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 |
| Global Phasing Ltd., Cambridge UK |
| http://www.globalphasing.com/people/osmart/ |
