AMBER Archive (2005)

Subject: RE: AMBER: average structure

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Sun Jun 19 2005 - 19:41:07 CDT

> 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
(http://www.rosswalker.co.uk/tutorials/amber_workshop/Tutorial_eight/index.h
tm) for details about the limitations of "average" structures and some other
types of analysis you can do.

All the best
Ross

/\
\/
|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel:- +1 858 784 8889 |
| EMail:- ross_at_rosswalker.co.uk |
| http://www.rosswalker.co.uk/ | PGP Key available on request |

Note: Electronic Mail is not secure, has no guarantee of delivery, may not
be read every day, and should not be used for urgent or sensitive issues.

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu