresentative of the solution structure. Your best bet though is just to
> try out some simulations and see what happens. You definitely want to avoid
> having to simulate a selenium compound if you can help it. It is very
> strange that the authors make no mention of it, do they refer to it in the
> pdb header?

Selenomethione residues are replacements for 'normal' methionine used to
gain the phase information required to solve the crystal structure. In
MD, they should just be replaced with normal methionine (unless you wish
to develop parameters for MSE). The tartaric acid is probably just from
the buffer used for the crystallisation. This can also probably be
safely left out. You need to read the crystallisation paper to see if
tartrate is mentioned in the condition where the crystals were grown.

> > As Amber can't recognize these molecules.
> Indeed, for the moment I assume you just removed them from the pdb...

      "I have not failed 10,000 times. I have successfully 
      found 10,000 ways that will not work" (Thomas Edison)
|  Andy Purkiss, School of Crystallography, Birkbeck College, London  |
|           E-mail                   |
|      Phone 020 7631 6869 (Work) or 0776 490 360 (Mobile)            |
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Received on Tue Jul 13 2004 - 10:53:00 PDT
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