CCL: MM RMSD



Dear Nico:
 Your exact problem is addressed by our automation environment, ChemAlive C
 currently in beta.
  Run a few molecules through our interface:
 Http://www.chemslive.com/C/interfaceC.html
 We manage the MM conformational analysis using RDKIT and then RMSD filter.
 After this all confirmations are further optimized with PM6 semi-empirical
 level with CP2K and further RMSD filtered.
 These calculations are free.
 In the coming weeks we will be adding batch submission and DFT follow on
 calculation using a proprietary on-the-fly selector for the most relevant
 conformations at the DFT level.
 This will be free for a while :)
 Please register and let us know what you think.
 ChemAlive Team
 www.chemalive.com
 On Fri, 16 Jun 2017 at 16:54, Nico Grimblat nicogreen6 ~ gmail.com <
 owner-chemistry ~ ccl.net> wrote:
 >
 > 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>
 >
 >