From owner-chemistry-!at!-ccl.net Fri Jun 16 12:21:01 2017 From: "Peter Jarowski peterjarowski|,|gmail.com" To: CCL Subject: CCL: MM RMSD Message-Id: <-52851-170616114952-26578-4TrzJLB8RWfRgH6qPKwOpQ- -server.ccl.net> X-Original-From: Peter Jarowski Content-Type: multipart/alternative; boundary="001a11401772038ce8055215bc5b" Date: Fri, 16 Jun 2017 15:49:34 +0000 MIME-Version: 1.0 Sent to CCL by: Peter Jarowski [peterjarowski~!~gmail.com] --001a11401772038ce8055215bc5b Content-Type: text/plain; charset="UTF-8" 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> > > --001a11401772038ce8055215bc5b Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Dear Nico:=C2=A0

Your exact problem is addressed by our automation environme= nt, ChemAlive C currently in beta.=C2=A0

<= div dir=3D"auto">=C2=A0Run a few molecules through our interface:
Http://www.chemslive.com/C/interfaceC.html
<= div dir=3D"auto">
We manage the MM conformationa= l analysis using RDKIT and then RMSD filter. After this all confirmations a= re further optimized with PM6 semi-empirical level with CP2K and further RM= SD filtered.=C2=A0

These= calculations are free.

= In the coming weeks we will be adding batch submission and DFT follow on ca= lculation using a proprietary on-the-fly selector for the most relevant con= formations 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 nicog= reen6 ~ gmail.com <owner-chemistry ~ ccl.net> wrote:

Sent to CCL by: "Nico=C2=A0 Grimblat" [nicogreen6]![gmail.com]
Dear all,

I'm working with organic molecules performing conformational searches w= ith tinker employing MMFF and
MM3 with dielectric constant 80 to avoid hydrogen bonds.
This generates a lot of conformations, including some that the only differe= nce is a 60 variation of a H of
an hydroxy group.
Since I will be performing DFT optimization is extremely likely that the co= nfirmations 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 mo= lecule 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



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