From owner-chemistry@ccl.net Fri Jul 24 03:12:02 2009 From: "Daniel Jana dfjana_+_gmail.com" To: CCL Subject: CCL: Any ORCA user over there Message-Id: <-39841-090723175739-26502-8lIYfrNdvhtHlwjf2AkuRA_._server.ccl.net> X-Original-From: Daniel Jana Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 23 Jul 2009 22:29:47 +0200 MIME-Version: 1.0 Sent to CCL by: Daniel Jana [dfjana a gmail.com] Hello, Esteban Gabriel Vega Hissi egvega::gmail.com wrote: > Hi CCL readers, > I have recently downloaded QM program ORCA and I can't run it because > of a segmentation failure in my ubuntu 9 and red hat 9. > Any suggestions? I use Ubuntu 9.04 and just downloaded orca_i686_openmpi_exe_2.7.0b.tbz (the OpenMPI version for a x86 machine, last version of the program). Decompressed the file, put the folder in the PATH used the first input example (long time I haven't used ORCA), the HF single point of CO. Ran with no problems. Did you download the correct version? Cheers, Daniel From owner-chemistry@ccl.net Fri Jul 24 04:15:01 2009 From: "Pablo Vitoria Garcia pablo.vitoria#,#ehu.es" To: CCL Subject: CCL: Any ORCA user over there Message-Id: <-39842-090723185406-13844-B4jnB1a3r92AZNFFflyiRw|*|server.ccl.net> X-Original-From: Pablo Vitoria Garcia Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; format="flowed" Date: Fri, 24 Jul 2009 00:21:12 +0200 MIME-Version: 1.0 Sent to CCL by: Pablo Vitoria Garcia [pablo.vitoria a ehu.es] Hi Esteban, It certainly works in Mandriva (several releases), and I guess in most =20 Linux systems since it is statically linked. Did you download the right binaries for your system? There are 32 and =20 64 bit versions in the download page. Regards Pablo "Esteban Gabriel Vega Hissi egvega::gmail.com" =20 ha escrito: > Hi CCL readers, > I have recently downloaded QM program ORCA and I can't run it because of a > segmentation failure in my ubuntu 9 and red hat 9. > Any suggestions? > --=20 ******************************** Pablo Vitoria Garcia Servicios Generales de Rayos X Universidad del Pa=EDs Vasco (UPV/EHU) Fac. Ciencia y Tecnolog=EDa, Edificio CD3 c/ Barrio Sarriena s/n, 48940 Leioa (Bizkaia) Tfno. +34 946015334 Fax +34 946013500 ******************************** From owner-chemistry@ccl.net Fri Jul 24 07:28:01 2009 From: "Vincent.Leroux/./loria.fr" To: CCL Subject: CCL: Need clear, published examples of multi-objective medchem optimization Message-Id: <-39843-090724063105-13351-T6e7N3FE/I0xmQSJ/bwuvg{=}server.ccl.net> X-Original-From: Vincent.Leroux(~)loria.fr Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; format="flowed" Date: Fri, 24 Jul 2009 11:52:41 +0200 MIME-Version: 1.0 Sent to CCL by: Vincent.Leroux]=[loria.fr Hi James, When a compound has such properties as poor ADME-tox or poor =20 penetration, IMHO it does not qualify as a lead... You may find published examples of already interesting compound being =20 further optimized rather than examples of "bad" compounds being =20 miraculously turned into wonderdrugs after some tinkering. =20 STI-571/Gleevec is one good example of the former lead optimization =20 done right. Capdeville R, Buchdunger E, Zimmermann J, Matter A. Glivec (STI571, =20 imatinib), a rationally developed, targeted anticancer drug. Nat Rev =20 Drug Discov. 2002;1:493-502. Regards, VL "James Thomas Metz James.Metz!=3D!Abbott.com" =20 a =E9crit=A0: > > Sent to CCL by: "James Thomas Metz" [James.Metz#Abbott.com] > CCL, > > I am looking for published references to clear examples of =20 > multi-objective medicinal chemistry lead optimization. > > By this I mean, clear examples where a publication identifies a lead =20 > compound which may have mediocre activity in some biological screen =20 > or assay as well as a number of additional measured "defects" e.g., =20 > poor solubility, poor brain penetration, poor ADME properties, etc. =20 > Then the same or another publication clearly shows an optimized =20 > molecule(s) from the same (or closely related series) where a number =20 > of the defects have been simultaneously resolved in the same =20 > molecule(s) e.g., improved biological activity, and improved =20 > solubility, and improved PK, etc. > > It is essential that the publication(s) state the initial and the =20 > final experimentally determined values of the various properties =20 > being optimized. > > Unfortunately, many med chem publications typically follow the SAR =20 > for biological activity, then, perhaps give measured ADME values of =20 > a few interesting final molecules. Hence one does not know the ADME =20 > or other property status of the initial molecules. > > I am currently studying Walter Sneader's interesting books, "Drug =20 > Prototypes," and "Drug Discovery - A History," in an attempt to find =20 > this information, but not much success from a multi-objective =20 > standpoint, so far. > > I would be most grateful, if anyone could provide appropriate =20 > literature references or suggestions how to obtain this information. > > Thank you. > > Regards, > Jim Metz > > Abbott Laboratories > > > > -=3D This is automatically added to each message by the mailing script =3D= -> > > From owner-chemistry@ccl.net Fri Jul 24 10:51:01 2009 From: "Zhenbo Liu zhenboliu[#]qq.com" To: CCL Subject: CCL: bridge bond Message-Id: <-39844-090723235248-14321-kojDgO2lmW5IPM8On9tkaA#server.ccl.net> X-Original-From: "Zhenbo Liu" Date: Thu, 23 Jul 2009 23:52:44 -0400 Sent to CCL by: "Zhenbo Liu" [zhenboliu{=}qq.com] I know the three-center two-electron bridge bond in B2H6. But I want to know whether there are other kinds of bridge bond. Thank you very much. From owner-chemistry@ccl.net Fri Jul 24 11:33:01 2009 From: "Bahareh honarparvar bahareh_honarparvar],[yahoo.com" To: CCL Subject: CCL:G: bridge bond Message-Id: <-39845-090724112907-18856-jbP6fTte9h0bTMdhUivkUQ(_)server.ccl.net> X-Original-From: Bahareh honarparvar Content-Type: multipart/alternative; boundary="0-1184132604-1248449331=:64831" Date: Fri, 24 Jul 2009 08:28:51 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Bahareh honarparvar [bahareh_honarparvar() yahoo.com] --0-1184132604-1248449331=:64831 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Dear Dr.Zhenbo Liu zhenboliu, you can do NBO analysis with Gaussian program. Good luck Honarparvar --- On Fri, 7/24/09, Zhenbo Liu zhenboliu[#]qq.com wrote: > From: Zhenbo Liu zhenboliu[#]qq.com Subject: CCL: bridge bond To: "Honarparvar, Honarparvar " Date: Friday, July 24, 2009, 8:22 AM Sent to CCL by: "Zhenbo=A0 Liu" [zhenboliu{=3D}qq.com] I know the three-center two-electron bridge bond in B2H6. But I want to kno= w whether there are other kinds of bridge bond. Thank you very much. -=3D This is automatically added to each message by the mailing script =3D-=A0 =A0 =A0=A0 =A0 =A0Subscribe/Unsubscribe:=20 =A0 =A0 =A0Job: http://www.ccl.net/jobs=20=A0 =A0 =A0=0A=0A=0A --0-1184132604-1248449331=:64831 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
Dear Dr.Zhenbo Liu zhenboliu,
you can do N= BO analysis with Gaussian program.
Good luck
Honarparvar

--- O= n Fri, 7/24/09, Zhenbo Liu zhenboliu[#]qq.com <owner-chemistry(~)ccl= .net> wrote:

From: Zhenbo Liu zh= enboliu[#]qq.com <owner-chemistry(~)ccl.net>
Subject: CCL: bridge bo= nd
To: "Honarparvar, Honarparvar " <bahareh_honarparvar(~)yahoo= .com>
Date: Friday, July 24, 2009, 8:22 AM


Sent to CCL by: "Zhenbo  Liu" [zhenboliu{=3D}qq.com]
I kn= ow the three-center two-electron bridge bond in B2H6. But I want to know wh= ether there are other kinds of bridge bond. Thank you very much.


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=0A=0A --0-1184132604-1248449331=:64831-- From owner-chemistry@ccl.net Fri Jul 24 15:08:00 2009 From: "Jan Labanowski janl- -speakeasy.net" To: CCL Subject: CCL: Environmental Toxicity Prediction Challenge Message-Id: <-39846-090724150600-10522-GNMRUcyRUaIRAk0WnAy9kw|*|server.ccl.net> X-Original-From: Jan Labanowski Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="iso-8859-1" Date: Fri, 24 Jul 2009 15:05:45 EDT MIME-Version: 1.0 Sent to CCL by: Jan Labanowski [janl]|[speakeasy.net] Forwarding at request of Dr. Tetko: Environmental Toxicity Prediction Challenge This challenge is organized by ICANN'09: International Conference on Artifi= cial Neural Networks, European Neural Network Society (ENNS) and CADASTER proje= ct. Goals of this study: Develop in silico models to predict environmental toxi= city of molecules against T. pyriformis using data from [1]. Estimate the predi= ction intervals for new compounds. Further information can be found at http://www.cadaster.eu. Five datasets of descriptors are available:=20 Quantum Chemistry, E-state, DRAGON, SimulationsPlus and MOE descriptors Important key dates August 31 The submission of results is closed.=20 September 14-17 2009 The winner will be announced at the ICANN'09 conference (there is no requirement to participate to this conference) The winner will be identified according to the criteria defined below. It is expected that the winner as well as other participants will submit articles describing their methodological approaches for publication in a peer-revie= wed journal (under discussion).=20 Criteria for success Firstly, methods with Root Mean Squared Error (RMSE) non-significantly dif= ferent to the method with lowest RMSE (according to the bootstrap test, p<0.05) w= ill be identified as the first-pass winners.=20 Secondly, the method providing the best likelihood criteria between estimat= ed and observed confidences for the blind test set as described in [2] will be=20 identified amid the first-pass winners.=20 Igor V. Tetko, Terry W. Schultz and Wlodzislaw Duch=20 [1] Zhu, H.; Tropsha, A.; Fourches, D.; Varnek, A.; Papa, E.; Gramatica, P.; Oberg, T.; Dao, P.; Cherkasov, A.; Tetko, I. V. Combinatorial QSAR Modeling= of Chemical Toxicants Tested against Tetrahymena pyriformis J. Chem. Inf. Mode= l. 2008, 48 (4), 766-784. [2] Tetko, I. V.; Sushko, I.; Pandey, A. K.; Zhu, H.; Tropsha, A.; Papa, E.= ;=20 Oberg, T.; Todeschini, R.; Fourches, D.; Varnek, A., Critical assessment of= QSAR models of environmental toxicity against Tetrahymena pyriformis: focusing = on applicability domain and overfitting by variable selection J. Chem. Inf. Mo= del. 2008, 48 (9), 1733-46. Dr. Igor V. Tetko Institute of Bioinformatics and Systems Biology Helmholtz Zentrum Muenchen=20 German Research Center for Environmental Health Ingolstaedter Landstrasse 1, D-85764 Neuherberg, Germany Tel./Fax: +49-89-3187-3575/x85 e-mail: itetko#,#vcclab.org, itetko#,#gmail.com http://www.vcclab.org http://www.cadaster.eu -- see prediction challenge! From owner-chemistry@ccl.net Fri Jul 24 18:07:01 2009 From: "Ben Janesko bjanesko * rice.edu" To: CCL Subject: CCL:G: Transition state optimization with Gaussian 03 and frozen atoms Message-Id: <-39847-090724145608-9392-6u5dFZE0AXeoDNfgL2Ieew/./server.ccl.net> X-Original-From: Ben Janesko Content-Transfer-Encoding: 7bit Content-Type: text/plain Date: Fri, 24 Jul 2009 13:18:31 -0500 Mime-Version: 1.0 Sent to CCL by: Ben Janesko [bjanesko_+_rice.edu] Hello. I would like to optimize the transition state of a reaction on a metal cluster. I want to freeze the cluster geometry. Is this possible with Gaussian 03? It doesn't appear to work with the QST2 and QST3 methods. Ben Janesko From owner-chemistry@ccl.net Fri Jul 24 20:17:00 2009 From: "Susan R Atlas susie[*]sapphire.phys.unm.edu" To: CCL Subject: CCL: compilation of parallel VASP on SGI Altix ICE architecture Message-Id: <-39848-090724201553-18995-hEB99NJTILi2NMW/jy0j9Q ~ server.ccl.net> X-Original-From: "Susan R Atlas" Date: Fri, 24 Jul 2009 20:15:49 -0400 Sent to CCL by: "Susan R Atlas" [susie|*|sapphire.phys.unm.edu] Hi, A member of my group is trying to build (parallel) VASP on an SGI Altix ICE cluster, and is running into serious problems with the BLACS and ScaLAPACK underlying components. We are using the Intel 11.0 compiler on Xeon 5300 series CPUs, SLES Linux OS. The interconnect is Infiniband and MPI is MVAPICH 1.0 from OSU. The BLACS configuration utilities either lead to error messages or failures on the self-tests; if we push through the ScaLAPACK build with one of these BLACS, the ScaLAPACK self-tests generate numerous segfaults. Does anyone have experience with compiling VASP (and in particular the underlying BLACS and ScaLAPACK) on this SGI architecture/environment? Any advice and/or scripts would be greatly appreciated. Thanks, Susan