From owner-chemistry@ccl.net Mon Jun 14 08:55:01 2010 From: "Paolo Tosco paolo.tosco::unito.it" To: CCL Subject: CCL:G: Open3DQSAR 1.2 released Message-Id: <-42106-100614081048-13658-htjth6KDOE13Obn5B+J3vg/./server.ccl.net> X-Original-From: "Paolo Tosco" Date: Mon, 14 Jun 2010 08:10:46 -0400 Sent to CCL by: "Paolo Tosco" [paolo.tosco-,-unito.it] Dear CCLers, Open3DQSAR 1.2 has been released: http://www.open3dqsar.org Open3DQSAR is an open-source software aimed at pharmacophore exploration of a set of ligands endowed with biological activity by high-throughput chemometric analysis of molecular interaction fields (MIFs). Open3DQSAR can generate steric potential, electron density and MM/QM electrostatic potential fields; furthermore, it can import GRID and CoMFA/CoMSIA MIFs. On these MIFs, Open3DQSAR performs fast, automated PLS chemometric analysis allowing to quickly generate and challenge the predictivity of many 3D-QSAR models using different training/test set combinations, superposition schemes, variable selection and data scrambling procedures, etc. High computational performance is attained through implementation of parallelized algorithms for MIF generation, PLS model building and validation, variable selection. New features in Open3DQSAR 1.2 include: - Seamless integration with OpenBabel, PyMOL, gnuplot - Multi-threaded computation of MIFs (both MM and QM) - Support for MMFF94 and GAFF force-fields with automated assignment of atom types to the imported molecular structures - More comprehensive output, including SDF molecular databases, 3D maps and many different plots to ease immediate evaluation of results in PyMOL, MOE, Maestro, SYBYL and gnuplot - User-friendly interface to all major QM packages (e.g. GAUSSIAN, FIREFLY, GAMESS-US, MOLDEN) allows calculation of QM electron density and electrostatic potential 3D maps from within Open3DQSAR Open3DQSAR runs on all mainstream operating systems (Windows 32/64-bit, Linux 32/64-bit, Solaris x86 32/64-bit, Intel Mac OS X 32/64-bit). Open3DQSAR is available free of charge to eligible users according to the license terms; for information, see http://www.open3dqsar.org Tosco, P.; Balle, T. "Open3DQSAR: a new open-source software aimed at high-throughput chemometric analysis of molecular interaction fields", J. Mol. Model. 2010 http://dx.doi.org/10.1007/s00894-010-0684-x Kind regards, Paolo Tosco Department of Drug Science and Technology Faculty of Pharmacy, University of Turin Via Pietro Giuria 9, 10125 Torino, Italy Thomas Balle Department of Medicinal Chemistry The Faculty of Pharmaceutical Sciences, University of Copenhagen, 2 Universitetsparken, 2100 Copenhagen, Denmark From owner-chemistry@ccl.net Mon Jun 14 09:29:01 2010 From: "Rene Thomsen rt##molegro.com" To: CCL Subject: CCL: Molegro releases Molegro Data Modeller 2.5 Message-Id: <-42107-100614070410-5193-fcRFIQgMr8yUZ8OxQLZjYA=-=server.ccl.net> X-Original-From: "Rene Thomsen" Date: Mon, 14 Jun 2010 07:04:09 -0400 Sent to CCL by: "Rene Thomsen" [rt^molegro.com] Aarhus, Denmark, June 14th, 2010 - Molegro is pleased to announce a new release of Molegro Data Modeller, a cross-platform application for Data Mining, Data Modelling, and Data Visualization. The built-in features for visualization of chemical structures (SDF and SMILES) make it particularly suitable for QSAR / QSPR modelling and for detailed analysis of docking results from Molegro Virtual Docker. The highly interactive user interface of Molegro Data Modeller is ideal for fast and intuitive data exploration, as opposed to complex workflow based solutions or command-driven statistical products. Molegro Data Modeller is available for Windows, Linux, and Mac OS X. New features in version 2.5: * A new 'Import Dataset Wizard' allows for previewing CSV datasets before import. It is also possible to filter the dataset based on a descriptor and to import a row range of a dataset. * New 'Apply Model to External Dataset' dialog for applying regression and classification models to external CSV files without importing all the data into main memory. This makes it possible to make predictions on large datasets only limited by disk size. * Offline model predictions from the command line making it possible to integrate MDM in automated workflows. * 'Compare Training / Test Set' dialog for measuring how close data points in a given test set are to the data points used for model training. The dialog can be used to check if test data belongs to the same domain as the training data - if not, model predictions might not be reliable. * 'Diversity Statistics' dialog for analysing the diversity of a given data set. * Minor user interface improvements and bug fixes (see Release Notes for details). For more information, or to download a trial version, please visit our company website at: http://www.molegro.com or contact: Rene Thomsen, CEO Molegro C. F. Moelles Alle 8, Bldg. 1110 DK-8000 Aarhus Denmark E-mail: rt-*-molegro.com Phone: (+45) 89 42 31 65 About Molegro Molegro is a Danish company founded in 2005. Our company concentrates on developing high- performance drug discovery solutions leading to a faster drug-development process. Our goal is to provide scientifically superior products focusing on both state-of-the-art algorithms and an intuitive graphical user interface experience. From owner-chemistry@ccl.net Mon Jun 14 10:04:00 2010 From: "Liu Jing jliu/./cuhk.edu.hk" To: CCL Subject: CCL: TDDFT Message-Id: <-42108-100614052615-14954-5vS6KWq4jxHSy5grIG7/Bg::server.ccl.net> X-Original-From: Liu Jing Content-Type: multipart/alternative; boundary=00c09f8997034c36580488f93b21 Date: Mon, 14 Jun 2010 16:25:29 +0800 MIME-Version: 1.0 Sent to CCL by: Liu Jing [jliu%a%cuhk.edu.hk] --00c09f8997034c36580488f93b21 Content-Type: text/plain; charset=ISO-8859-1 Dear all, Can you tell me how to set the spin multiplicity of the excited states when a open- shell system is concerned? Thank you and good luck. Yours Jing --00c09f8997034c36580488f93b21 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Dear all,
=A0=A0
=A0=A0Can you tell me how to set the spin multiplicity of the excited = states when a open-
shell system is concerned?
=A0
=A0Thank you and good luck.
=A0
Yours Jing
--00c09f8997034c36580488f93b21-- From owner-chemistry@ccl.net Mon Jun 14 14:31:00 2010 From: "Jamin Krinsky jamink()berkeley.edu" To: CCL Subject: CCL:G: TDDFT Message-Id: <-42109-100614142847-23733-mS9ApYfjGbfLXSKjJNKWxA- -server.ccl.net> X-Original-From: Jamin Krinsky Content-Type: multipart/alternative; boundary=0016363b8fb8475202048901a898 Date: Mon, 14 Jun 2010 11:28:36 -0700 MIME-Version: 1.0 Sent to CCL by: Jamin Krinsky [jamink-,-berkeley.edu] --0016363b8fb8475202048901a898 Content-Type: text/plain; charset=ISO-8859-1 Dear Jing, If you are using Gaussian, you cannot request excited-state multiplicities different from the ground state for open-shell molecules (the "singlets" and "triplets" options are ignored). You can of course calculate the ground-state configuration for each multiplicity and compare energies of those... Some other programs (Q-Chem included I think) will let you do spin-flip TDDFT, but you'd want to read up on the subject before attempting it (I don't know much about it). Regards, Jamin On Mon, Jun 14, 2010 at 1:25 AM, Liu Jing jliu/./cuhk.edu.hk < owner-chemistry*ccl.net> wrote: > Dear all, > > Can you tell me how to set the spin multiplicity of the excited states > when a open- > shell system is concerned? > > Thank you and good luck. > > Yours Jing > -- Jamin L Krinsky, Ph.D. Molecular Graphics and Computation Facility 175 Tan Hall, University of California, Berkeley, CA 94720 jamink*berkeley.edu, 510-643-0616 http://glab.cchem.berkeley.edu --0016363b8fb8475202048901a898 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear Jing,

If you are using Gaussian, you cannot request excited-sta= te multiplicities different from the ground state for open-shell molecules = (the "singlets" and "triplets" options are ignored). Yo= u can of course calculate the ground-state configuration for each multiplic= ity and compare energies of those... Some other programs (Q-Chem included I= think) will let you do spin-flip TDDFT, but you'd want to read up on t= he subject before attempting it (I don't know much about it).

Regards,
Jamin


On Mon, Jun 14,= 2010 at 1:25 AM, Liu Jing jliu/./cuhk.edu.h= k <owne= r-chemistry*ccl.net> wrote:
Dear all,
=A0=A0
=A0=A0Can you tell me how to set the spin multiplicity of the excited = states when a open-
shell system is concerned?
=A0
=A0Thank you and good luck.
=A0
Yours Jing



--
Jamin L Krinsky, Ph.D.<= br>Molecular Graphics and Computation Facility
175 Tan Hall, University = of California, Berkeley, CA 94720
jamink*berkeley.edu, 510-643-0616
http://glab.cchem.berkeley.edu

--0016363b8fb8475202048901a898-- From owner-chemistry@ccl.net Mon Jun 14 22:02:01 2010 From: "Liu Jing jliu]^[cuhk.edu.hk" To: CCL Subject: CCL:G: TDDFT Message-Id: <-42110-100614213746-31673-59G+DNnuzv/WVZ3Bmt9D9A(!)server.ccl.net> X-Original-From: Liu Jing Content-Type: multipart/alternative; boundary=00163630f75f62b44a048907a68f Date: Tue, 15 Jun 2010 09:37:36 +0800 MIME-Version: 1.0 Sent to CCL by: Liu Jing [jliu#,#cuhk.edu.hk] --00163630f75f62b44a048907a68f Content-Type: text/plain; charset=ISO-8859-1 Dear Jamin, Thank you for your quick reply. Would you like to say sth about the oscillator strengths. In my calculation this value is equal to zero for the first excited state, does it mean this transition is forbidden? Regards Liu, Jing 2010/6/15 Jamin Krinsky jamink()berkeley.edu > Dear Jing, > > If you are using Gaussian, you cannot request excited-state multiplicities > different from the ground state for open-shell molecules (the "singlets" and > "triplets" options are ignored). You can of course calculate the > ground-state configuration for each multiplicity and compare energies of > those... Some other programs (Q-Chem included I think) will let you do > spin-flip TDDFT, but you'd want to read up on the subject before attempting > it (I don't know much about it). > > Regards, > Jamin > > > On Mon, Jun 14, 2010 at 1:25 AM, Liu Jing jliu/./cuhk.edu.hk < > owner-chemistry]~[ccl.net> wrote: > >> Dear all, >> >> Can you tell me how to set the spin multiplicity of the excited states >> when a open- >> shell system is concerned? >> >> Thank you and good luck. >> >> Yours Jing >> > > > > -- > Jamin L Krinsky, Ph.D. > Molecular Graphics and Computation Facility > 175 Tan Hall, University of California, Berkeley, CA 94720 > jamink]~[berkeley.edu, 510-643-0616 > http://glab.cchem.berkeley.edu > > --00163630f75f62b44a048907a68f Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Dear Jamin,
=A0=A0=A0 Thank you for your quick reply.
=A0=A0=A0 Would you like to say sth about the oscillator strengths. In= my
calculation this value is equal to zero for the first excited state, d= oes
it mean this transition is forbidden?
=A0
Regards
Liu, Jing
2010/6/15 Jamin Krinsky jamink()berkeley.edu <owner-chemistry(-)ccl.net>
Dear Jing,

If you are usi= ng Gaussian, you cannot request excited-state multiplicities different from= the ground state for open-shell molecules (the "singlets" and &q= uot;triplets" options are ignored). You can of course calculate the gr= ound-state configuration for each multiplicity and compare energies of thos= e... Some other programs (Q-Chem included I think) will let you do spin-fli= p TDDFT, but you'd want to read up on the subject before attempting it = (I don't know much about it).

Regards,
Jamin


On Mon, Jun 14, 2010 at 1:25 AM, Liu Jing jliu/.= /cuhk.edu.hk <owner-chemistry]~[ccl.net> wrote:
Dear all,
=A0=A0
=A0=A0Can you tell me how to set the spin multiplicity of the excited = states when a open-
shell system is concerned?
=A0
=A0Thank you and good luck.
=A0
Yours Jing



--
Jamin L Krinsky, Ph.D.
Molecular Graphics and Com= putation Facility
175 Tan Hall, University of California, Berkeley, CA 9= 4720
jamink]~[berkele= y.edu, 510-643-0616
http://glab.cchem.berkeley.edu


--00163630f75f62b44a048907a68f--