From owner-chemistry@ccl.net Sat Mar 26 06:34:00 2011 From: "Tobias Schwabe tobba_._uni-muenster.de" To: CCL Subject: CCL: Absorption spectrum with TDDFT Message-Id: <-44224-110326063100-12697-VbpTwCKsLUDflnEjpc8CtA#server.ccl.net> X-Original-From: Tobias Schwabe Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-15; format=flowed Date: Sat, 26 Mar 2011 11:30:49 +0100 MIME-Version: 1.0 Sent to CCL by: Tobias Schwabe [tobba**uni-muenster.de] Dear Joaquin, based on your information it is not quite easy to give any detailed advise to improve your results. But maybe some general remarks will do? An error of 0.5 eV is not that unusual. But it does not have to be a problem. What is the goal of your study? Maybe the error is systematic (based on comparison to other experiments/computations for similar molecules), so that you predictions based on your calculation still have some conclusiveness. For valence excitations one often observes a systematic error cancellation for basis set effects so that you might get away with the low level basis set. This is not the case for geometries. If not done so before, try to use a good triple-zeta basis set for your geometry optimization. Excitation energies can be quite sensible to geometric parameters. It is known that DFT has some problems with charge transfer effects. Use functionals with higher amount of HF exchange. In your case: BH-LYP, which is known to yield better results than B3-LYP. Or, even more promising, apply CAM-B3-LYP. It should only be more demanding in computational time, but not in hardware requirements. And finally: is your system really that large? Nowadays there are some very efficient methods around which show better performance than standard TD-DFT. You could try a double-hybrid approach: J. Chem. Phys. 127, (2007), 154116-18. DOI:10.1063/1.2772854 which is available in ORCA. Or maybe you can even afford RI-CC2: J. Chem. Phys. 113, (2000), 5154-5161. DOI:10.1063/1.1290013 which is available in the TURBOMOLE code, for example. I hope that helps a bit. Regards, Tobias From owner-chemistry@ccl.net Sat Mar 26 20:06:00 2011 From: "Carsten Detering detering++biosolveit.de" To: CCL Subject: CCL: Release of new Hyde Affinity Assessment in LeadIT Message-Id: <-44225-110326184037-10718-aG3Y9N5jKyF1D8pdWlWCcQ%server.ccl.net> X-Original-From: "Carsten Detering" Date: Sat, 26 Mar 2011 18:40:34 -0400 Sent to CCL by: "Carsten Detering" [detering-x-biosolveit.de] BioSolveIT is proud to announce the release of LeadIT's new *Affinity Assessment HYDE* at the upcoming Spring ACS Meeting in Anaheim, CA. For more initial information on Hyde: www.biosolveit.com/hyde Come see what it's all about on - Monday, March 28, 11:05am, Room 213B Anaheim Convention Center There will also be a workshop dedicated to LeadIT on - Tuesday, March 29, 4pm, Room 211B (watch for signs) The workshop will be kicked off with Chris Lipinski talking about "Medicinal and computational chemistry: preserving teamwork" Other topics covered in the workshop: -FBLD with core hopping, linking merging and growing fragments -HYDE affinity assessment of results We will see you there! PS If you can't make it to Anaheim, there will be a series of webinars covering Hyde Affinity Assessment. Check our website for announcements: www.biosolveit.com -- __________________________________________________________________ Dr. Carsten Detering; Appl. Scientist detering[-]biosolveit.com Phone EU: +49-2241-2525-0 / Fax: -525 www.biosolveit.com Phone US: +1-617-297-2770 BioSolveIT GmbH - An der Ziegelei 79 - 53757 St.Augustin - Germany Geschftsfhrer Dr. Christian Lemmen Amtsgericht Siegburg HRB 6261 From owner-chemistry@ccl.net Sat Mar 26 20:41:00 2011 From: "Carsten Detering detering++biosolveit.de" To: CCL Subject: CCL: Lead Optimization with Hyde Affinity Assessment Message-Id: <-44226-110326184542-19595-NTUNpc5PjXoJlHlL7cdmaA,+,server.ccl.net> X-Original-From: "Carsten Detering" Date: Sat, 26 Mar 2011 18:45:40 -0400 Sent to CCL by: "Carsten Detering" [detering-,-biosolveit.de] BioSolveIT is proud to announce the release of LeadIT's new *Affinity Assessment HYDE* at the upcoming Spring ACS Meeting in Anaheim, CA. For more initial information on Hyde: www.biosolveit.com/hyde Come see what it's all about on - Monday, March 28, 11:05am, Room 213B Anaheim Convention Center There will also be a workshop dedicated to LeadIT on - Tuesday, March 29, 4pm, Room 211B (watch for signs) The workshop will be kicked off with Chris Lipinski talking about "Medicinal and computational chemistry: preserving teamwork" Other topics covered in the workshop: -FBLD with core hopping, linking merging and growing fragments -HYDE affinity assessment of results We will see you there! PS If you can't make it to Anaheim, there will be a series of webinars covering Hyde Affinity Assessment. Check our website for announcements: www.biosolveit.com -- __________________________________________________________________ Dr. Carsten Detering; Appl. Scientist detering,+,biosolveit.com Phone EU: +49-2241-2525-0 / Fax: -525 www.biosolveit.com Phone US: +1-617-297-2770 BioSolveIT GmbH - An der Ziegelei 79 - 53757 St.Augustin - Germany Geschftsfhrer Dr. Christian Lemmen Amtsgericht Siegburg HRB 6261 From owner-chemistry@ccl.net Sat Mar 26 21:28:00 2011 From: "Nancy nancy5villa]~[gmail.com" To: CCL Subject: CCL: RMSD Calculation Message-Id: <-44227-110326212632-1801-flvDCICoSzbki9b1gOXkzg,+,server.ccl.net> X-Original-From: Nancy Content-Type: multipart/alternative; boundary=00151747ba0e0cf633049f6cb78e Date: Sat, 26 Mar 2011 21:26:23 -0400 MIME-Version: 1.0 Sent to CCL by: Nancy [nancy5villa^gmail.com] --00151747ba0e0cf633049f6cb78e Content-Type: text/plain; charset=ISO-8859-1 Hi All, I need to determine the RMSD of a small molecule cocrystallized ligand, against a large number of predicted docked conformations. Please let me know what is the best method for doing this. Thank you very much, Nancy --00151747ba0e0cf633049f6cb78e Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi All,

I need to determine the RMSD of a small molecule= cocrystallized ligand, against a large number of predicted docked conforma= tions. =A0Please let me know what is the best method for doing this.

Thank you very much,
Nancy

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