From chemistry-request@ccl.net Thu Sep 18 23:00:06 2003 Received: from ccl.net (pagergate.ccl.net [192.148.249.4]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h8J2xZAg023437 for ; Thu, 18 Sep 2003 22:59:35 -0400 Received: from krakow.ccl.net (krakow.ccl.net [192.148.249.195]) by ccl.net (8.11.6+Sun/8.11.6/OSC 2.1) with ESMTP id h8J2xXm17330; Thu, 18 Sep 2003 22:59:33 -0400 (EDT) Date: Thu, 18 Sep 2003 22:59:32 -0400 (EDT) From: "Dr. Jan K Labanowski" To: chemistry(at)ccl.net Subject: Japan Catalyst User Group Meeting - Dec 10-11, 2003 (fwd) Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=X-UNKNOWN Content-Transfer-Encoding: 8BIT X-Spam-Status: No, hits=1.3 required=7.0 tests=OPPORTUNITY_2,USER_AGENT_PINE version=2.55 X-Spam-Level: * X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Accelrys Japan Catalyst User Group Meeting & Advanced User Training December 10-11, 2003 Tokyo American Club Tokyo, Japan This is to announce the upcoming Japan Catalyst User Group Meeting to be held in Tokyo American Club, Tokyo, Japan. This two days event will include the Advanced User Training on Catalyst on the second day. Registration, abstract submission, and agenda information for this event can be found at the URL below: http://www.accelrys.com/usergroups/catalyst/ This annual event offers a unique opportunity to: interact with the Accelrys R&D staff, learn the latest developments in Catalyst, share insights and issues with other scientists working in similar fields, and influence the direction of future Accelrysb product development. We look forward to seeing many of you in Tokyo, Japan on Dec 11-12, 2003. Best Regards, Samuel Toba Product Specialist, Catalyst Accelrys From chemistry-request@ccl.net Thu Sep 18 13:07:57 2003 Received: from www2.cle.lionbioscience.com (pub-www2.cle.lionbioscience.com [216.183.176.227]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h8IH7PAg008304 for ; Thu, 18 Sep 2003 13:07:25 -0400 Received: from pion.cle.lionbioscience.com (pion.cle.lionbioscience.com [10.20.1.32]) by www2.cle.lionbioscience.com (Postfix) with ESMTP id 74656C0D7; Thu, 18 Sep 2003 13:07:24 -0400 (EDT) Received: from localhost (localhost.localdomain [127.0.0.1]) by pion.cle.lionbioscience.com (Postfix) with ESMTP id 63195E4081; Thu, 18 Sep 2003 13:07:24 -0400 (EDT) Received: from pion.cle.lionbioscience.com ([127.0.0.1]) by localhost (pion.cle.lionbioscience.com [127.0.0.1]) (amavisd-new, port 10024) with LMTP id 04737-01-7; Thu, 18 Sep 2003 13:07:24 -0400 (EDT) Received: from wolf (cisco-26.us.lionbioscience.com [10.19.3.26]) by pion.cle.lionbioscience.com (Postfix) with ESMTP id 0593AE4057; Thu, 18 Sep 2003 13:07:22 -0400 (EDT) From: Mitchell Miller To: CHEMICAL INFORMATION SOURCES DISCUSSION LIST , chemistry*at*ccl.net Subject: Symposium on Linking Bioinformatics to Cheminformatics at ACS National Meeting in Anaheim March 28 - April 1, 2004 Date: Thu, 18 Sep 2003 11:07:16 -0600 Organization: LION bioscience, Inc. X-Mailer: Oracle Outlook Connector 3.4 40812 MIME-Version: 1.0 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Message-Id: <20030918170722.0593AE4057*at*pion.cle.lionbioscience.com> X-Virus-Scanned: by amavisd-new at cle.lionbioscience.com X-Spam-Status: No, hits=4.4 required=7.0 tests=FORGED_MUA_OUTLOOK,HTML_70_80,HTML_MESSAGE,MIME_HTML_ONLY, MIME_LONG_LINE_QP version=2.55 X-Spam-Level: **** X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp)

Colleagues,

At the next ACS National Meeting (= Anaheim M= arch 28 - April 1, 2004),= the Division of Chemical Information will conduct a symposium on =

The Bigger Picture: Linking Bioinformatics to Cheminformatics.

and you are invited to submit an abstract.=

Theme: Most life-science research organizations have inf= ormation systems for sequence data and for compound data. This symposium will explore what is being done to bridge these two types of systems and provide= an integrated view that facilitates faster compound discovery. We welcom= e talks about information systems in production, development, or planning. Yo= u can even talk about what you wish you could build if…

Here are the details:

- The best way to submit an abstract is on-line using OA= SYS (http://oasys.acs.org/)

- Please e-mail or call me if you have trouble with OASY= S.

- The deadline for submissions is 1 De= cember 2003.&= nbsp; (You can submit an abstract now and then make changes until 1 December.)<= /font>

- Target presentation length is 20 minutes, with 5 minut= es for questions. Please let me know if you need more time.

- We especially welcome presentations from research organizations working with bioinformatics and cheminformatics.

- When planning your presentation, consider a back-up pe= rson > from your organization who could deliver your talk if for any reason you ca= nnot make it to the meeting.

Questions are welcome!

Regards,

Mitch

Mitchell Miller, Ph.D.

Director Cheminformatics

LION bioscience

mitchell.miller@lionbioscience= .com

Tel. +1 801 569 1390

Fax. +1 801 365 3949

From chemistry-request@ccl.net Thu Sep 18 15:09:11 2003 Received: from cytosin.uni-konstanz.de (cytosin.uni-konstanz.de [134.34.240.61]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h8IJ8dAg019365 for ; Thu, 18 Sep 2003 15:08:39 -0400 Received: from viribus.rz.uni-konstanz.de (viribus.rz.uni-konstanz.de [134.34.240.50]) by cytosin.uni-konstanz.de (Postfix) with ESMTP id A845FA8DD4F for ; Thu, 18 Sep 2003 21:08:38 +0200 (MEST) Received: from localhost (localhost [127.0.0.1]) by localhost.viribus.rz.uni-konstanz.de (Postfix) with ESMTP id 933CF1F805B for ; Thu, 18 Sep 2003 21:08:38 +0200 (CEST) Received: from viribus.rz.uni-konstanz.de ([127.0.0.1]) by localhost (viribus.rz.uni-konstanz.de [127.0.0.1]) (amavisd-new, port 10024) with LMTP id 21919-05-28 for ; Thu, 18 Sep 2003 21:08:38 +0200 (CEST) Received: from charlie (charlie.chemie.uni-konstanz.de [134.34.112.36]) by viribus.rz.uni-konstanz.de (Postfix) with ESMTP id 699BC1F8004 for ; Thu, 18 Sep 2003 21:08:38 +0200 (CEST) Message-ID: <200309182108410374.07471E02*at*mailhub.uni-konstanz.de> X-Mailer: Calypso Version 3.30.00.00 (1) Date: Thu, 18 Sep 2003 21:08:41 +0200 Reply-To: Eike.Huebner*at*uni-konstanz.de From: "pop14848" To: chemistry*at*ccl.net Subject: CCL: Opteron Mime-Version: 1.0 Content-Type: text/plain; charset="ISO-8859-1" X-Virus-Scanned: by amavisd-new at Mailservice RZ Uni-Konstanz X-Spam-Status: No, hits=3.5 required=7.0 tests=RCVD_IN_OSIRUSOFT_COM,X_OSIRU_OPEN_RELAY version=2.55 X-Spam-Level: *** X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id h8IJ9BAg019384 Hello, has anyone made some experience with the AMD Opterons processors? I am especially interested in some results of running GAMESS on Opterons processors, using the 32bit "compatibility" mode and the 64bit mode (if someone had the needed 64bit compiler (Licence) to get this running). Additionally it would be interesting if someone used schrodinger products such as Jaguar on this platform. Last I would be interested in the operating system environment? On which 64Bit Linux versions do these processors run (stable)? BTW (I am not really used to 64Bit environments, at least not in installing the OS) am I right that the 64Bit versions are mosty quite expensive? Searching a bit around I found that the moste free linux implementations such as Suse, redhat etc. seem to have quite high prices for the 64Bit versions. Thank you very much in advance, Eike Huebner From chemistry-request@ccl.net Thu Sep 18 20:25:20 2003 Received: from gip2.u-picardie.fr (gip2.u-picardie.fr [193.49.184.4]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h8J0OlAg010008 for ; Thu, 18 Sep 2003 20:24:48 -0400 Received: by gip2.u-picardie.fr (Postfix, from userid 33) id 43E526D25; Fri, 19 Sep 2003 02:24:47 +0200 (CEST) To: chemistry*at*ccl.net Subject: Hydrogens in InsightII Message-ID: <1063931087.3f6a4ccf3569d*at*webmail.u-picardie.fr> Date: Fri, 19 Sep 2003 02:24:47 +0200 (CEST) From: FyD MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit User-Agent: IMP/PHP IMAP webmail program 2.2.6 X-Spam-Status: No, hits=0.0 required=7.0 tests=USER_AGENT version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Dear All, I would interested in knowing 'the command' in insightII which allows to automatically REMOVE all the hydrogens (of an oligonucleotide) in order to save the structure (to the PDB format) without these hydrogens, keeping only the heavy atoms. Thanks, regards, Francois From chemistry-request@ccl.net Thu Sep 18 04:21:59 2003 Received: from fornells.imim.es (fornells.imim.es [193.147.240.141]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h8I8LFAg030511 for ; Thu, 18 Sep 2003 04:21:16 -0400 Received: by fornells.imim.es with Internet Mail Service (5.5.2656.59) id ; Thu, 18 Sep 2003 10:22:23 +0200 Received: from imim.es (homer.imim.es [193.146.190.141]) by hpserv.imim.es with SMTP (Microsoft Exchange Internet Mail Service Version 5.5.2656.59) id SDP83MRK; Thu, 18 Sep 2003 10:25:48 +0200 From: Fabien Fontaine To: Mingyue Zheng Cc: CHEMISTRY*at*ccl.net Message-ID: <3F696A3B.7000303*at*imim.es> Date: Thu, 18 Sep 2003 10:18:03 +0200 Organization: IMIM/UPF User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.0.2) Gecko/20030208 Netscape/7.02 X-Accept-Language: en-us, en MIME-Version: 1.0 Subject: Re: CCL:molecule substructure searching algorithms References: <002601c37d22$96bc9fd0$4c137fca*at*simm.ac.cn> Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=1.4 required=7.0 tests=EMAIL_ATTRIBUTION,QUOTED_EMAIL_TEXT,RCVD_IN_OSIRUSOFT_COM, REFERENCES,REPLY_WITH_QUOTES,USER_AGENT_MOZILLA_UA, X_ACCEPT_LANG,X_OSIRU_OPEN_RELAY version=2.55 X-Spam-Level: * X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) The best open source code to do this is the openbabel library http://openbabel.sourceforge.net/ which use the daylight SMART chemical language http://www.daylight.com/dayhtml/doc/theory/theory.smarts.html Regards Fabien Mingyue Zheng wrote: > This message uses a character set that is not supported by the Internet > Service. To view the original message content, open the attached > message. If the text doesn't display correctly, save the attachment to > disk, and then open it using a viewer that can display the original > character set. <> > > > ------------------------------------------------------------------------ > > Received: from server.ccl.net ([192.153.40.39]) by fornells.imim.es with SMTP (Microsoft Exchange Internet Mail Service Version 5.5.2656.59) > id SDPJDJ5Z; Wed, 17 Sep 2003 20:26:14 +0200 > Received: (from root@localhost) > by server.ccl.net (8.12.8/8.12.8) id h8HI2h85008570 > for ccl2; Wed, 17 Sep 2003 14:02:43 -0400 > Received: from mail.shcnc.ac.cn (server.shcnc.ac.cn [159.226.128.1]) > by server.ccl.net (8.12.8/8.12.8) with ESMTP id h8HDoRAg027782 > for ; Wed, 17 Sep 2003 09:50:28 -0400 > Received: from DATA4 (unknown [202.127.19.76]) > by mail.shcnc.ac.cn (4U Message Server) with SMTP id 6335E4594 > for ; Wed, 17 Sep 2003 21:48:23 +0800 (CST) > Message-ID: <002601c37d22$96bc9fd0$4c137fca*at*simm.ac.cn> > X-Reply-To: "Mingyue Zheng" > From: "Mingyue Zheng" > To: > Subject: CCL:molecule substructure searching algorithms > Date: Wed, 17 Sep 2003 21:50:00 +0800 > Organization: SIMM > MIME-Version: 1.0 > Content-Type: text/plain; > charset="GB18030" > X-Priority: 3 > X-MSMail-Priority: Normal > X-Mailer: Microsoft Outlook Express 6.00.2800.1158 > X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1106 > X-Spam-Status: No, hits=3.0 required=7.0 > tests=BASE64_ENC_TEXT,RCVD_IN_RFCI > version=2.55 > X-Spam-Level: *** > X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) > Content-Transfer-Encoding: 8bit > X-MIME-Autoconverted: from base64 to 8bit by server.ccl.net id h8HDoxAg028012 > Sender: "Computational Chemistry List" > Errors-To: chemistry-request*at*ccl.net > Precedence: bulk > > Hi all CCLers: > > I want to write a program calculatting pKa of molecule based on it's structure. > > The first problem harassing me is how to efficiently recognize and sign a specific > functional group in a molecule. > > Is here anyone who could tell me where can I find some open source code for > molecule substructure searching algorithms, or any free program dealing with it? > > Thank you in advance! > Regards! > > > > (UTF-8) > *********************************************************************** > Mingyue Zheng > Drug Design & Discovery Center > SIMM,China Acadmy of Science > 555 Zu Chong Zhi Road, Zhangjiang Hi-Tech Park,Shanghai 201203,China > Tel: 86-21-50806600 Fax: 86-21-50807088 > myzheng*at*mail.shcnc.ac.cn > myzheng*at*iris3.simm.ac.cn > *********************************************************************** > > > > -= 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, jkl*at*ccl.net (read about it on CCL Home Page) > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > -- Fabien Fontaine Engineer in Biotechnology Computer-Assisted Drug Design Laboratory Research Group on Biomedical Informatics (GRIB) - IMIM/UPF Passeig Maritim de la Barceloneta, 37-49 Tel: +34 93 224 08 94 E-08003 Barcelona (Spain) Fax: +34 93 224 08 75 e-mail: ffontaine*at*imim.es http://www.imim.es/grib From chemistry-request@ccl.net Fri Sep 19 01:25:47 2003 Received: from scheraga2.chem.cornell.edu (scheraga2.chem.cornell.edu [128.253.229.65]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h8J5PgAg002837 for ; Fri, 19 Sep 2003 01:25:42 -0400 Received: by scheraga2.chem.cornell.edu (Postfix, from userid 103) id 9746A1C081; Fri, 19 Sep 2003 01:25:42 -0400 (EDT) Received: from localhost (localhost [127.0.0.1]) by scheraga2.chem.cornell.edu (Postfix) with ESMTP id 89BEF2CB7F; Fri, 19 Sep 2003 01:25:42 -0400 (EDT) Date: Fri, 19 Sep 2003 01:25:42 -0400 (EDT) From: Cezary Czaplewski To: pop14848 Cc: Subject: Re: CCL:Opteron In-Reply-To: <200309182108410374.07471E02..at..mailhub.uni-konstanz.de> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Spam-Status: No, hits=3.4 required=7.0 tests=IN_REP_TO,MAILTO_TO_SPAM_ADDR,RCVD_IN_OSIRUSOFT_COM, USER_AGENT_PINE,X_OSIRU_OPEN_RELAY version=2.55 X-Spam-Level: *** X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Hi, quite recently I did some benchmarks, but only using static 32-bit binaries on Opteron with 64bit GinGin64 system (dahlia) : 1. Single point HF energy calculation for Ace-Gly-NMe in 6-31G* (155 basis functions) g03: mem=100MW TEST 6-31G* nosym scf=(tight,incore) gamess: MEMORY=20000000 DIRSCF=.TRUE. itek g03 Itanium2 1400MHz efc 7.1 26.5 dahlia g03 Opteron 1400MHz pgi4 49.5 m211 g03 k7mp 2133MHz(MP 2600+) pgi4 83.3 m211 gamess k7mp 2133MHz(MP 2600+) ifc7.1 92.5 dahlia gamess Opteron 1400MHz ifc7.1 128.5 matrix g03 p4xenon 1800MHz pgi4 144.0 (*) itek gamess Itanium2 1400MHz efc 7.1 150.8 matrix gamess p4xenon 1800MHz ifc7.1 165.6 (*) uses 50MW, machine has not enough memory for scf=incore (g03 needs 75MW) so you cannot compare it with other results of g03, gamess is happy with 20 MW for DIRSCF=.TRUE. 2. Single point MP2 energy calculation for Ace-Gly-NMe in 6-31G* (155 basis functions) g03: mem=100mw rwf=a,250MW,b,250MW,c,250MW TEST rmp2/6-31G* nosym scf=(tight,incore) MaxDisk=750MW gamess: MEMORY=50000000 DIRSCF=.TRUE. itek g03 Itanium2 1400MHz efc 7.1 51.7 dahlia g03 Opteron 1400MHz pgi4 150.7 m211 gamess k7mp 2133MHz(MP 2600+) ifc7.1 154.2 dahlia gamess Opteron 1400MHz ifc7.1 191.0 itek gamess Itanium2 1400MHz efc 7.1 194.8 matrix gamess p4xenon 1800MHz ifc7.1 238.1 m211 g03 k7mp 2133MHz(MP 2600+) pgi4 251.6 matrix g03 p4xenon 1800MHz pgi4 255.3(*) (*) as above 3. Manfreds Gaussian Benchmark http://www.chemie.uni-dortmund.de/groups/ocb/projekte/mg98b.html 243 basis functions 399 primitive gaussians RHF/3-21G* Freq [sec] itek g03 Itanium2 1400MHz efc 7.1 2843 dahlia g03 Opteron 1400MHz pgi 4 9332 m211 g03 k7mp 2133MHz(MP 2600+) pgi 4 10289 galera g03 p3xenon 700MHz pgi 3 19317 m001 g03 p3 650MHz pgi 4 22824 4. test397.com from gaussian03 882 basis functions, 1440 primitive gaussians rb3lyp/3-21g force test scf=novaracc [sec] itek g03 Itanium2 1400MHz efc 7.1 6733 dahlia g03 Opteron 1400MHz pgi 4 17879 m211 g03 k7mp 2133MHz(MP 2600+) pgi 4 20521 galera g03 p3xenon 700MHz pgi 3 39353 5. Gaussian calculations of NMR chemical shifts for GlyGlyAlaAla 207 basis functions, 339 primitive gaussians %MEM=800MB B3LYP/GEN NMR [sec] itek LINUX Itanium2 1400MHz efc 7.1 275 dahlia g03 Opteron 1400MHz pgi 4 808 MEM=2000MB dahlia g03 Opteron 1400MHz pgi 4 849 m211 g03 k7mp 2133MHz(MP 2600+) pgi 4 948 matrix LINUX p4xenon 1800MHz pgi 4 975 MEM=256MB some details: g03 is GAUSSIAN 03 rev. B04 with gaussian blas compiled with 32-bit pgi4.0 gamess is VERSION 6 SEP 2001 (R4) compiled with 32-bit ifc 7.1 Itanium2 (itek) uses gamess VERSION = 14 JAN 2003 (R3) compiled with 64-bit efc and GAUSSIAN 03 rev. B04 with mkl60 compiled with 64-bit efc 7.1 P3xenon (galera) uses gamess VERSION = 6 SEP 2001 (R4) compiled with ifc 6.0 and GAUSSIAN 03 rev B.01 with gaussian blas compiled with pgi 3.3 czarek ---------------------------------------------------------------------- Dr. Cezary Czaplewski Department of Chemistry Box 431 Baker Lab of Chemistry University of Gdansk Cornell University Sobieskiego 18, 80-952 Gdansk, Poland Ithaca, NY 14853 phone: +48 58 3450 430 phone: (607) 255-0556 fax: +48 58 341-0357 fax: (607) 255-4137 e-mail: czarek..at..chem.univ.gda.pl e-mail: cc178..at..cornell.edu ---------------------------------------------------------------------- From chemistry-request@ccl.net Fri Sep 19 12:32:42 2003 Received: from smtp1.utdallas.edu (smtp1.utdallas.edu [129.110.10.12]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h8JGWAmK031132 for ; Fri, 19 Sep 2003 12:32:10 -0400 Received: from utdallas.edu (pascal.utdallas.edu [129.110.22.64]) by smtp1.utdallas.edu (Postfix) with ESMTP id 4D0A6388DE4 for ; Fri, 19 Sep 2003 11:32:09 -0500 (CDT) Sender: wfisher=at=utdallas.edu Message-ID: <3F6B2F36.6A1D52AB=at=utdallas.edu> Date: Fri, 19 Sep 2003 11:30:46 -0500 From: Wayne Fisher X-Mailer: Mozilla 4.79 [en] (X11; U; HP-UX B.11.11 9000/785) X-Accept-Language: en MIME-Version: 1.0 To: "chemistry=at=ccl.net" Subject: CCL:Control convergene threshold in Gaussian Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=-0.6 required=7.0 tests=EMAIL_ATTRIBUTION,USER_AGENT_MOZILLA_XM,X_ACCEPT_LANG version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Colleagues, On 16 Sep 2003 Zhi-Xiang Wang wrote: Date: Tue, 16 Sep 2003 09:51:20 -0400 (EDT) From: Zhi-Xiang Wang To: chemistry=at=ccl.net Subject: CCL:Control convergene threshold in Gaussian Hi Do we have a method to make the convergene threshold in Gaussian like that Threshold Maximum Force .000050 RMS Force .000300 Maximum Displacement .018800 RMS Displacement .012000 Instead of the default values Item Threshold Maximum Force .000450 RMS Force .000300 Maximum Displacement .001800 RMS Displacement .001200 Thanks Zhixiang In a subsequent private communication he wrote: Unfortunately, I have't got the right answer for this question. However I know we can use iop(1/7=mmm) to adjust the threshold. The default value mmm=300. The problem for me is when I use smaller mmm, both the maxium and rms force and the maxium and rms displacement decrease, instead of an increasing in maxium and rms displacement as I want. Hope it is useful for you. ZX Unfortunately it does not seem that these thresholds are independently variable in Gaussian 03. The variable for the RMS Force, ConvF, is set by default to 3/10000 unless IOp(1/7) overrides the default. In that case IOp(1/7)=mmm sets ConvF and thus the threshold for RMS Force to mmm/10000. Also note that, according to the Gaussian 03 IOps Reference manual, IOp(1/7=-1) sets ConvF to 1/600. ConvX, the variable for RMS Displacement, appears to be hard coded as ConvF*4, so the threshold for RMS Displacement will always be four times that of the RMS Force. Further, the variables for Maximum Force and Maximum Displacement are set as follows: Maximum Force = ConvF*CnvFMX Maximum Displacement = ConvX*CnvFMX and CnvFMX is set as data to 1.5. Thus we always have the following relationships: RMS Force = set by default or IOp(1/7) Maximum Force = RMS Force*1.5 Maximum Displacement = RMS Force*6 RMS Displacement = RMS Force*4 Best regards, Wayne Fisher The University of Texas at Dallas From chemistry-request@ccl.net Fri Sep 19 13:59:55 2003 Received: from ms2.usu.edu (ms2.usu.edu [129.123.104.12]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h8JHxNmK001068 for ; Fri, 19 Sep 2003 13:59:23 -0400 Received: from webster.usu.edu (webster.usu.edu [129.123.1.90]) by ms2.usu.edu (8.12.8/8.12.8) with ESMTP id h8JHw4GC023843 for ; Fri, 19 Sep 2003 11:58:04 -0600 X-WebMail-UserID: Alexandrova Date: Fri, 19 Sep 2003 11:58:04 -0600 Sender: Anastassia Alexandrova From: Anastassia Alexandrova To: CHEMISTRY$at$ccl.net X-EXP32-SerialNo: 00002751 Subject: CCL: CASSCF scf-convergency criteria Message-ID: <3F6C2ABA$at$webster.usu.edu> Mime-Version: 1.0 Content-Type: text/plain; charset="ISO-8859-1" Content-Transfer-Encoding: 7bit X-Mailer: WebMail (Hydra) SMTP v3.62 X-MailScanner: Found to be clean X-Spam-Status: No, hits=0.0 required=7.0 tests=none version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Hello, All! Does any one know how to change (decrease) the scf-convergency criteria in CASSCF calculations in Gaussian 03? Thanks in advance Anastassia N. Alexandrova Dr. Boldyrev's research group Utah State University From chemistry-request@ccl.net Fri Sep 19 12:42:02 2003 Received: from bureau6.utcc.utoronto.ca (bureau6.utcc.utoronto.ca [128.100.132.16]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h8JGfTmK031897 for ; Fri, 19 Sep 2003 12:41:30 -0400 Received: from mditdell.mdit.utoronto.ca ([128.100.251.12] HELO MditDell ident: IDENT-NOT-QUERIED [port 1177]) by bureau6.utcc.utoronto.ca with SMTP id <464317-137>; Fri, 19 Sep 2003 12:41:16 -0400 From: "William Wei" To: "CCLers" Subject: Relaxed PES Scans Vs Partial Optimizations Date: Fri, 19 Sep 2003 12:45:03 -0500 Message-ID: MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook IMO, Build 9.0.2416 (9.0.2910.0) Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2727.1300 X-Spam-Status: No, hits=-0.4 required=7.0 tests=MSGID_GOOD_EXCHANGE version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) After reading the "gaussian 98 user's reference" about PES scan, seems "opt=ModRedundant" does the same thing with "opt=Z-matrix" specifying the "S". Could anybody tell me what is the different? Thanks. Best regards, William ------------------------- William Wei Molecular Design and Information Technology (MDIT) center Faculty of Pharmacy, University of Toronto 19 Russell Street, Toronto, ON. M5S 2S2 Tel: 1-416-946-8469 Fax: 1-416-978-8511 Email: william.wei[at]utoronto.ca william[at]phm.utoronto.ca From chemistry-request@ccl.net Fri Sep 19 12:41:46 2003 Received: from sycorax.delfa.net (relay4.delfa.net [193.125.210.9]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h8JGfEmK031873 for ; Fri, 19 Sep 2003 12:41:14 -0400 X-Envelope-To: Received: from dux.ru (dux.ru [193.125.210.65]) by sycorax.delfa.net (8.12.10/8.12.10/Sycorax.Delfa) with ESMTP id h8JGfDGP008400 for ; Fri, 19 Sep 2003 20:41:13 +0400 Received: from dux.ru (localhost [127.0.0.1]) by dux.ru (8.12.6/8.12.6) with ESMTP id h8JGfC5l090605 for ; Fri, 19 Sep 2003 20:41:12 +0400 (MSD) (envelope-from dima=at=xenon.spb.ru) Received: (from uucp@localhost) by dux.ru (8.12.6/8.12.1/Submit) with UUCP id h8JGfC5A090603 for chemistry=at=ccl.net; Fri, 19 Sep 2003 20:41:12 +0400 (MSD) (envelope-from dima=at=xenon.spb.ru) Received: from troll ([192.168.5.1] helo=xenon.spb.ru ident=dima) by shadow with esmtp (Exim 3.35 #1 (Debian)) id 1A0OD1-00054f-00 for ; Fri, 19 Sep 2003 20:34:15 +0400 Message-ID: <3F6B2FEA.3060700=at=xenon.spb.ru> Date: Fri, 19 Sep 2003 20:33:46 +0400 From: Dmitry Rozmanov User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.4) Gecko/20030908 Debian/1.4-4 X-Accept-Language: ru, en MIME-Version: 1.0 To: CCL Subject: Compiling GAMESS with IFC 7.0 Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=-0.1 required=7.0 tests=USER_AGENT_MOZILLA_UA,X_ACCEPT_LANG version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Dear Colleagues, I have compiled the latest GAMESS with Intel fortran compiler 7.0. It works but in output file I see a lot of error messages like these: FLUSH--FAILED:: Invalid argument FLUSH--FAILED:: Unknown error 153 FLUSH--FAILED:: No such file or directory Interesting thing is that calculation finish successfully and the results look ok. So what are these errors could be? How can I fight them out? Thank you in advance. ---Dmitry. From chemistry-request@ccl.net Fri Sep 19 11:33:50 2003 Received: from camay.yandex.ru (camay.yandex.ru [213.180.193.64]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h8JFXimK027811 for ; Fri, 19 Sep 2003 11:33:44 -0400 Received: from YAMAIL (camay.yandex.ru) by mail.yandex.ru id ; Fri, 19 Sep 2003 19:33:29 +0400 Date: Fri, 19 Sep 2003 19:33:28 +0400 (MSD) From: "My-boxic" Reply-To: My-boxic[at]yandex.ru Sender: My-boxic[at]yandex.ru Message-Id: <3F6B21C8.000009.32224[at]camay.yandex.ru> MIME-Version: 1.0 X-Mailer: Yamail [ http://yandex.ru ] Errors-To: My-boxic[at]yandex.ru To: chemistry[at]ccl.net X-source-ip: 212.192.241.134 Content-Type: text/plain; charset="US-ASCII" Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=3.5 required=7.0 tests=RCVD_IN_OSIRUSOFT_COM,X_OSIRU_OPEN_RELAY version=2.55 X-Spam-Level: *** X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Can I docking ligand connected atom B or another atom (for example, different metal or S,Si,P) by Autodock 3 ??? Can I calculated grid map for atom B??? Student Maria. From chemistry-request@ccl.net Fri Sep 19 12:41:14 2003 Received: from julesburg.uits.indiana.edu (julesburg.uits.indiana.edu [129.79.1.75]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h8JGegmK031865 for ; Fri, 19 Sep 2003 12:40:43 -0400 Received: from grapeape.uits.iupui.edu (grapeape.uits.iupui.edu [134.68.220.203]) by julesburg.uits.indiana.edu (8.12.10/8.12.10/IUPO) with ESMTP id h8JGebRA019683 for ; Fri, 19 Sep 2003 11:40:39 -0500 (EST) Received: from iupui.edu ([134.68.57.154]) by grapeape.uits.iupui.edu (8.12.10/8.12.10/IUPO) with ESMTP id h8JGeTdX004569 for ; Fri, 19 Sep 2003 11:40:39 -0500 (EST) Sender: qin|at|grapeape.uits.iupui.edu Message-ID: <3F6B3185.E28B599A|at|iupui.edu> Date: Fri, 19 Sep 2003 11:40:37 -0500 From: "Q." X-Mailer: Mozilla 4.78 [en] (X11; U; Linux 2.4.7-10 i686) X-Accept-Language: en MIME-Version: 1.0 To: chemistry|at|ccl.net Subject: CCL:autodock3 parameter change Content-Type: multipart/mixed; boundary="------------4CACA8D5965A76C9AC39C9E5" X-Spam-Status: No, hits=-0.1 required=7.0 tests=USER_AGENT_MOZILLA_XM,X_ACCEPT_LANG version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) This is a multi-part message in MIME format. --------------4CACA8D5965A76C9AC39C9E5 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit --------------4CACA8D5965A76C9AC39C9E5 Content-Type: message/rfc822 Content-Transfer-Encoding: 7bit Content-Disposition: inline Return-Path: X-Sieve: cmu-sieve 2.0 Return-Path: Received: from round.uits.indiana.edu (round.uits.indiana.edu [129.79.1.72]) by imap1.iupui.edu (8.12.10/8.12.10/imap1) with ESMTP id h8JGJe6K025583 for ; Fri, 19 Sep 2003 11:19:40 -0500 (EST) Received: from ns0.scripps.edu (ns0.scripps.edu [192.42.82.58]) by round.uits.indiana.edu (8.12.10/8.12.10/IUPO) with ESMTP id h8JGJbfs006087 for ; Fri, 19 Sep 2003 11:19:37 -0500 (EST) Received: from antigen.scripps.edu (antigen.scripps.edu [137.131.200.100]) by ns0.scripps.edu (8.11.7/TSRI-4.2rx) with SMTP id h8JGJbO11669 for ; Fri, 19 Sep 2003 09:19:37 -0700 (PDT) Received: from relay2.scripps.edu(137.131.200.30) by antigen.scripps.edu via csmap id 24409; Fri, 19 Sep 2003 09:16:51 -0700 (PDT) Received: from spiderweb.scripps.edu (spiderweb [137.131.200.42]) by relay2.scripps.edu (8.11.7/TSRI-4.4.1rAVB) with ESMTP id h8JGFIR21223; Fri, 19 Sep 2003 09:15:19 -0700 (PDT) Received: (from majordom@localhost) by spiderweb.scripps.edu (SGI-8.9.3/TSRI-3.1w) id JAA23269 for autodock-outgoing; Fri, 19 Sep 2003 09:10:24 -0700 (PDT) Received: from relay2.scripps.edu (relay2 [137.131.200.30]) by spiderweb.scripps.edu (SGI-8.9.3/TSRI-3.1w) with ESMTP id JAA91991 for ; Fri, 19 Sep 2003 09:10:20 -0700 (PDT) Received: from antigen.scripps.edu (antigen [137.131.200.100]) by relay2.scripps.edu (8.11.7/TSRI-4.4.1rAVB) with SMTP id h8JGAKR20702 for ; Fri, 19 Sep 2003 09:10:20 -0700 (PDT) Received: from relay1.scripps.edu(137.131.200.29) by antigen.scripps.edu via csmap id 23453; Fri, 19 Sep 2003 09:11:49 -0700 (PDT) Received: from julesburg.uits.indiana.edu (julesburg.uits.indiana.edu [129.79.1.75]) by relay1.scripps.edu (8.11.7/TSRI-4.4.1rAVB) with ESMTP id h8JGAJI28331 for ; Fri, 19 Sep 2003 09:10:19 -0700 (PDT) Received: from auggiedoggie.uits.iupui.edu (auggiedoggie.uits.iupui.edu [134.68.220.202]) by julesburg.uits.indiana.edu (8.12.10/8.12.10/IUPO) with ESMTP id h8JGAFRA007774 for ; Fri, 19 Sep 2003 11:10:15 -0500 (EST) Received: from iupui.edu ([134.68.57.154]) by auggiedoggie.uits.iupui.edu (8.12.10/8.12.10/IUPO) with ESMTP id h8JGAHGh012545 for ; Fri, 19 Sep 2003 11:10:17 -0500 (EST) Message-ID: <3F6B2A71.C69F1EE7|at|iupui.edu> Date: Fri, 19 Sep 2003 11:10:25 -0500 From: "Q." X-Mailer: Mozilla 4.78 [en] (X11; U; Linux 2.4.7-10 i686) X-Accept-Language: en MIME-Version: 1.0 To: autodock Subject: ADL: parameters Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Sender: owner-autodock|at|scripps.edu Precedence: bulk Reply-To: "Q." Dear All, I have a very hydrophobic ligand that only makes one h-bond to the protein through a sp2 N atom. There is a crystal structure the protein/ligand complex. However, when I use autodock 3, the lowest docked comformation is 3 anstrom away from the crystallofraphic position. The 1 anstrom rmsd comformation has two fold less of delta G than the experimental value. Buzko et. al. (2002) had once modified the parameters in autodock 2.4 to get the "right" docking position. They changed enthalpic well depth for H-bond from 5 to 7. Now what is the justification to make such a change? If I want to modify the 12-10 parameter or 12-6 parameter in autodock 3, although the manual said not to change them lightly, how can I do it right? As a matter of factor, I have tried to increase to epsilonij for h-bond to about 5~7, it did predict the right docking comformation with reasonable binding free energy. However, these values are far away from the one used in Autodock3, which is 0.328. Any suggestions are appreciated. Qin Zou , Ph D. Indiana University -- ADL: AutoDock List --- http://www.scripps.edu/pub/olson-web/doc/autodock/ --- --------------4CACA8D5965A76C9AC39C9E5-- From chemistry-request@ccl.net Fri Sep 19 07:50:38 2003 Received: from GWIA.HSC.WVU.EDU (gateway.hsc.wvu.edu [157.182.105.18]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h8JBo7mK015657 for ; Fri, 19 Sep 2003 07:50:07 -0400 Received: from HSC-DOM5-MTA by GWIA.HSC.WVU.EDU with Novell_GroupWise; Fri, 19 Sep 2003 07:50:16 -0400 Message-Id: X-Mailer: Novell GroupWise Internet Agent 6.0.3 Date: Fri, 19 Sep 2003 07:49:56 -0400 From: "Peter Gannett" To: , Subject: Re: CCL:Hydrogens in InsightII Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Disposition: inline X-Spam-Status: No, hits=0.0 required=7.0 tests=none version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id h8JBocmK015678 Francois: It would probably be easier to write the pdb file and then use the egrep command with the -v option, which can be used to exclude all lines containing hydrogens, and then dump it to a new file. Pete Gannett >>> FyD 09/18/03 08:24PM >>> Dear All, I would interested in knowing 'the command' in insightII which allows to automatically REMOVE all the hydrogens (of an oligonucleotide) in order to save the structure (to the PDB format) without these hydrogens, keeping only the heavy atoms. Thanks, regards, Francois -= 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, jkl|at|ccl.net (read about it on CCL Home Page) -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ From chemistry-request@ccl.net Fri Sep 19 15:45:10 2003 Received: from sandmail01.sd.accelrys.com (fw1.sd.accelrys.com [209.120.169.30]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h8JJibmK006154 for ; Fri, 19 Sep 2003 15:44:37 -0400 In-Reply-To: To: , Subject: Re: CCL: Removing all Hydrogens in InsightII MIME-Version: 1.0 X-Mailer: Lotus Notes Release 6.0.1CF1 March 04, 2003 Message-ID: From: Ken Butenhof Date: Fri, 19 Sep 2003 15:44:33 -0400 X-MIMETrack: Serialize by Router on sandmail01/Server/Accelrys(Release 6.0.2CF1|June 9, 2003) at 09/19/2003 12:44:37, Serialize complete at 09/19/2003 12:44:37 Content-Type: multipart/alternative; boundary="=_alternative 006C64E285256DA6_=" X-Spam-Status: No, hits=1.9 required=7.0 tests=ASCII_FORM_ENTRY,HTML_20_30,HTML_MESSAGE,IN_REP_TO version=2.55 X-Spam-Level: * X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) This is a multipart message in MIME format. --=_alternative 006C64E285256DA6_= Content-Type: text/plain; charset="US-ASCII" Francois: The best procedure is to first display ONLY hydrogens (Molecule/Display, with Display_Only option on), select the displayed atom (by dragging a selection box around the displayed atoms you wish to delete) then hit the delete key. You can then display all atoms and save. Ken _______________________________________________ Kenneth Butenhof phone: 800 756-4674 Principal Scientist email: kenb-.at.-accelrys.com Accelrys Inc. web: www.accelrys.com "Peter Gannett" Sent by: "Computational Chemistry List" 09/19/2003 07:49 AM To , cc Subject CCL:Hydrogens in InsightII Francois: It would probably be easier to write the pdb file and then use the egrep command with the -v option, which can be used to exclude all lines containing hydrogens, and then dump it to a new file. Pete Gannett >>> FyD 09/18/03 08:24PM >>> Dear All, I would interested in knowing 'the command' in insightII which allows to automatically REMOVE all the hydrogens (of an oligonucleotide) in order to save the structure (to the PDB format) without these hydrogens, keeping only the heavy atoms. Thanks, regards, Francois -= 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, jkl-.at.-ccl.net (read about it on CCL Home Page) -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ --=_alternative 006C64E285256DA6_= Content-Type: text/html; charset="US-ASCII"
Francois:

The best procedure is to first display ONLY hydrogens (Molecule/Display, with Display_Only option on), select the displayed atom (by dragging a selection box around the displayed atoms you wish to delete) then hit the delete key. You can then display all atoms and save.

Ken
_______________________________________________
Kenneth Butenhof phone: 800 756-4674
Principal Scientist email: kenb-.at.-accelrys.com
Accelrys Inc. web: www.accelrys.com

"Peter Gannett" <pgannett-.at.-hsc.wvu.edu>
Sent by: "Computational Chemistry List" <chemistry-request-.at.-ccl.net>
09/19/2003 07:49 AM

To
<chemistry-.at.-ccl.net>, <fyd-.at.-u-picardie.fr>

cc

Subject
CCL:Hydrogens in InsightII

Francois: It would probably be easier to write the pdb file and then use the egrep command with the -v option, which can be used to exclude all lines containing hydrogens, and then dump it to a new file. Pete Gannett >>> FyD <fyd-.at.-u-picardie.fr> 09/18/03 08:24PM >>> Dear All, I would interested in knowing 'the command' in insightII which allows to automatically REMOVE all the hydrogens (of an oligonucleotide) in order to save the structure (to the PDB format) without these hydrogens, keeping only the heavy atoms. Thanks, regards, Francois -= 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, jkl-.at.-ccl.net (read about it on CCL Home Page) -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+
--=_alternative 006C64E285256DA6_=--