[gmx-users] Hydrogen bonding

David van der Spoel spoel at xray.bmc.uu.se
Wed Jan 30 13:19:07 CET 2002

On Wed, 30 Jan 2002, Andrew Horsfield wrote:

>> 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.
Resolution != error. The error is much smaller, and could be assessed by 
looking at B factors.

>I started from a rigid docking calculation, optimised the resulting
>geometry, solvated the complex, and re-optimised.
So how good was the agreement (RMS,H-bonding) straight after docking?

Groeten, David.
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://zorn.bmc.uu.se/~spoel

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