RE: AMBER: average structure

From: Ross Walker <>
Date: Sun, 19 Jun 2005 17:41:07 -0700

> I have done 1ns simulation with explicit water model, and I
> want to get the average structure after equilibration from
> 50ps to 500ps using ptraj (amber8) using the input below.
> After I load the average.pdb into leap to get the prmtop
> file, i got a lot of warnings like this:
> WARNING: There is a bond of 0.049558 angstroms between:
> ------- .R<GLU 84>.A<CA 3> and .R<GLU 84>.A<CB 5>
> WARNING: There is a bond of 0.230554 angstroms between:
> ------- .R<GLU 84>.A<CA 3> and .R<GLU 84>.A<C 14>
> WARNING: There is a bond of 0.035128 angstroms between:
> ------- .R<GLU 84>.A<N 1> and .R<GLU 84>.A<H 2>

This is because an average structure is just that, an average. Do really
expect it to have meaninful significance in terms of a structure? Have you
tried looking at this structure (the pdb) in something like VMD? I think you
will be surprised at what you see...

E.g. If I take a rigid methyl group and spin it about about the carbon atom
what is the average positions of the hydrogens? The average position will be
a point at the centre of rotation. Truly the average but not a chemically
meaningful structure...

Check out this tutorial
tm) for details about the limitations of "average" structures and some other
types of analysis you can do.

All the best

|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel:- +1 858 784 8889 |
| EMail:- |
| | PGP Key available on request |

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Received on Mon Jun 20 2005 - 01:53:00 PDT
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