CCL: MM RMSD
- From: Peter Jarowski <peterjarowski.:.gmail.com>
- Subject: CCL: MM RMSD
- Date: Fri, 16 Jun 2017 15:49:34 +0000
Your exact problem is addressed by our automation environment, ChemAlive C
currently in beta.
Run a few molecules through our interface:
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.
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,