CCL: MM RMSD



 Sent to CCL by: Michel Petitjean [petitjean.chiral*gmail.com]
 Pls. have a look at the DIVCF software:
 http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html
 It clusters the conformers and exhibits the "mean" conformer within
 each cluster.
 The number of clusters is computed from the input data.
 No cut-off is needed.
 Best regards,
 Michel Petitjean
 MTi, INSERM UMR-S 973, University Paris 7,
 35 rue Helene Brion, 75205 Paris Cedex 13, France.
 Phone: +331 5727 8434; Fax: +331 5727 8372
 E-mail: petitjean.chiral- -gmail.com (preferred),
         michel.petitjean- -univ-paris-diderot.fr
 http://petitjeanmichel.free.fr/itoweb.petitjean.html
 2017-06-16 11:39 GMT+02:00 Nico Grimblat nicogreen6 ~ gmail.com
 <owner-chemistry- -ccl.net>:
 > Sent to CCL by: "Nico  Grimblat" [nicogreen6]![gmail.com]
 > Dear all,
 >
 > I'm working with organic molecules performing conformational searches with
 tinker employing MMFF and MM3 with dielectric constant 80 to avoid hydrogen
 bonds.
 > This generates a lot of conformations, including some that the only
 difference is a 60 variation of a H of an hydroxy group.
 > Since I will be performing DFT optimization is extremely likely that the
 confirmations that have such difference will be the same after optimization.
 > Based on this idea, I was thinking in performing a RMSD comparison in order
 to compare by a script all molecules and remove the ones that will end up in the
 same optimised molecule as others.
 > What is the cutoff that will remove this kind of conformations and be able
 to keep the ones that are different enough to question the geometry of the
 optimised molecule.
 >
 > Kind regards,
 >
 > Nico