From chemistry-request@server.ccl.net Thu Jun 15 08:44:12 2000 Received: from ucidoor.unitedcatalysts.com ([208.23.162.2]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id IAA31666 for ; Thu, 15 Jun 2000 08:44:11 -0400 Received: by ucidoor.unitedcatalysts.com; (8.8.8/1.3/10May95) id IAA29346; Thu, 15 Jun 2000 08:49:39 -0400 (EDT) Received: from 10.1.0.50 by ucismtp02.unitedcatalysts.com (InterScan E-Mail VirusWall NT); Thu, 15 Jun 2000 08:41:48 -0400 (Eastern Daylight Time) Received: from lvlxch01.unitedcatalysts.com ([10.1.0.88]) by lvlmail.unitedcatalysts.com (PMDF V5.2-32 #33820) with ESMTP id <0FW700N2A4UWIA@lvlmail.unitedcatalysts.com>; Thu, 15 Jun 2000 08:47:20 -0400 (EDT) Received: by LVLXCH01 with Internet Mail Service (5.5.2650.21) id ; Thu, 15 Jun 2000 08:42:10 -0400 Content-return: allowed Date: Thu, 15 Jun 2000 08:42:04 -0400 From: "Shobe, Dave" Subject: RE: Basis set problem (Summary) To: "'Iris Chan'" , chemistry@ccl.net Message-id: <157A51F55AAAD3119CD70008C7B1629D638390@LVLXCH01> MIME-version: 1.0 X-Mailer: Internet Mail Service (5.5.2650.21) Content-type: text/plain; charset="iso-8859-1" You don't need the pseudo keyword to get the ECP part of lanl2dz? I thought that gen just retrieved the explicit-electron basis set of this basis/ECP combination. --David Shobe -----Original Message----- From: Iris Chan [mailto:kiki@iris.chem.cuhk.edu.hk] Sent: Thursday, June 15, 2000 3:30 PM To: chemistry@ccl.net Subject: CCL:Basis set problem (Summary) Hi, The responses is so quick!. Thanks for the help from Dr. Ida Ma and Li Zhenhua. According to their suggestion, the problem can be solved as follows: ---------------------------------------- #P ub3lyp/gen opt Geometry of LaCl3 0 1 La Cl 1 r Cl 1 r 2 a Cl 1 r 2 a 3 d r=2.5 a=120. d=180. La 0 LANL2DZ **** Cl 0 6-311+G(d) **** ---------------------------------------- Regards, Iris -= This is automatically added to each message by mailing script =- CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net From chemistry-request@server.ccl.net Wed Jun 14 23:34:46 2000 Received: from canter-n-siegel.schrodinger.com (canter-n-siegel.schrodinger.com [192.156.98.248]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id XAA28873 for ; Wed, 14 Jun 2000 23:34:45 -0400 Received: (from info@localhost) by canter-n-siegel.schrodinger.com (8.8.5/8.8.5) id UAA21788 for chemistry@ccl.net; Wed, 14 Jun 2000 20:24:11 -0700 From: Schrodinger Info account Message-Id: <200006150324.UAA21788@canter-n-siegel.schrodinger.com> Subject: ANNC: Schrodinger releases ADME prediction software To: chemistry@ccl.net Date: Wed, 14 Jun 2000 20:24:11 -0700 (PDT) X-Mailer: ELM [version 2.5 PL0b2] MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear Colleague, We would like to introduce you to QikProp, a new property prediction program, recently developed by Professor William Jorgensen at Yale University. QikProp represents an integrated, comprehensive product specifically focused upon drug discovery that extends and complements existing methods (see E.M. Duffy, W.L. Jorgensen, J. Am. Chem.Soc. 2000, 122, 2878-2888; W.L. Jorgensen, E.M. Duffy, Bioorg. & Med. Chem. Let. 2000, 10 (11), 1155-1158). QikProp provides fast predictions (10,000 molecules/hour) for seventeen physically significant descriptors and seven pharmaceutically relevant properties useful in predicting ADME (adsorption, distribution, metabolism, and excretion) characteristics of drug candidates. To our knowledge, QikProp is the only currently available property prediction program that determines Caco-2 permeability and blood-brain barrier permeability. QikProp's use of whole-molecule descriptors that have a straightforward physical interpretation (as opposed to fragment-based descriptors) could provide a useful pathway for medicinal chemists to modify ADME properties. QikProp has been thoroughly evaluated at many major pharmaceutical companies and found to be extremely useful in the context of both high-throughput library screening and lead optimization. Contact us today to receive your free evaluation copy of QikProp! For more information, please visit http://www.schrodinger.com, or contact info@schrodinger.com. From chemistry-request@server.ccl.net Thu Jun 15 08:57:20 2000 Received: from hcm-fw1-ext.hcm-fw1.vnn.vn ([203.162.44.33]) by server.ccl.net (8.8.7/8.8.7) with SMTP id IAA31756 for ; Thu, 15 Jun 2000 08:57:14 -0400 Received: from vnuserv.vnuhcm.edu.vn by hcm-fw1-ext.hcm-fw1.vnn.vn via smtpd (for server.ccl.net [192.153.40.39]) with SMTP; 15 Jun 2000 12:53:15 UT Received: from Mail-Gateway.hcmuns.edu.vn (Services.hcmuns.edu.vn [172.29.16.4]) by vnuserv.vnuhcm.edu.vn (8.9.3/8.8.7) with ESMTP id NAA01280; Thu, 15 Jun 2000 13:08:46 GMT Received: from vnuserv.vnuhcm.edu.vn. by VNU-Gateway with ESMTP Ver (1.1Plus) for recipient addresses : Received: from mailbox.hcmuns.edu.vn (Mailbox.hcmuns.edu.vn [172.29.1.10]) by HCMU Mail-Gateway At Fri, 16 Jun 2000 02:56:32 +0700 (VN) VietNam Received: from chemsrv (www-chemdep.hcmuns.edu.vn [172.29.2.231]) by mailbox.hcmuns.edu.vn (8.8.5/SCA-6.6) with SMTP id UAA11933 for ; Thu, 15 Jun 2000 20:01:21 +0700 (VN) Message-ID: <005d01bfd6c8$e12ae030$e7021dac@chem.hcmuns.edu.vn> Reply-To: "quanph" From: "quanph" To: Subject: Databases . . . Date: Thu, 15 Jun 2000 19:54:44 +0700 Dear all, Does anyone know any structure and biological acitivities databases of medicinal or chemical, or where I may get more information? Thank you in advance, Phung Quan From chemistry-request@server.ccl.net Thu Jun 15 16:17:47 2000 Received: from helix.nih.gov (helix.nih.gov [128.231.2.3]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id QAA01148 for ; Thu, 15 Jun 2000 16:17:47 -0400 Received: from I.T.S.ME ([137.187.209.93]) by helix.nih.gov (8.9.3/8.9.3) with ESMTP id QAA3865380; Thu, 15 Jun 2000 16:17:43 -0400 (EDT) Date: Thu, 15 Jun 2000 16:17:32 -0400 (Eastern Daylight Time) From: "M. Nicklaus" To: quanph cc: chemistry@ccl.net, mn1@helix.nih.gov Subject: Re: CCL:Databases . . . In-Reply-To: <005d01bfd6c8$e12ae030$e7021dac@chem.hcmuns.edu.vn> Message-ID: X-X-Sender: mn1@helix.nih.gov MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Thu, 15 Jun 2000, quanph wrote: > Does anyone know any structure and biological acitivities databases of > medicinal or chemical, or where I may get more information? You can download chemical structural data together with biological activity data (cancer and AIDS) from our web server, at http://cactus.cit.nih.gov/ncidb/download.html. Marc ------------------------------------------------------------------------ Marc C. Nicklaus National Institutes of Health E-mail: mn1@helix.nih.gov Bldg 37, Rm 5B29 Phone: (301) 402-3111 37 Convent Dr, MSC 4255 Fax: (301) 402-2275 BETHESDA, MD 20892-4255 USA http://rex.nci.nih.gov/RESEARCH/basic/medchem/mcnbio.htm Laboratory of Medicinal Chemistry, National Cancer Institute ------------------------------------------------------------------------ From chemistry-request@server.ccl.net Thu Jun 15 17:01:18 2000 Received: from ucidoor.unitedcatalysts.com ([208.23.162.2]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id RAA01714 for ; Thu, 15 Jun 2000 17:01:18 -0400 Received: by ucidoor.unitedcatalysts.com; (8.8.8/1.3/10May95) id RAA16135; Thu, 15 Jun 2000 17:06:57 -0400 (EDT) Received: from 10.1.0.50 by ucismtp02.unitedcatalysts.com (InterScan E-Mail VirusWall NT); Thu, 15 Jun 2000 16:59:04 -0400 (Eastern Daylight Time) Received: from lvlxch01.unitedcatalysts.com ([10.1.0.88]) by lvlmail.unitedcatalysts.com (PMDF V5.2-32 #33820) with ESMTP id <0FW7000NXRVP6T@lvlmail.unitedcatalysts.com>; Thu, 15 Jun 2000 17:04:37 -0400 (EDT) Received: by LVLXCH01 with Internet Mail Service (5.5.2650.21) id ; Thu, 15 Jun 2000 16:59:27 -0400 Content-return: allowed Date: Thu, 15 Jun 2000 16:59:21 -0400 From: "Shobe, Dave" Subject: RE: Databases . . . To: "'quanph'" , chemistry@ccl.net Message-id: <157A51F55AAAD3119CD70008C7B1629D638395@LVLXCH01> MIME-version: 1.0 X-Mailer: Internet Mail Service (5.5.2650.21) Content-type: text/plain; charset="iso-8859-1" For the most common chemicals (including most commercially available drugs) there's the Merck Index. A larger number of chemicals is found in the Dictionary of Natural Products (which is much more expensive and therefore less likely to be found in your library; plus it only includes chemicals that have been isolated from natural sources). Chemical Abstracts indexes the primary literature (i.e. journal articles and the like) on biological effects of chemicals. STN--the producers of Chemical Abstracts--has various other pharmaceutical-related databases, which are described at http://www.cas.org/PHARM/pharm.html. Maybe you are looking for information on QSAR (quantitative structure-activity relationships). I can't help you much there, although it's on my list of things I'd like to know more about. :-) Hope this helps, --David Shobe -----Original Message----- From: quanph [mailto:quanph@hcmuns.edu.vn] Sent: Thursday, June 15, 2000 8:55 AM To: chemistry@ccl.net Subject: CCL:Databases . . . Dear all, Does anyone know any structure and biological acitivities databases of medicinal or chemical, or where I may get more information? Thank you in advance, Phung Quan -= This is automatically added to each message by mailing script =- CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net From chemistry-request@server.ccl.net Thu Jun 15 20:16:48 2000 Received: from markov.chem.rochester.edu (markov.chem.rochester.edu [128.151.176.16]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id UAA02633 for ; Thu, 15 Jun 2000 20:16:48 -0400 Received: (from serg@localhost) by markov.chem.rochester.edu (8.10.1/8.10.1) id e5H0GeM28186; Thu, 16 Jun 2000 20:16:40 -0400 (EDT) Date: Thu, 16 Jun 2000 20:16:40 -0400 (EDT) From: Sergei Tretiak To: CHEMISTRY@ccl.net Subject: g98A9 on sun In-Reply-To: <38BAB281.6C0D3662@trentu.ca> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Netters: I am trying to compile g98A9 at Sun (SunOS 5.8 with Sun Performance Library). Compiler produces following errors (lines from bldg98.log): cc -I/nh/nest/u/serg/Gaussian/g98A9_sun//g98 -DDEFMAXSHL=20000 -DDEFMAXATM=20000 -DDEFMAXNZ=20000 -DDEFMAXINFO=200 -DDEFNVDIM=257 -DDEFARCREC=1024 -DDEFLMAX=13 -DDEFCACHE=256 -DDEFN3MIN=10 -DDEFMAXOP=120 -DDEFMAXTIT=100 -DDEFMAXRTE=4000 -DDEFMAXOV=500 -DDEFMAXIOP=100 -DDEFMAXCHR=1024 -DDEFMAXHEV=2000 -DDEFMAXLECP=10 -DDEFMAXFUNIT=5 -DDEFMAXFFILE=10000 -DDEFMAXFPS=1300 -DDEFMXTS=1500 -DDEFMXBAS=500 -DDEFMXOPT=50 -DDEFMXBOND=12 -DDEFMXSPH=250 -DDEFMXINV=1500 -DI64 -DPACK64 -D_SUN_ -D_SUN_64 -DGAUSS_PAR -DGAUSS_THPAR -xtarget=ultra -xarch=v9 -c bsd/mdutil.c "bsd/mdutil.c", line 776: warning: modification of typedef with "int" ignored "bsd/mdutil.c", line 776: identifier redeclared: ssize_t current : int previous: long : "/usr/include/stdio_impl.h", line 20 "bsd/mdutil.c", line 1687: undefined symbol: O_RDWR "bsd/mdutil.c", line 1688: undefined symbol: O_RDONLY "bsd/mdutil.c", line 1698: undefined symbol: O_CREAT "bsd/mdutil.c", line 1698: undefined symbol: O_TRUNC "bsd/mdutil.c", line 1703: undefined symbol: LOCK_EX "bsd/mdutil.c", line 1703: undefined symbol: LOCK_NB "bsd/mdutil.c", line 1712: undefined symbol: LOCK_EX "bsd/mdutil.c", line 1712: undefined symbol: LOCK_NB "bsd/mdutil.c", line 1720: undefined symbol: LOCK_SH "bsd/mdutil.c", line 1720: undefined symbol: LOCK_NB "bsd/mdutil.c", line 1725: undefined symbol: LOCK_EX "bsd/mdutil.c", line 1725: undefined symbol: LOCK_NB "bsd/mdutil.c", line 1790: undefined symbol: LOCK_UN "bsd/mdutil.c", line 2048: undefined symbol: L_XTND "bsd/mdutil.c", line 3458: warning: inconsistent redeclaration of extern: sbrk cc: acomp failed for bsd/mdutil.c make: *** [mdutil.o] Error 2 ar rv ../util.a mdutil.o ar: mdutil.o: No such file or directory else if ( 0 ) then rm mdutil.o rm: mdutil.o: No such file or directory endif Obviousely cc could not compile mdutil.c. I wonder if somebody had an experience with this error. Thanks. Sergei From chemistry-request@server.ccl.net Thu Jun 15 18:20:31 2000 Received: from dqo.fcq.unc.edu.ar (root@dqo.fcq.unc.edu.ar [200.16.18.55]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id SAA02282 for ; Thu, 15 Jun 2000 18:20:29 -0400 Received: from fer-net.fcq.unc.edu.ar (IDENT:marcos@fer-net.fcq.unc.edu.ar [200.16.18.6]) by dqo.fcq.unc.edu.ar (8.9.3/8.9.3) with SMTP id TAA24530 for ; Thu, 15 Jun 2000 19:19:06 -0400 From: Marcos Villarreal To: chemistry@ccl.net Subject: decane Date: Thu, 15 Jun 2000 19:14:41 -0400 X-Mailer: KMail [version 1.0.17] Content-Type: text/plain MIME-Version: 1.0 Message-Id: <00061519182400.01043@fer-net.fcq.unc.edu.ar> Content-Transfer-Encoding: 8bit Hello, were could I find an equilibrated box of decane (all or united atom) to perform a molecular dynamics? Thanks in advance, ----------------------------------------------- PhD student Marcos Villarreal Departamento de Quimica Biologica. Facultad de Ciencias Quimicas. Universidad Nacional de Cordoba. Argentina.