From owner-chemistry@ccl.net Fri Jun 16 12:56:00 2017 From: "Michel Petitjean petitjean.chiral-*-gmail.com" To: CCL Subject: CCL: MM RMSD Message-Id: <-52852-170616122322-6884-fbewr/jwGETcj4/FGzizEQ^^^server.ccl.net> X-Original-From: Michel Petitjean Content-Type: text/plain; charset="UTF-8" Date: Fri, 16 Jun 2017 18:23:16 +0200 MIME-Version: 1.0 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 : > 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