[gmx-users] Hydrogen bonding

Andrew Horsfield horsfield at fecit.co.uk
Wed Jan 30 11:08:56 CET 2002

On Wed, 30 Jan 2002, Daan van Aalten wrote:

> I would say that's a pretty good agreement.


> You don;t mention a few things, however:
> - what is the RESOLUTION of the complex structure you are structure with?
>   Uncertainty of coordinates in X-ray structures can easily be up to 0.2
>   Anstroms!

It is a 0.2nm (i.e. 2.0 Angstroms) resolution X-ray structure. This is
very coarse compared to the errors I am noting. They used structure
refinement to determine the coordinates - I am not familiar enough with
the method to know by how much this reduces error bars.

> - were the given values after EM or after MD?

Conjugate gradient energy minimization.

> - how did you generate your topology?

I started from a rigid docking calculation, optimised the resulting
geometry, solvated the complex, and re-optimised.



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