[gmx-users] em and backbone

David spoel at xray.bmc.uu.se
Sat Jun 7 20:13:01 CEST 2003

On Sat, 2003-06-07 at 19:53, jxs818 at bham.ac.uk wrote:
> Hi all, 
>  I have producted a homology model of a enzyme i am 
> working on. Although there is very good sequence 
> similarity between target and template there is a region 
> which contains a proline which is at different positions 
> throughout the family. I have performed em (cg and steep) 
> on the protein, but on comparing the pre & post em 
> structures i can not see any change in the area of this 
> proline. Should I expect to ?? or does the MD take care of 
> this??
> As always any help will be emotionally recieved

No, don't expect EM to do anything visible. Usually rmsd after em is <
0.1 Å

MD may or may not change the conformation. If it does you know something
wasn't good in the structure, otherwise you still know nothing...

> JOhn  
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Groeten, David.
Dr. David van der Spoel, 	Dept. of Cell and Molecular Biology
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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