From: Oliver Smart
Date: 11 January 2012 14:31
On Mon, 9 Jan 2012, krish wrote:
....
You can use Phenix.elbow or phenix.reel to load the coordinates of the small moleucle and optimize with AM1 (semi-empirical), then you should get reasonable geometirc parameters suc as bond length, bond angles and etc.
Hope this helps !
Cheers,
Krishna
Krishna Chinthalapudi, PhD
Hannover Medical School
Shveta and Krishna,
Just to point out that an alternative to using QM methods as a source of ligand restraints for refinement is to directly use the methods to represent the ligand chemistry during refinement. BUSTER provides the facility to do this see:
http://www.globalphasing.com/buster/wiki/index.cgi?AutobusterLigandQMIntroduction
It is pretty easy to do, particularly for semi-empirical QM methods (such as AM1 or the superior RM1). An advantage is that instead of coming up with approximate restraints sourced from AM1 then the actual method itself is used.
Regards,
Oliver | Dr Oliver Smart
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