From chemistry-request@ccl.net Fri Jul 2 09:06:42 2004 Received: from mx4.trentu.ca (mx4.trentu.ca [192.75.12.5]) by server.ccl.net (8.12.8/8.12.8) with SMTP id i62E6eFY028667 for ; Fri, 2 Jul 2004 09:06:41 -0500 Received: (qmail 10619 invoked by uid 510); 2 Jul 2004 14:12:00 -0000 Received: from elewars!at!trentu.cA by mx4.trentu.ca by uid 501 with qmail-scanner-1.20rc3 (f-prot: 4.4.1/3.14.11. spamassassin: 2.62. Clear:RC:1:. Processed in 0.019618 secs); 02 Jul 2004 14:12:00 -0000 Received: from unknown (HELO trentu.cA) (209.42.102.47) by mx4.trentu.ca with SMTP; 2 Jul 2004 14:12:00 -0000 Message-ID: <40E56E3F.10400!at!trentu.cA> Date: Fri, 02 Jul 2004 10:16:31 -0400 From: Errol Lewars User-Agent: Mozilla/5.0 (Windows; U; WinNT4.0; en-US; rv:1.6) Gecko/20040113 X-Accept-Language: en-us, en MIME-Version: 1.0 To: Yan Zhao , chemistry!at!ccl.net Subject: Re: CCL:gaussian03 optimization to transition state References: <200407012308.i61N818h020314!at!trojan.software.umn.edu> In-Reply-To: <200407012308.i61N818h020314!at!trojan.software.umn.edu> Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=0.0 required=7.5 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net 2004 July 2 People new to gaussian may wish to note that Gaussian *never* seems to find a transition state unless the NoEigentest (see below) keyword is included. I don't know why this is not the default. A good option is often Opt(TS, NoEigenTest, mndofc, MaxCycle=99). EL ===== Yan Zhao wrote: >Substitute "POpt=(Saddle=1)" for "opt=(ts,noeigentest,maxcycle=100)", then >it will not stop because the wrong number of Negaative eigenvalues, if the >optimization does not converge, you probably should try some better initial >guesses of the geometry or add "calcfc" in the opt keyword. > >Yan > >On 1 Jul 2004, Carsten Detering wrote: > > >>Hi all, >> >> I would like to optimize a complex involving a bifurcated hydrogen >>bond between three nitrogen atoms (trimethylamine and triazen) to a >>saddle point (which I know exists from previous Mopac calculations). >>Taking this header line in the input file >> >>B3LYP/6-31g* POpt=(Saddle=1) nosymmetry test >> >>the optimization finishes with an error >> >>optimization stopped >> --wrong number of Negative eigenvalues: Desired= 1 Actual= 2 >> --Flag reset to prevent archiving >> >>Then I get, at the bottom, the typical proverb that you see only when a >>calculation has successfully finished, and then >> >>Could anybody make some suggestions how to fix this? >> >>Thanks a lot in advance, >> >>Carsten >> >> >>To send e-mail to subscribers of CCL put the string CCL: on your Subject: >>line >> >>Send your subscription/unsubscription requests to: >> >> >CHEMISTRY-REQUEST!at!ccl.net > > >> >> >> >> >> >> >> >*************************************** >Yan Zhao yzhao!at!chem.umn.edu >Smith Hall 232 (612)-625-5311 >Department of Chemistry >University of Minnesota >207 Pleasant St SE >Minneapolis, MN 55455 >*************************************** > > > >-= This is automatically added to each message by the mailing script =- >To send e-mail to subscribers of CCL put the string CCL: on your Subject: line >and send your message to: CHEMISTRY!at!ccl.net > >Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST!at!ccl.net >HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs > >If your mail is bouncing from CCL.NET domain send it to the maintainer: >Jan Labanowski, jlabanow!at!nd.edu (read about it on CCL Home Page) >-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > > > > From chemistry-request@ccl.net Thu Jul 1 19:52:57 2004 Received: from postoffice7.mail.cornell.edu (postoffice7.mail.cornell.edu [132.236.56.22]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i620qu8a009764 for ; Thu, 1 Jul 2004 19:52:56 -0500 Received: from cornell.edu (67-41-237-93.slkc.qwest.net [67.41.237.93]) by postoffice7.mail.cornell.edu (8.12.10/8.12.6) with ESMTP id i620w56p023394; Thu, 1 Jul 2004 20:58:15 -0400 (EDT) Message-ID: <40E4B31A.7000302!at!cornell.edu> Date: Thu, 01 Jul 2004 18:58:02 -0600 From: Richard Wood User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.4) Gecko/20030624 Netscape/7.1 (ax) X-Accept-Language: en-us, en MIME-Version: 1.0 To: "chemistry!at!ccl.net" Subject: HyperChem units Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit X-PMX-Version: 4.6.0.99824, Antispam-Core: 4.6.0.101390, Antispam-Data: 2004.7.1.105720 X-Spam-Status: No, hits=4.2 required=7.5 tests=FROM_ENDS_IN_NUMS, RCVD_IN_DYNABLOCK,RCVD_IN_SORBS,TO_ADDRESS_EQ_REAL autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Hi all When one does an ab-initio calculation using HyperChem, what are the units? I can't find the answer to this question anywhere. Thanks in advance. Richard -- Richard L. Wood, Ph. D. Computational Chemist SynVax, Inc. N. Logan, UT 84341 From chemistry-request@ccl.net Fri Jul 2 15:55:05 2004 Received: from schrodinger.com (thermidore.schrodinger.com [192.156.98.99]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i62Kt0FY022761 for ; Fri, 2 Jul 2004 15:55:04 -0500 Received: from SVETLA (svetla.schrodinger.com [192.156.98.141]) by schrodinger.com (8.12.6/8.12.8) with SMTP id i62L0O27008207 for ; Fri, 2 Jul 2004 14:00:25 -0700 (PDT) (envelope-from announce..at..schrodinger.com) From: Schrodinger Announcements To: CCL Subject: Schrodinger Drug Design Seminar in WA, July 28 Date: Fri, 02 Jul 2004 16:57:26 -0400 Message-ID: <0702104165726.138@SVETLA> X-Spam-Status: No, hits=1.0 required=7.5 tests=NO_COST autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Schrodinger is hosting a seminar on Wednesday, July 28, at the Doubletree Hotel Bellevue in Bellevue, Washington. The Summer 2004 Drug Design Seminar will feature presentations on our latest advances and applications in structure-based and ligand-based drug design. There is no charge for attending, but space is limited, so please register in advance at our website: http://www.schrodinger.com/Announce/Workshop/W2004/wa_seminar04.html From chemistry-request@ccl.net Fri Jul 2 05:09:02 2004 Received: from smtp.uibk.ac.at (lmr1.uibk.ac.at [138.232.1.142]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i62A8vFY015292 for >ccl.net>; Fri, 2 Jul 2004 05:09:01 -0500 Received: from chemistry.upatras.gr (yy1-c724.uibk.ac.at [138.232.32.48]) by smtp.uibk.ac.at (8.12.10/8.12.10/F1) with ESMTP id i62AEJvD012262 for >ccl.net>; Fri, 2 Jul 2004 12:14:19 +0200 Message-ID: <40E5357B.3010205<>chemistry.upatras.gr> Date: Fri, 02 Jul 2004 12:14:19 +0200 From: Demetrios Xenides >chemistry.upatras.gr> User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.4) Gecko/20030624 Netscape/7.1 X-Accept-Language: en-us, en MIME-Version: 1.0 To: chemistry<>ccl.net Subject: error in orthogonality Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit X-Spam-Score: -3.0 () RCV_SMTP_UIBK X-Scanned-By: MIMEDefang 2.42 at uibk.ac.at X-Spam-Status: No, hits=0.0 required=7.5 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Hi all!!! Gaussian plays tricks again. The same file in G94 runs without any problem but in G98 it reduces the number of the basis used... I am trying to run a single point calculation using an uncontracted basis set by partridge. same command line for both #p rhf/gen scf(conver=10) nosymm field=read -------------------------------------------- MESSAGE IN ------------------------------------ ---------------------------------------------------G98-------------------------------------------- Two-electron integral symmetry is turned off. 187 basis functions 196 primitive gaussians 26 alpha electrons 26 beta electrons nuclear repulsion energy 147.4020983233 Hartrees. Leave Link 301 at Fri Jul 2 09:46:53 2004, MaxMem= 6291456 cpu: 0.1 (Enter /usr/local/g98/l302.exe) One-electron integrals computed using PRISM. Error in orthogonal basis= 1.61D-07 with 187 functions, increasing threshold to 2.00D-04. Error in orthogonal basis= 1.61D-07 with 187 functions, increasing threshold to 4.00D-04. Error in orthogonal basis= 1.61D-07 with 187 functions, increasing threshold to 8.00D-04. Error in orthogonal basis= 1.61D-07 with 187 functions, increasing threshold to 1.60D-03. Error in orthogonal basis= 1.61D-07 with 187 functions, increasing threshold to 3.20D-03. Error in orthogonal basis= 1.61D-07 with 187 functions, increasing threshold to 6.40D-03. Error in orthogonal basis= 1.61D-07 with 187 functions, increasing threshold to 1.28D-02. Error in orthogonal basis= 1.61D-07 with 187 functions, increasing threshold to 2.56D-02. Error in orthogonal basis= 4.12D-08 with 186 functions, increasing threshold to 5.12D-02. Error in orthogonal basis= 3.10D-09 with 182 functions, increasing threshold to 1.02D-01. NBasis= 187 RedAO= T NBF= 187 NBsUse= 167 1.02D-01 NBFU= 167 -------------------------------------------- MESSAGE IN ------------------------------------ ---------------------------------------------------G94W------------------------------------------ Two-electron integral symmetry is turned off. 187 basis functions 187 primitive gaussians 26 alpha electrons 26 beta electrons nuclear repulsion energy 147.4020983233 Hartrees. Leave Link 301 at Fri Jul 02 10:22:17 2004, MaxMem= 4000000 cpu:1.0 (Enter C:\G94W\l302.exe) One-electron integrals computed using PRISM. The smallest eigenvalue of the overlap matrix is 2.425E-04 Leave Link 302 at Fri Jul 02 10:22:17 2004, MaxMem= 4000000 cpu:1.0 (Enter C:\G94W\l303.exe) any hint? Cheers Demetrios From chemistry-request@ccl.net Fri Jul 2 10:59:30 2004 Received: from mhub-w3.tc.umn.edu (mhub-w3.tc.umn.edu [160.94.160.33]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i62FxTFY003303 for >ccl.net>; Fri, 2 Jul 2004 10:59:30 -0500 Received: from pobox.com (abacavir.pharmacy.umn.edu [160.94.172.208] (may be forged)) by mhub-w3.tc.umn.edu with ESMTP; Fri, 2 Jul 2004 11:04:53 -0500 (CDT) X-Umn-Remote-Mta: [N] abacavir.pharmacy.umn.edu [160.94.172.208] #+HF+LO Message-ID: <40E588A8.7080507<>pobox.com> Date: Fri, 02 Jul 2004 11:09:12 -0500 From: Eric Bennett >pobox.com> User-Agent: Mozilla/5.0 (X11; U; IRIX64 IP30; en-US; rv:1.4.1) Gecko/20040326 X-Accept-Language: en-us, en MIME-Version: 1.0 To: Michel Petitjean >itodys.jussieu.fr>, chemistry<>ccl.net Subject: Re: software to convert XYZ format to PDB ? References: <200407020730.i627U68E052048<>ds10.itodys.jussieu.fr> In-Reply-To: <200407020730.i627U68E052048<>ds10.itodys.jussieu.fr> Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=0.0 required=7.5 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Michel Petitjean wrote: >To: chemistry<>ccl.net >Subject: CCL:software to convert XYZ format to PDB ? > >Konrad Hinsen >cnrs-orleans.fr> wrote: > > >> If I had to do this (fortunately I don't), I'd first identify the >> >>peptide planes as patterns of pairwise distances (they are quite >>rigid). I'd then identify the sidechains atom by atom starting from the >>C-alphas, again by distance criteria. Not a trivial task, but not an >>impossible one either. >> >> > >Sure... if you have the side chains ! (were not indicated in the example) >It needs other assumptions: true residues, no HETATM, lexicographical >ordering coherent with the PDB conventions... > > There are programs (such as ARP/wARP) which start with NO atom information, not even coordinates, and can correctly build a protein structure based on an electron density map using pattern recognition techniques. The ambiguities there, such as ASP vs. ASN, are not present when you know the elements, as we do here. ARP/wARP is also gaining ligand building capabilities and already handles water molecules. ARP is part of CCP4 so you get source code with it. http://www.embl-hamburg.de/ARP/ Of course if you have any unexplained data (whether electron density or known atom positions) that do not fit the pattern of an amino acid, you can just leave them alone and inform the user. -- Eric Bennett, Center for Drug Design, U of Minnesota From chemistry-request@ccl.net Fri Jul 2 21:21:19 2004 Received: from postoffice7.mail.cornell.edu (postoffice7.mail.cornell.edu [132.236.56.22]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i632LH9h013703 for ; Fri, 2 Jul 2004 21:21:18 -0500 Received: from cornell.edu (67-41-237-93.slkc.qwest.net [67.41.237.93]) by postoffice7.mail.cornell.edu (8.12.10/8.12.6) with ESMTP id i632Ohin020483; Fri, 2 Jul 2004 22:26:38 -0400 (EDT) Message-ID: <40E618DF.4000703=at=cornell.edu> Date: Fri, 02 Jul 2004 20:24:31 -0600 From: Richard Wood User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.4) Gecko/20030624 Netscape/7.1 (ax) X-Accept-Language: en-us, en MIME-Version: 1.0 To: "chemistry=at=ccl.net" Subject: Installing AutoDock under Cygwin Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit X-PMX-Version: 4.6.0.99824, Antispam-Core: 4.6.0.101390, Antispam-Data: 2004.7.2.105835 X-Spam-Status: No, hits=4.2 required=7.5 tests=FROM_ENDS_IN_NUMS, RCVD_IN_DYNABLOCK,RCVD_IN_SORBS,TO_ADDRESS_EQ_REAL autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Hi all Has anyone out there installed Autodock under Cygwin? If so, I'd appreciate some advice/pointers as I'm about to attempt to do it. Thanks in advance. Richard -- Richard L. Wood, Ph. D. Computational Chemist SynVax, Inc. N. Logan, UT 84341 From chemistry-request@ccl.net Thu Jul 1 23:18:43 2004 Received: from ccu.umanitoba.ca ([219.253.216.92]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i624Ie8a022384 for ; Thu, 1 Jul 2004 23:18:41 -0500 Subject: =?iso-8859-1?B?R2V0IGEgYmlnIEgwdXNlIE4ub3c=?= Date: Fri, 02 Jul 2004 04:35:07 +0000 To: chemistry=at=ccl.net MIME-Version: 1.0 Message-ID: From: "Albert M. Kendall" Content-Type: text/plain Content-Transfer-Encoding: 8bit X-Spam-Status: No, hits=4.9 required=7.5 tests=BLANK_LINES_70_80,NO_RDNS2, RM_st_iso8859 autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Hello, I sent you an email a few days ago because you now qualify for a new mortgage. You could get a $300,000 for as little as $700 a month! credit is no problem, you can pull cash out or refinance. Best Regards, Christine Morgan http://itel.online-loanz.com/s5/o0o.php?jq1=51 No thanks http://kdihe.online-loanz.com/r1/index.html The Environmental Protection Agency said Tuesday that 243 counties -- mostly in the eastern third of the country -- will probably be found in violation of the federal air standard for soot. State officials will have to develop plans aimed at cutting the pollution by 2010 or 2015, depending on the severity of the air quality problem, or face sanctions, including possible loss of highway funds.Reducing microscopic soot, EPA Administrator Mike Leavitt told reporters, is "the single most important action we can take to make our air healthier."But getting those reductions has been far from easy.The EPA issued a new air quality standard for "fine particulates" -- particles less than one-seventh as wide as a human hair -- in 1997, only to have it challenged by industry. The legal fight went to the U.S. Supreme Court, and eventually the EPA prevailed. From chemistry-request@ccl.net Fri Jul 2 10:24:22 2004 Received: from smtp.uibk.ac.at (lmr1.uibk.ac.at [138.232.1.142]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i62FOKFY001272 for ; Fri, 2 Jul 2004 10:24:21 -0500 Received: from uibk.ac.at (yy1-c724.uibk.ac.at [138.232.32.48]) by smtp.uibk.ac.at (8.12.10/8.12.10/F1) with ESMTP id i62FTivD020579 for ; Fri, 2 Jul 2004 17:29:44 +0200 Message-ID: <40E57F68.9020203=at=uibk.ac.at> Date: Fri, 02 Jul 2004 17:29:44 +0200 From: Demetrios Xenides User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.4) Gecko/20030624 Netscape/7.1 X-Accept-Language: en-us, en MIME-Version: 1.0 To: chemistry=at=ccl.net Subject: Gaussian's tricks Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit X-Spam-Score: -3.1 () FROM_ENDS_IN_NUMS,FROM_ENDS_IN_NUMS_UIBK,RCV_SMTP_UIBK X-Scanned-By: MIMEDefang 2.42 at uibk.ac.at X-Spam-Status: No, hits=0.0 required=7.5 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Hi all!!! Gaussian plays tricks again. The same file in G94 runs without any problem but in G98 it reduces the number of the basis used... I am trying to run a single point calculation using an uncontracted basis set by partridge. same command line for both #p rhf/gen scf(conver=10) nosymm field=read -------------------------------------------- MESSAGE IN ------------------------------------ ---------------------------------------------------G98-------------------------------------------- Two-electron integral symmetry is turned off. 187 basis functions 196 primitive gaussians 26 alpha electrons 26 beta electrons nuclear repulsion energy 147.4020983233 Hartrees. Leave Link 301 at Fri Jul 2 09:46:53 2004, MaxMem= 6291456 cpu: 0.1 (Enter /usr/local/g98/l302.exe) One-electron integrals computed using PRISM. Error in orthogonal basis= 1.61D-07 with 187 functions, increasing threshold to 2.00D-04. Error in orthogonal basis= 1.61D-07 with 187 functions, increasing threshold to 4.00D-04. Error in orthogonal basis= 1.61D-07 with 187 functions, increasing threshold to 8.00D-04. Error in orthogonal basis= 1.61D-07 with 187 functions, increasing threshold to 1.60D-03. Error in orthogonal basis= 1.61D-07 with 187 functions, increasing threshold to 3.20D-03. Error in orthogonal basis= 1.61D-07 with 187 functions, increasing threshold to 6.40D-03. Error in orthogonal basis= 1.61D-07 with 187 functions, increasing threshold to 1.28D-02. Error in orthogonal basis= 1.61D-07 with 187 functions, increasing threshold to 2.56D-02. Error in orthogonal basis= 4.12D-08 with 186 functions, increasing threshold to 5.12D-02. Error in orthogonal basis= 3.10D-09 with 182 functions, increasing threshold to 1.02D-01. NBasis= 187 RedAO= T NBF= 187 NBsUse= 167 1.02D-01 NBFU= 167 -------------------------------------------- MESSAGE IN ------------------------------------ ---------------------------------------------------G94W------------------------------------------ Two-electron integral symmetry is turned off. 187 basis functions 187 primitive gaussians 26 alpha electrons 26 beta electrons nuclear repulsion energy 147.4020983233 Hartrees. Leave Link 301 at Fri Jul 02 10:22:17 2004, MaxMem= 4000000 cpu:1.0 (Enter C:\G94W\l302.exe) One-electron integrals computed using PRISM. The smallest eigenvalue of the overlap matrix is 2.425E-04 Leave Link 302 at Fri Jul 02 10:22:17 2004, MaxMem= 4000000 cpu:1.0 (Enter C:\G94W\l303.exe) any hint? Cheers Demetrios From chemistry-request@ccl.net Fri Jul 2 12:12:08 2004 Received: from marge.theochem.uni-frankfurt.de (marge.theochem.uni-frankfurt.de [141.2.216.130]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i62HC7FY007979 for ; Fri, 2 Jul 2004 12:12:07 -0500 Received: from gorbunov (helo=localhost) by marge.theochem.uni-frankfurt.de with local-esmtp (Exim 4.11) id 1BgRfH-0008LU-00 for chemistry(at)ccl.net; Fri, 02 Jul 2004 19:17:31 +0200 Date: Fri, 2 Jul 2004 19:17:31 +0200 (MEST) From: Roman Gorbunov To: chemistry(at)ccl.net Subject: Dielectric constant and pH. Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Sender: Roman Gorbunov X-Spam-Status: No, hits=0.9 required=7.5 tests=MY_BAD_DOT autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Hi all, I need to know dependence of the dielectric constant of water on pH-value. Can you help me? Thank you in advance for any comments, Roman Gorbunov. From chemistry-request@ccl.net Fri Jul 2 04:53:39 2004 Received: from mxout2.netvision.net.il (mxout2.netvision.net.il [194.90.9.21]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i629rbFY014163 for ; Fri, 2 Jul 2004 04:53:38 -0500 Received: from fedor ([217.132.138.29]) by mxout2.netvision.net.il (iPlanet Messaging Server 5.2 HotFix 1.21 (built Sep 8 2003)) with ESMTPA id <0I0700ENRYE9R1(at)mxout2.netvision.net.il> for chemistry(at)ccl.net; Fri, 02 Jul 2004 12:58:57 +0300 (IDT) Date: Fri, 02 Jul 2004 13:26:24 +0200 From: Michael Subject: CCL: Re[2]: software to convert XYZ format to PDB ? To: chemistry(at)ccl.net Message-id: <003201c46027$68c99950$b400a8c0@fedor> MIME-version: 1.0 X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2800.1409 X-Mailer: Microsoft Outlook Express 6.00.2800.1409 Content-type: text/plain; charset=iso-8859-1 Content-transfer-encoding: 7BIT X-Priority: 3 X-MSMail-priority: Normal X-Spam-Status: No, hits=5.6 required=7.5 tests=NO_RDNS2,RCVD_IN_DYNABLOCK, RCVD_IN_SORBS autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Hello Michael, Obviously there are side residues also with hydrogens, and you know this > from my replay that I send to you responding on your first remark. I simply did not present the whole protein pdb in the three different formats (XYZ, defected pdb, and correct pdb) in order to save place in the email. I wrote in my original message presented for CCL that it is a fragment from the whole protein. I thought that to see the problem it is sufficient to present only four lines from the whole protein. Following your logic: Imagine that you are the programmer: how could you know from the atomic symbols and the X,Y,Z coordinates what could be the residue ? The N,CA,C,O coordinates of all residues of all known proteins in the PDB offer quite similar 3D patterns. Sure... if you have the side chains ! (were not indicated in the example) It needs other assumptions: true residues, no HETATM, lexicographical ordering coherent with the PDB conventions... why didn't you suggest that the protein was consisted from only four atoms presented in my email? Kind regards, Michael To: chemistry(at)ccl.net Subject: CCL:software to convert XYZ format to PDB ? Konrad Hinsen wrote: > On Jul 1, 2004, at 11:57, Michel Petitjean wrote: > > Imagine that you are the programmer: how could you know from > > the atomic symbols and the X,Y,Z coordinates what could be > > the residue ? The N,CA,C,O coordinates of all residues of > > all known proteins in the PDB offer quite similar 3D patterns. > > If I had to do this (fortunately I don't), I'd first identify the > peptide planes as patterns of pairwise distances (they are quite > rigid). I'd then identify the sidechains atom by atom starting from the > C-alphas, again by distance criteria. Not a trivial task, but not an > impossible one either. Sure... if you have the side chains ! (were not indicated in the example) It needs other assumptions: true residues, no HETATM, lexicographical ordering coherent with the PDB conventions... Michel Petitjean, Email: petitjean(at)itodys.jussieu.fr ITODYS (CNRS, UMR 7086) ptitjean(at)ccr.jussieu.fr 1 rue Guy de la Brosse Phone: +33 (0)1 44 27 48 57 75005 Paris, France. FAX : +33 (0)1 44 27 68 14 http://petitjeanmichel.free.fr/itoweb.petitjean.html -= This is automatically added to each message by the mailing script =- To send e-mail to subscribers of CCL put the string CCL: on your Subject: line and send your message to: CHEMISTRY(at)ccl.net Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST(at)ccl.net HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs From chemistry-request@ccl.net Thu Jul 1 20:09:47 2004 Received: from brass.metals.hope.edu (brass.metals.hope.edu [198.110.98.36]) by server.ccl.net (8.12.8/8.12.8) with SMTP id i6219k8b011045 for ; Thu, 1 Jul 2004 20:09:46 -0500 Received: from hope.edu ([198.110.98.17]) by brass.metals.hope.edu (SAVSMTP 3.1.1.32) with SMTP id M2004070121124229122 ; Thu, 01 Jul 2004 21:12:42 -0400 Received: from [198.110.101.2] (polik*at*hope.edu) by hope.edu; Thu, 1 Jul 2004 21:12:58 -0400 X-WM-Posted-At: hope.edu; Thu, 1 Jul 04 21:12:58 -0400 Message-Id: <5.2.0.9.2.20040701210918.02627eb8*at*webmail.hope.edu> X-Sender: polik*at*webmail.hope.edu (Unverified) X-Mailer: QUALCOMM Windows Eudora Version 5.2.0.9 Date: Thu, 01 Jul 2004 21:14:49 -0400 To: Carsten Detering , chemistry*at*ccl.net From: "William F. Polik" Subject: CCL:gaussian03 optimization to transition state In-Reply-To: <40E45989.9090503*at*u.washington.edu> Mime-Version: 1.0 Content-Type: multipart/alternative; boundary="=====================_431109562==.ALT" X-Spam-Status: No, hits=3.0 required=7.5 tests=HTML_MESSAGE,NO_RDNS2 autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net --=====================_431109562==.ALT Content-Type: text/plain; charset="us-ascii"; format=flowed Carsten, The success of a transition state optimization depends on how close you start to the optimized geometry. The optimized geometries are likely to be different in a MOPAC semi-empirical calculation than in a B3LYP/6-31g* calculation. However, you might better your odds at converging by trying B3LYP/6-31g* OPT=(TS,CalcFC,NoEigenTest) which requests that Gaussian calculate, rather than approximate, the force constants used in the optimization and not initially fail if more than one negative frequency is found. Will Polik At 02:35 PM 7/1/2004, Carsten Detering wrote: > I would like to optimize a complex involving a bifurcated hydrogen bond > between three nitrogen atoms (trimethylamine and triazen) to a saddle > point (which I know exists from previous Mopac calculations). Taking this > header line in the input file > >B3LYP/6-31g* POpt=(Saddle=1) nosymmetry test > >the optimization finishes with an error > >optimization stopped > --wrong number of Negative eigenvalues: Desired= 1 Actual= 2 > --Flag reset to prevent archiving > >Then I get, at the bottom, the typical proverb that you see only when a >calculation has successfully finished, and then > >Could anybody make some suggestions how to fix this? > >Thanks a lot in advance, > >Carsten ================================ Dr. William F. Polik Hofma Professor of Chemistry Department of Chemistry Hope College 35 East 12th Street Holland, MI 49422-9000 USA polik*at*hope.edu http://www.chem.hope.edu/~polik tel: (616) 395-7639 fax: (616) 395-7118 ================================ --=====================_431109562==.ALT Content-Type: text/html; charset="us-ascii" Carsten,

The success of a  transition state optimization depends on how close you start to the optimized geometry.  The optimized geometries are likely to be different in a MOPAC semi-empirical calculation than in a B3LYP/6-31g* calculation.  However, you might better your odds at converging by trying

B3LYP/6-31g* OPT=(TS,CalcFC,NoEigenTest)

which requests that Gaussian calculate, rather than approximate, the force constants used in the optimization and not initially fail if more than one negative frequency is found.

Will Polik

At 02:35 PM 7/1/2004, Carsten Detering wrote:
 I would like to optimize a complex involving a bifurcated hydrogen bond between three nitrogen atoms (trimethylamine and triazen) to a saddle point (which I know exists from previous Mopac calculations). Taking this header line in the input file

B3LYP/6-31g* POpt=(Saddle=1) nosymmetry test

the optimization finishes with an error

optimization stopped
        --wrong number of Negative eigenvalues: Desired= 1 Actual= 2
        --Flag reset to prevent archiving

Then I get, at the bottom, the typical proverb that you see only when a calculation has successfully finished, and then

Could anybody make some suggestions how to fix this?

Thanks a lot in advance,

Carsten

================================
Dr. William F. Polik
Hofma Professor of Chemistry

Department of Chemistry
Hope College
35 East 12th Street
Holland, MI  49422-9000
USA

polik*at*hope.edu
http://www.chem.hope.edu/~polik
tel: (616) 395-7639
fax: (616) 395-7118
================================
 --=====================_431109562==.ALT-- From chemistry-request@ccl.net Fri Jul 2 05:12:13 2004 Received: from mail2.iitk.ac.in (delhi-203.197.196-2.vsnl.net.in [203.197.196.2] (may be forged)) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i62AC8FY015654 for ; Fri, 2 Jul 2004 05:12:11 -0500 Received: from antivirus.cc.iitk.ac.in (antivirus.cc.iitk.ac.in [172.31.1.102]) by mail2.iitk.ac.in (8.12.8/8.12.8) with SMTP id i62AdQSa021670 for ; Fri, 2 Jul 2004 16:09:46 +0530 Received: (from apah [172.31.1.6]) by antivirus.cc.iitk.ac.in (SAVSMTP 3.1.0.29) with SMTP id M2004070215522727958 ; Fri, 02 Jul 2004 15:52:27 +0530 Date: Fri, 2 Jul 2004 15:28:27 +0530 (IST) From: Bhabani Shankar X-X-Sender: mbhabani*at*apah.cc.iitk.ac.in To: Bhabani Shankar Mallik phd chm cc: chemistry*at*ccl.net Subject: BSSE correction in g03 In-Reply-To: <200407020925.i629PO424025*at*socrates-a.ucl.ac.uk> Message-ID: References: <200407020925.i629PO424025*at*socrates-a.ucl.ac.uk> MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Spam-Status: No, hits=0.0 required=7.5 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Can anybody suggest how to calculate BSSE correction in g03 ? I want to calculate BSSE corection for ion-water system. thanks Bhabani From chemistry-request@ccl.net Sat Jul 3 04:41:07 2004 Received: from mb2i1.ns.pitt.edu (mb2i1.ns.pitt.edu [136.142.185.162]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i639f6w7029565 for ; Sat, 3 Jul 2004 04:41:06 -0500 Received: from CONVERSION-DAEMON by pitt.edu (PMDF V5.2-32 #41462) id <01LC0IDBQKMO004NTS!at!mb2i1.ns.pitt.edu> for chemistry!at!ccl.net; Sat, 3 Jul 2004 05:46:07 EDT Received: from visual1.chem.pitt.edu ([136.142.109.16]) by pitt.edu (PMDF V5.2-32 #41462) with ESMTP id <01LC0ID7T4QG004PKV!at!mb2i1.ns.pitt.edu>; Sat, 03 Jul 2004 05:46:03 -0400 (EDT) Date: Sat, 03 Jul 2004 05:47:56 -0400 From: Kadir Diri Subject: Re: CCL:BSSE correction in g03 In-reply-to: To: Bhabani Shankar Cc: chemistry!at!ccl.net Message-id: <40E680CC.3060006!at!visual1.chem.pitt.edu> MIME-version: 1.0 Content-type: text/plain; charset=us-ascii; format=flowed Content-transfer-encoding: 7bit User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.4) Gecko/20030624 Netscape/7.1 (ax) X-Accept-Language: en-us, en References: <200407020925.i629PO424025!at!socrates-a.ucl.ac.uk> X-Spam-Status: No, hits=3.0 required=7.5 tests=NO_RDNS2 autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Hi! Gaussian has the "counterpoise" keyword to calculate that. Check the online manual for details and examples, it is very straightforward: http://www.gaussian.com/g_ur/k_counterpoise.htm kadir Bhabani Shankar wrote: >Can anybody suggest how to calculate BSSE correction >in g03 ? I want to calculate BSSE corection for ion-water >system. > >thanks >Bhabani > > > >-= This is automatically added to each message by the mailing script =- >To send e-mail to subscribers of CCL put the string CCL: on your Subject: line >and send your message to: CHEMISTRY!at!ccl.net > >Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST!at!ccl.net >HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs > >If your mail is bouncing from CCL.NET domain send it to the maintainer: >Jan Labanowski, jlabanow!at!nd.edu (read about it on CCL Home Page) >-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > > > From chemistry-request@ccl.net Sat Jul 3 04:36:20 2004 Received: from mb2i1.ns.pitt.edu (mb2i1.ns.pitt.edu [136.142.185.162]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i639aJw7028896 for ; Sat, 3 Jul 2004 04:36:19 -0500 Received: from CONVERSION-DAEMON by pitt.edu (PMDF V5.2-32 #41462) id <01LC0I7VY8OW004MH5(at)mb2i1.ns.pitt.edu> for chemistry(at)ccl.net; Sat, 3 Jul 2004 05:41:44 EDT Received: from visual1.chem.pitt.edu ([136.142.109.16]) by pitt.edu (PMDF V5.2-32 #41462) with ESMTP id <01LC0I7TD0VY004IV8(at)mb2i1.ns.pitt.edu>; Sat, 03 Jul 2004 05:41:42 -0400 (EDT) Date: Sat, 03 Jul 2004 05:43:35 -0400 From: Kadir Diri Subject: Re: CCL:Gaussian's tricks In-reply-to: <40E57F68.9020203(at)uibk.ac.at> To: Demetrios Xenides Cc: chemistry(at)ccl.net Message-id: <40E67FC7.9050802(at)visual1.chem.pitt.edu> MIME-version: 1.0 Content-type: text/plain; charset=ISO-8859-1; format=flowed Content-transfer-encoding: 7bit User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.4) Gecko/20030624 Netscape/7.1 (ax) X-Accept-Language: en-us, en References: <40E57F68.9020203(at)uibk.ac.at> X-Spam-Status: No, hits=3.0 required=7.5 tests=NO_RDNS2 autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Hi! Looks like you have linear dependency problems in your basis set. You have to improve it. Maybe G94 was not checking for that, or had different tolerence compared to G98. kadir Demetrios Xenides wrote: > Hi all!!! > Gaussian plays tricks again. The same file in G94 runs without any > problem but in G98 it reduces the number of the basis used... I am > trying to run a single point calculation using an uncontracted basis > set by partridge. > > same command line for both > #p rhf/gen scf(conver=10) nosymm field=read > > > -------------------------------------------- MESSAGE IN > ------------------------------------ > ---------------------------------------------------G98-------------------------------------------- > > Two-electron integral symmetry is turned off. > 187 basis functions 196 primitive gaussians > 26 alpha electrons 26 beta electrons > nuclear repulsion energy 147.4020983233 Hartrees. > Leave Link 301 at Fri Jul 2 09:46:53 2004, MaxMem= 6291456 > cpu: 0.1 > (Enter /usr/local/g98/l302.exe) > One-electron integrals computed using PRISM. > Error in orthogonal basis= 1.61D-07 with 187 functions, increasing > threshold to 2.00D-04. > Error in orthogonal basis= 1.61D-07 with 187 functions, increasing > threshold to 4.00D-04. > Error in orthogonal basis= 1.61D-07 with 187 functions, increasing > threshold to 8.00D-04. > Error in orthogonal basis= 1.61D-07 with 187 functions, increasing > threshold to 1.60D-03. > Error in orthogonal basis= 1.61D-07 with 187 functions, increasing > threshold to 3.20D-03. > Error in orthogonal basis= 1.61D-07 with 187 functions, increasing > threshold to 6.40D-03. > Error in orthogonal basis= 1.61D-07 with 187 functions, increasing > threshold to 1.28D-02. > Error in orthogonal basis= 1.61D-07 with 187 functions, increasing > threshold to 2.56D-02. > Error in orthogonal basis= 4.12D-08 with 186 functions, increasing > threshold to 5.12D-02. > Error in orthogonal basis= 3.10D-09 with 182 functions, increasing > threshold to 1.02D-01. > NBasis= 187 RedAO= T NBF= 187 > NBsUse= 167 1.02D-01 NBFU= 167 > > -------------------------------------------- MESSAGE IN > ------------------------------------ > ---------------------------------------------------G94W------------------------------------------ > > > Two-electron integral symmetry is turned off. > 187 basis functions 187 primitive gaussians > 26 alpha electrons 26 beta electrons > nuclear repulsion energy 147.4020983233 Hartrees. > Leave Link 301 at Fri Jul 02 10:22:17 2004, MaxMem= 4000000 cpu:1.0 > (Enter C:\G94W\l302.exe) > One-electron integrals computed using PRISM. > The smallest eigenvalue of the overlap matrix is 2.425E-04 > Leave Link 302 at Fri Jul 02 10:22:17 2004, MaxMem= 4000000 cpu:1.0 > (Enter C:\G94W\l303.exe) > > any hint? > > Cheers > Demetrios > > > > -= This is automatically added to each message by the mailing script =- > To send e-mail to subscribers of CCL put the string CCL: on your > Subject: line > and send your message to: CHEMISTRY(at)ccl.net > > Send your subscription/unsubscription requests to: > CHEMISTRY-REQUEST(at)ccl.net HOME Page: http://www.ccl.net | Jobs Page: > http://www.ccl.net/jobs > If your mail is bouncing from CCL.NET domain send it to the maintainer: > Jan Labanowski, jlabanow(at)nd.edu (read about it on CCL Home Page) > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > From chemistry-request@ccl.net Sat Jul 3 08:42:23 2004 Received: from hawk.dcu.ie (mail.dcu.ie [136.206.1.5]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i63DgMw7027352 for ; Sat, 3 Jul 2004 08:42:22 -0500 Received: from [136.206.86.70] by hawk.dcu.ie with HTTP; Sat, 3 Jul 2004 14:47:48 +0100 Date: Sat, 3 Jul 2004 14:47:48 +0100 Message-ID: <40E08A770000560B_at_hawk.dcu.ie> From: "Noel O'Boyle" Subject: Calculation of exchange energy To: chemistry_at_ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" X-Spam-Status: No, hits=0.0 required=7.5 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id i63DgNw7027358 Dear CCLers, I am using Gaussian03 (B3LYP) to study the adsorption of a molecule on a surface. I would like to measure the strength of the interaction by means of an exchange energy. Is there any way to get a value for the exchange energy from a Gaussian calculation? I was hoping to use Morokuma decomposition - but there doesn't seem to be any software available for doing this (using results from Gaussian). Thanks, Noel From chemistry-request@ccl.net Sat Jul 3 11:31:20 2004 Received: from hotmail.com (bay22-dav11.bay22.hotmail.com [64.4.16.191]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i63GVHKg004934 for ; Sat, 3 Jul 2004 11:31:17 -0500 Received: from mail pickup service by hotmail.com with Microsoft SMTPSVC; Sat, 3 Jul 2004 09:36:45 -0700 Received: from 210.83.210.9 by bay22-dav11.bay22.hotmail.com with DAV; Sat, 03 Jul 2004 16:36:44 +0000 X-Originating-IP: [210.83.210.9] X-Originating-Email: [liuxin_dut~at~hotmail.com] X-Sender: liuxin_dut~at~hotmail.com From: "li" To: Subject: CCL: how to study the bonding characteristics among atoms! Date: Sun, 4 Jul 2004 00:36:43 +0800 MIME-Version: 1.0 Content-Type: text/plain; charset="gb2312" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2800.1409 X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2800.1409 Message-ID: X-OriginalArrivalTime: 03 Jul 2004 16:36:45.0020 (UTC) FILETIME=[ED85D9C0:01C4611B] X-Spam-Status: No, hits=2.0 required=7.5 tests=MIME_BASE64_TEXT autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from base64 to 8bit by server.ccl.net id i63GVKKg004942 Hi! Everyone! I am studying the bonding characteristics among atoms in solids such as zinc sulfide. And I am trying to find an efficient way to describe the bonding characteristics between or among atoms, expecially for those with special hybridization states such as d5-d5, d10-d10, and d0-d0. Any suggestions from you would be appreciated! Thank you in advance for your future help! Sincerely yours