From chemistry-request@ccl.net Tue Apr 5 22:44:00 2005 Received: from web53707.mail.yahoo.com (web53707.mail.yahoo.com [206.190.37.28]) by server.ccl.net (8.13.1/8.13.1) with SMTP id j362hsno013471 for ; Tue, 5 Apr 2005 22:43:54 -0400 Received: (qmail 7528 invoked by uid 60001); 6 Apr 2005 01:43:53 -0000 Comment: DomainKeys? See http://antispam.yahoo.com/domainkeys DomainKey-Signature: a=rsa-sha1; q=dns; c=nofws; s=s1024; d=yahoo.com; b=OhkS8doZFHTAQsd7WPsv/UDFGocLe8yZlrqloAw6z76lQ4f3SvKGF8lCKO8VS1kOHHhu6t2nqovsTCoYAEY0lVQBl0Am2O5HyAPE05Sezzr2n0O+2wkG59sz2JFpMw51wEcqix3tup81O11lvr2lKB5HAYlWTs1Wo1Gr47P4jZI= ; Message-ID: <20050406014353.7526.qmail..at..web53707.mail.yahoo.com> Received: from [130.18.145.140] by web53707.mail.yahoo.com via HTTP; Tue, 05 Apr 2005 18:43:53 PDT Date: Tue, 5 Apr 2005 18:43:53 -0700 (PDT) From: Delwar Hossain Subject: Problem in geomtry optimization using G03 To: chemistry..at..ccl.net MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="0-1146862885-1112751833=:6196" X-Spam-Status: No, score=2.8 required=5.0 tests=DEAR_SOMETHING, DNS_FROM_RFC_ABUSE,FROM_ENDS_IN_NUMS,HTML_MESSAGE,TRACKER_ID autolearn=no version=3.0.1 X-Spam-Level: ** X-Spam-Checker-Version: SpamAssassin 3.0.1 (2004-10-22) on server.ccl.net --0-1146862885-1112751833=:6196 Content-Type: text/plain; charset=us-ascii Dear Sir, I would be grateful to you if anyone kindly helps me giving information how to solve the problem mentioned below. I try to optimize the structure using G03. Some times the after several steps (i) the Maximum force and RMS Force remains unchanged until maximum step number reached and finally the job stoped. (ii) Some times the Maximum Displacement and RMS displacement remain unchanged. (iii) Some times I saw the warning s" energy rises" and " no minima in search direction". I am including two steps for the first case: GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad Internal Forces: Max 0.003648311 RMS 0.000547824 Step number 61 out of a maximum of 100 All quantities printed in internal units (Hartrees-Bohrs-Radians) Energy Rises -- skip Quadratic search. Skip linear search -- no minimum in search direction. Steepest descent instead of Quadratic search. Steepest descent step scaled to max of 0.05000. Item Value Threshold Converged? Maximum Force 0.003648 0.000450 NO RMS Force 0.000548 0.000300 NO Maximum Displacement 0.000705 0.001800 YES RMS Displacement 0.000125 0.001200 YES GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad Internal Forces: Max 0.003648313 RMS 0.000547986 Step number 62 out of a maximum of 100 All quantities printed in internal units (Hartrees-Bohrs-Radians) Energy Rises -- skip Quadratic search. Skip linear search -- no minimum in search direction. Steepest descent instead of Quadratic search. Steepest descent step scaled to max of 0.05000. Item Value Threshold Converged? Maximum Force 0.003648 0.000450 NO RMS Force 0.000548 0.000300 NO Maximum Displacement 0.000675 0.001800 YES RMS Displacement 0.000119 0.001200 YES Thanking you in advance for your generous help. With best regards, Delwar Hossain Chemistry Department Mississippi State University e-mail: hossaind2004..at..yahoo.com --------------------------------- Do you Yahoo!? Yahoo! Mail - now with 250MB free storage. Learn more. --0-1146862885-1112751833=:6196 Content-Type: text/html; charset=us-ascii

Dear Sir,

I would be grateful to you if anyone kindly helps me giving information how to solve the problem mentioned below. I try to optimize the structure using G03. Some times the after several steps (i) the Maximum force and RMS Force remains unchanged until maximum step number reached and finally the job stoped. (ii) Some times the Maximum Displacement and RMS displacement remain unchanged. (iii) Some times I saw the warning s" energy rises" and " no minima in search direction".

I am including two steps for the first case:

 

GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad

 Internal  Forces:  Max     0.003648311 RMS     0.000547824

 Step number  61 out of a maximum of 100

 All quantities printed in internal units (Hartrees-Bohrs-Radians)

 Energy Rises -- skip Quadratic search.

 Skip linear search -- no minimum in search direction.

 Steepest descent instead of Quadratic search.

 Steepest descent step scaled to max of 0.05000.

         Item                           Value            Threshold    Converged?

 Maximum Force                  0.003648        0.000450       NO

 RMS     Force                      0.000548        0.000300       NO

 Maximum Displacement     0.000705        0.001800      YES

 RMS     Displacement          0.000125       0.001200      YES

GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad

 Internal  Forces:  Max     0.003648313 RMS     0.000547986

 Step number  62 out of a maximum of 100

 All quantities printed in internal units (Hartrees-Bohrs-Radians)

 Energy Rises -- skip Quadratic search.

 Skip linear search -- no minimum in search direction.

 Steepest descent instead of Quadratic search.

 Steepest descent step scaled to max of 0.05000.

 

        Item                                   Value             Threshold            Converged?

 Maximum Force                    0.003648           0.000450                 NO

 RMS     Force                        0.000548           0.000300                 NO

 Maximum Displacement       0.000675           0.001800                YES

 RMS     Displacement           0.000119            0.001200               YES

 

 

Thanking you in advance for your generous help.

 

With best regards,

Delwar Hossain

Chemistry Department

Mississippi State University

e-mail: hossaind2004..at..yahoo.com

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Yahoo! Mail - now with 250MB free storage. Learn more. --0-1146862885-1112751833=:6196-- From chemistry-request@ccl.net Wed Apr 6 11:53:44 2005 Received: from smtp.uibk.ac.at (lmr1.uibk.ac.at [138.232.1.142]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j36Frfo2014066 for ; Wed, 6 Apr 2005 11:53:41 -0400 Received: from uibk.ac.at (yy1-c724.uibk.ac.at [138.232.32.48]) by smtp.uibk.ac.at (8.12.11/8.12.11/F1) with ESMTP id j36EksKK010819 for ; Wed, 6 Apr 2005 16:46:54 +0200 Message-ID: <4253F65E.4050708 _()_ uibk.ac.at> Date: Wed, 06 Apr 2005 16:46:54 +0200 From: Demetrios Xenides Reply-To: Demetrios.Xenides _()_ uibk.ac.at 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: ccl: density=ccsd in g03 Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit X-Spam-Score: -5.3 () ALL_TRUSTED,FROM_ENDS_IN_NUMS,RCV_SMTP_UIBK X-Scanned-By: MIMEDefang 2.51 at uibk.ac.at on 138.232.1.140 X-Spam-Status: No, score=0.0 required=5.0 tests=none autolearn=failed version=3.0.1 X-Spam-Checker-Version: SpamAssassin 3.0.1 (2004-10-22) on server.ccl.net Hi all, I am trying to perform a density=ccsd calculation in G03. It is said (Gaussian manual) that this feature is available in this version. For your convenience here is the command line that I am using: Mem=700mb %rwf=o01,2gb,o02,2gb,o03,2gb,o04,2gb,o05,2gb,o06,2gb,o07,2gb,o08,2gb,o09,2gb %Nprocshared=6 %Nosave #p ccsd/gen geom=coord density=ccsd units=au nosymm scfcon=10 Do I have to mention that it simply does not work? Am I missing something? Do I also have to mention that I have already sent an email to Gaussian and I haven't got any reply? Looking forward for your suggestions. Cheers Demetrios p.s.1 I tried to do the same but instead of using density=ccsd to use density=current; it produced the CC results!!! From chemistry-request@ccl.net Wed Apr 6 15:55:00 2005 Received: from server.ccl.net (ccl [127.0.0.1]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j36Jswsr022799 for ; Wed, 6 Apr 2005 15:54:58 -0400 Received: (from apache@localhost) by server.ccl.net (8.13.1/8.13.1/Submit) id j36Jswoa022798 for chemistry~at~ccl.net; Wed, 6 Apr 2005 15:54:58 -0400 Date: Wed, 6 Apr 2005 15:54:58 -0400 Message-Id: <200504061954.j36Jswoa022798~at~server.ccl.net> X-Authentication-Warning: server.ccl.net: apache set sender to chemistry-request~at~ccl.net using -f From: "Principal, , Component" To: chemistry~at~ccl.net X-Web-Message-Number: 050406155409-22761 Subject: W:Free code for solvent accessible surface area X-Spam-Status: No, score=-0.6 required=5.0 tests=ALL_TRUSTED, FORGED_YAHOO_RCVD autolearn=failed version=3.0.1 X-Spam-Checker-Version: SpamAssassin 3.0.1 (2004-10-22) on server.ccl.net Is there any free code available for calculating SASA, apart from that suggested by M Petitjean. Fortran, C, C++, Java, Python, Perl anything will do. Thanks in advance From chemistry-request@ccl.net Wed Apr 6 19:11:43 2005 Received: from race1.oit.umass.edu (race1.oit.umass.edu [128.119.101.37]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j36NBc2O029557 for ; Wed, 6 Apr 2005 19:11:38 -0400 Received: from localhost (mail-www2.oit.umass.edu [128.119.100.12]) by race1.oit.umass.edu (8.13.2/8.13.3) with ESMTP id j36LKZOL026844; Wed, 6 Apr 2005 17:20:36 -0400 Received: from tasha.biochem.umass.edu (tasha.biochem.umass.edu [128.119.35.170]) by mail-www2.oit.umass.edu (IMP) with HTTP for ; Wed, 6 Apr 2005 17:20:35 -0400 Message-ID: <1112822435.425452a3c9f6e..at..mail-www2.oit.umass.edu> Date: Wed, 6 Apr 2005 17:20:35 -0400 From: rsmock..at..student.umass.edu To: CHEMISTRY..at..server.ccl.net, Jeffrey.Gosper..at..brunel.ac.uk Subject: bug in babelwin MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit User-Agent: Internet Messaging Program (IMP) 3.2 X-Originating-IP: 128.119.35.170 X-Scanned-By: MIMEDefang 2.48 on 128.119.101.37 X-Spam-Status: No, score=0.2 required=5.0 tests=NO_REAL_NAME autolearn=no version=3.0.1 X-Spam-Checker-Version: SpamAssassin 3.0.1 (2004-10-22) on server.ccl.net There is a minor bug with the code in cca/software/UNIX/babel/babelwin.zip Conversion to Sybil mol2 format does not work. I think it is just a typo in the code, which puts "-omo2" in the command line. Open Babel uses the syntax "-omol2" (the difference is letter l not number 1). Rob Smock rsmock..at..student.umass.edu From chemistry-request@ccl.net Wed Apr 6 19:18:29 2005 Received: from erouter2.it-datacntr.louisville.edu (ulbcenter-01-b08.it-datacntr.louisville.edu [136.165.5.83]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j36NIRfZ029741 for >ccl.net>; Wed, 6 Apr 2005 19:18:27 -0400 Received: from gwise.louisville.edu (gwise.louisville.edu [136.165.1.45]) by erouter2.it-datacntr.louisville.edu (Postfix) with ESMTP id 251566F603 for >ccl.net>; Wed, 6 Apr 2005 12:06:56 -0400 (EDT) Received: from sgate-MTA by gwise.louisville.edu with Novell_GroupWise; Wed, 06 Apr 2005 12:06:55 -0400 Message-Id: >gwise.louisville.edu> X-Mailer: Novell GroupWise Internet Agent 6.5.3 Beta Date: Wed, 06 Apr 2005 12:06:24 -0400 From: "Lei Wang" >louisville.edu> To: >ccl.net> Subject: fingerprint generation software Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Disposition: inline X-Spam-Status: No, score=0.0 required=5.0 tests=none autolearn=failed version=3.0.1 X-Spam-Checker-Version: SpamAssassin 3.0.1 (2004-10-22) on server.ccl.net Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id j36NITfZ029745 I want to generate finger-prints for my chemical database. and want to use such info to do sub-structure or similarity search. What software could I use? Thanks! Lei From chemistry-request@ccl.net Wed Apr 6 17:01:48 2005 Received: from smtp.uibk.ac.at (lmr1.uibk.ac.at [138.232.1.142]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j36L1gid025488 for >ccl.net>; Wed, 6 Apr 2005 17:01:42 -0400 Received: from localhost (lwm1.uibk.ac.at [138.232.1.160]) by smtp.uibk.ac.at (8.12.11/8.12.11/F1) with ESMTP id j36JuQ8n005719 for >ccl.net>; Wed, 6 Apr 2005 21:56:26 +0200 Received: from ysh15-247-242.uibk.ac.at (ysh15-247-242.uibk.ac.at [138.232.247.242]) by web-mail1.uibk.ac.at (IMP) with HTTP for >mail1.uibk.ac.at>; Wed, 6 Apr 2005 21:56:26 +0200 Message-ID: <1112817386.42543eea6bf3d<>web-mail1.uibk.ac.at> Date: Wed, 6 Apr 2005 21:56:26 +0200 From: Demetrios Xenides >uibk.ac.at> To: chemistry<>ccl.net Subject: CCL MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit User-Agent: Internet Messaging Program (IMP) 3.2.6 X-Originating-IP: 138.232.247.242 X-Forwarded-For: X-Spam-Score: -8.8 () ALL_TRUSTED,RCV_SMTP_UIBK,RCV_WEBMAIL X-Scanned-By: MIMEDefang 2.51 at uibk.ac.at on 138.232.1.140 X-Spam-Status: No, score=0.0 required=5.0 tests=none autolearn=failed version=3.0.1 X-Spam-Checker-Version: SpamAssassin 3.0.1 (2004-10-22) on server.ccl.net Let me correct my previous posting, in the sense that they answered to me after some hours (of course I have taken into account the difference in hour). In any case here is what they told me (it contains both answers-replies): ######################################################################### Dear Demetrios, Yes, the result is the CCSD density in both of these input files - density=current is synonymous with density=cc in this case. The label in the output is the same regardless of whether you are using CCD, CCSD, or a QCI method. The only post-HF density available during these calculations is for the method used to calculate the energy. For example, only the CCSD density is available during a CCSD calculation - the CCD density is not available. Regards, Jim On Apr 6, 2005, at 11:32 AM, Demetrios Xenides wrote: > Dear Jim, > and the result is the CCSD density? this is what I got > > %%%%%%%%%%%%%%%% example 1 %%%%%%%%%%%%%%%%% > > #p ccsd/gen geom=coord density=current units=au nosymm scfcon=10 > . > . > . > Population analysis using the QCI/CC density. > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > %%%%%%%%%%%%%%%% example 2 %%%%%%%%%%%%%%%%% > #p ccsd/gen geom=coord density=cc units=au nosymm scfcon=10 > . > . > . > Population analysis using the QCI/CC density. > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > Regards > Demetrios > > > > Customer Service - Jim wrote: > >> Dear Dr. Xenides, >> On can calculate the CCSD density, but not during a CCSD(T) >> calculation. You'll have to use "CCSD Density=CC" to get the CCSD >> density. >> >> Regards, >> Jim Hess >> >> +++++++++++++++++++++++++ >> James Hess, Ph.D. >> Customer Support Scientist >> Gaussian, Inc. >> e-mail: help<>gaussian.com >> +++++++++++++++++++++++++ >> >> On Apr 6, 2005, at 5:57 AM, Demetrios Xenides wrote: >> >>> Below is the result of your feedback form. It was submitted by >>> Demetrios Xenides (Demetrios.Xenides<>uibk.ac.at) on Wednesday, April >>> 06, 2005 at 05:57:51 >>> --------------------------------------------------------------------- >>> -- >>> ---- >>> >>> >>> email: Demetrios.Xenides=at=uibk.ac.at >>> >>> realname: Demetrios Xenides >>> >>> org: University of Innsbruck >>> >>> fax: none >>> >>> gver: G03 >>> >>> grev: c02 >>> >>> os: SGI64 >>> >>> osver: IRIX 6.5.16m >>> >>> proc: MIPS R14000 >>> >>> message: I am trying to run a job with the folloing command line >>> #p ccsd-t/gen geom=coord density=ccsd units=au nosymm scfcon=10 >>> >>> and I get the message >>> >>> Last state="Den1" >>> TCursr=34585 LCursr= 33 >>> >>> If I am not wrong in G03 you can calculate the density at the CCSD >>> level of theory. Am I missing something? >>> Regards, >>> Demetrios Xenides >>> >> >> > From chemistry-request@ccl.net Wed Apr 6 17:47:54 2005 Received: from pickering.cc.nd.edu (pickering.cc.nd.edu [129.74.250.225]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j36LlkPk027148 for ; Wed, 6 Apr 2005 17:47:50 -0400 Received: from vegeta (vegeta.chem.nd.edu [129.74.80.114]) (authenticated bits=0) by pickering.cc.nd.edu (Switch-3.1.7/Switch-3.1.7) with ESMTP id j36LlMgh008100 (version=TLSv1/SSLv3 cipher=RC4-MD5 bits=128 verify=NO); Wed, 6 Apr 2005 16:47:23 -0500 (EST) Message-Id: <200504062147.j36LlMgh008100=at=pickering.cc.nd.edu> From: "Chris Harrison" To: "'Attila, , Borics'" , Subject: RE: W:Solvation models in Gaussian 03 Date: Wed, 6 Apr 2005 16:47:22 -0500 MIME-Version: 1.0 Content-Type: text/plain; charset="US-ASCII" Content-Transfer-Encoding: 7bit X-Mailer: Microsoft Office Outlook, Build 11.0.6353 In-Reply-To: <200504051907.j35J7tk8024956=at=server.ccl.net> X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2900.2180 Thread-Index: AcU6Ke3xb0icXfjpS06XLCAhz9fc1gAxnvYg X-ND-MTA-Date: Wed, 06 Apr 2005 16:47:25 -0500 (EST) X-ND-Virus-Scan: engine v4.3.20; dat v4463 X-Spam-Status: No, score=0.0 required=5.0 tests=none autolearn=failed version=3.0.1 X-Spam-Checker-Version: SpamAssassin 3.0.1 (2004-10-22) on server.ccl.net Attila, I have experienced similar errors with g03 SCRF (PCM & CPCM, HOH & ether) optimizations using B3LYP/3-21G* thru B3LYP/6-311++G(3df,2d), however, only with systems containing more than one molecule. I assumed it might be related to a poor description of electron density between the separate molecules and inability to resolve the constructed tessarae/spheres with that density. As were your results, my gas phase results seem more consistent with experiment than the optimized solvated structures that didn't crash. I too would be very interested in an explanation and solution. Chris Harrison charris5=at=nd.edu Wiest Lab Dept Chem & Biochemistry Univ Notre Dame Notre Dame, IN 46556 > I do geometry optimizations on ~60 atom systems using B3LYP and B3PW91 > hybrid > functionals on the 6-31G* basis set. I do gas phase optimizations without > any problem, but when it comes to SCRF solvation (DMSO, CDCl3, etc.), my > jobs often crash, with error messages like: > > AdVTs1: ISph= 830 is engulfed by JSph= 831 but Ae( 830) is not yet > zero! > Error termination via Lnk1e in /usr/local//g03/l301.exe at Sun Feb 27 > 01:15:48 2005. > > or > > BldSpC: Error generating genealogic tree for sphere 894 at level 15 > Error termination via Lnk1e in /usr/local//g03/l301.exe at Sat Feb 26 > 09:50:34 2005. > > I believe this is related to the solvation model. > Another interesting feature of these solvated optimizations is that when > it completed without error it resulted in almost identical final structure > as in gas phase (with identical initial structures), which is, however, > possible but unlikely considering a 4 residue peptide. Frequency > calculations, howewer, on the almost superimposable output structures > revealed major differences, not only in frequencies, but IR intensities > and rotational strengths. Interestingly, gas phase calculations reproduced > experimental results better, than optimizations utilizing the SCRF method. > > So, my question is how good or reliable is this SCRF method incorporated > in G03? Is there any reliable solvation model within G03? What do you > suggest? > Thank You > > > Attila Borics > > > > -= 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 is mail bouncing from ccl.net domain due to spam filters, please > use the Web based form from CCL Home Page > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > From chemistry-request@ccl.net Wed Apr 6 21:19:17 2005 Received: from f05n15.cac.psu.edu (phpdb.aset.psu.edu [128.118.141.100]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j371JAhn003180 for ; Wed, 6 Apr 2005 21:19:11 -0400 Received: from 192.168.1.102 (69-162-2-232.stcgpa.adelphia.net [69.162.2.232]) by f05n15.cac.psu.edu (8.13.2/8.13.2) with ESMTP id j370BxeJ132256; Wed, 6 Apr 2005 20:11:59 -0400 Subject: Re: CCL:fingerprint generation software From: Rajarshi Guha Reply-To: rxg218_at_psu.edu To: Lei Wang Cc: chemistry_at_ccl.net In-Reply-To: References: Content-Type: text/plain Date: Wed, 06 Apr 2005 20:11:59 -0400 Message-Id: <1112832719.3743.11.camel_at_localhost.localdomain> Mime-Version: 1.0 X-Mailer: Evolution 2.0.2 (2.0.2-3) Content-Transfer-Encoding: 7bit X-Virus-Scanned: by amavisd-new X-Spam-Status: No, score=0.6 required=5.0 tests=FORGED_RCVD_HELO, FROM_ENDS_IN_NUMS autolearn=no version=3.0.1 X-Spam-Checker-Version: SpamAssassin 3.0.1 (2004-10-22) on server.ccl.net On Wed, 2005-04-06 at 12:06 -0400, Lei Wang wrote: > I want to generate finger-prints for my chemical database. and want > to use such info to do sub-structure or similarity search. What > software could I use? The CDK (http://cdk.sourceforge.net) will calculate fingerprints. ------------------------------------------------------------------- Rajarshi Guha GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04 06F7 1BB9 E634 9B87 56EE ------------------------------------------------------------------- All seems condemned in the long run to approximate a state akin to Gaussian noise. -- James Martin