From chemistry-request@ccl.net Tue Dec 14 09:59:10 2004 Received: from up.univ-mrs.fr (mailup.univ-mrs.fr [147.94.113.16]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id iBEEx9hd004553 for ; Tue, 14 Dec 2004 09:59:09 -0500 Received: from localhost (localhost [127.0.0.1]) by up.univ-mrs.fr (Postfix) with ESMTP id CCC941E8E4D; Tue, 14 Dec 2004 16:14:45 +0100 (CET) Received: from up.univ-mrs.fr ([127.0.0.1]) by localhost (mailup.univ-mrs.fr [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id 232948-06; Tue, 14 Dec 2004 16:14:45 +0100 (CET) Received: from [147.94.185.160] (unknown [147.94.185.160]) by up.univ-mrs.fr (Postfix) with ESMTP id 05B4A1CB498; Tue, 14 Dec 2004 16:14:45 +0100 (CET) Message-ID: <41BF0367.5020604(at)up.univ-mrs.fr> Date: Tue, 14 Dec 2004 16:14:47 +0100 From: =?ISO-8859-1?Q?Nicolas_Ferr=E9?= Organization: LCTMM User-Agent: Mozilla/5.0 (X11; U; Linux i686; fr-FR; rv:1.7.2) Gecko/20040804 X-Accept-Language: fr-fr, en-us, en MIME-Version: 1.0 To: help(at)gaussian.com Cc: CCL posting Subject: Gaussian03: MP2 before CI or CC X-Enigmail-Version: 0.85.0.0 X-Enigmail-Supports: pgp-inline, pgp-mime Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit X-Virus-Scanned: by amavisd-new at up.univ-mrs.fr X-Spam-Status: No, hits=4.0 required=7.5 tests=NO_RDNS,NO_RDNS2,RM_ft_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 Dear all, When you run a CI or CC job with g03, it starts by resolving the HF equations. In the next step, the integrals are expressed over MOs and then the first-order MP wavefunction (and the second-order MP energy) are computed, all of this done in the link 804. Finally, g03 uses these informations for the CI or CC job in the link 913. I would like to find references about this procedure. I guess it is related to the Davidson scheme for diagonalizing the CI matrix. But why always using the MP wavefunction instead of the HF one ? Is there an option in g03 for using the HF wavefunction ? What is more surprising is that the CI or CC energy depends on the MO eigenvalues ! I just slightly modified the code in link 801 for changing one eigenvalue (rwf 547) and the final CI or CC energy varies with this eigenvalue ! I checked the same behavior on different machines. Can someone explain what is happening ? I guess I am missing something but I cannot find what. -- Dr. Nicolas Ferre' Laboratoire de Chimie Theorique et de Modelisation Moleculaire UMR 6517 - CNRS Universite' de Provence Case 521 - Faculte' de Saint-Jerome Av. Esc. Normandie Niemen 13397 MARSEILLE Cedex 20 (FRANCE) Tel : (+33)4.91.28.27.33 Fax : (+33)4.91.28.87.58 Please avoid sending me Word or PowerPoint attachments. See http://www.gnu.org/philosophy/no-word-attachments.html From chemistry-request@ccl.net Tue Dec 14 16:37:28 2004 Received: from nrcmrdbh1.imsb.nrc.ca (nrcmrdbh1.imsb.nrc.ca [132.246.56.30]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id iBELbRFO009140 for ; Tue, 14 Dec 2004 16:37:27 -0500 Received: by nrcmrdbh1.imsb.nrc.ca with Internet Mail Service (5.5.2657.72) id ; Tue, 14 Dec 2004 16:53:05 -0500 Message-ID: From: "Drabik, Piotr" To: "'chemistry(at)ccl.net'" Subject: software for supramolecule building and optimization Date: Tue, 14 Dec 2004 16:53:01 -0500 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2657.72) Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01C4E221.AA1E5B3A" X-Spam-Status: No, hits=1.0 required=7.5 tests=HTML_20_30,HTML_MESSAGE autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net This message is in MIME format. Since your mail reader does not understand this format, some or all of this message may not be legible. ------_=_NextPart_001_01C4E221.AA1E5B3A Content-Type: text/plain Dear CCL'ers, does anyone have any suggestions of a code able to: (a) build a supramolecule; say, a nanotube or multimeric protein (given the structure of monomer and symmetry data) and (b) optimize/relax it with a solvation model (including explicit or implicit counterions)? list of pros and cons (open source/commercial; GUI; ease of building a supramolecular object; robustness of electrostatics treatment, etc.) and users' opinions & experiences independent of companies' claims would be appreciated. thanks, piotr ------_=_NextPart_001_01C4E221.AA1E5B3A Content-Type: text/html Content-Transfer-Encoding: quoted-printable software for supramolecule building and optimization

Dear CCL'ers,

does anyone have any suggestions of a code able = to:

(a) build a supramolecule; say, a nanotube or = multimeric protein (given the structure of monomer and symmetry data) = and
(b) optimize/relax it with a solvation model = (including explicit or implicit counterions)?

list of pros and cons (open source/commercial; GUI; = ease of building a supramolecular object; robustness of electrostatics = treatment, etc.) and users' opinions & experiences independent of = companies' claims would be appreciated.

thanks,
piotr

------_=_NextPart_001_01C4E221.AA1E5B3A-- From chemistry-request@ccl.net Tue Dec 14 15:07:27 2004 Received: from calmail-be1.berkeley.edu (mailfarm.Berkeley.EDU [128.32.61.106]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id iBEK7N6b004431 for ; Tue, 14 Dec 2004 15:07:23 -0500 Received: from [128.32.246.98] (account jayaeg(at)calmail.berkeley.edu) by calmail-be1.berkeley.edu (CommuniGate Pro WebUser 4.1.8) with HTTP id 3922350 for chemistry(at)ccl.net; Tue, 14 Dec 2004 12:23:01 -0800 From: "Jayasree Elambalassery" Subject: NTRerr called from fileIO:gaussian To: chemistry(at)ccl.net X-Mailer: CommuniGate Pro WebUser Interface v.4.1.8 Date: Tue, 14 Dec 2004 12:23:01 -0800 Message-ID: MIME-Version: 1.0 Content-Type: text/plain; charset="ISO-8859-1"; format="flowed" Content-Transfer-Encoding: 8bit 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 Dear CCL users, I have seen the same questions in CCL, but the replies were missing. Now I am facing these problems. I would really appreciate if you help me out though this has been asked many times. I am doing an MP2(full) transition state optimization and it ends with the following error ********* Illegal file or unit passed to FileIO.FileIO: IOper= 1 IFilNo(1)= 0 Len= 1050624 IPos= 0 Q= 1343154312 dumping /fiocom/, unit = 1 NFiles = -------------- ---------------------- Error termination in NtrErr: NtrErr Called from FileIO. *********************** In another optimization at ccsd(t) level using aug-cc-pvdz, I got an error Semi-Direct transformation. Attempt to create subfile not contained in parent. FileIO: IOper= 4 IFilNo(1)= 201 Len= 1585675872 IPos= 0 Q= -1073750520 dumping /fiocom/, unit = 1 NFiles = 7------------ ------------------- Error termination in NtrErr: NtrErr Called from FileIO. **************************************************** I have tried increasing the maxdisk and memory. But it didn't help. Can you suggest me something to solve this problem? Thank you very much Jayasree Elambalassery University of California Berkeley. From chemistry-request@ccl.net Tue Dec 14 17:41:16 2004 Received: from pickering.cc.nd.edu (pickering.cc.nd.edu [129.74.250.225]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id iBEMfDFO012897 for ; Tue, 14 Dec 2004 17:41:13 -0500 Received: from localhost (localhost [127.0.0.1]) by pickering.cc.nd.edu (Switch-3.1.7/Switch-3.1.7) with ESMTP id iBEMup4d008675; Tue, 14 Dec 2004 17:56:51 -0500 (EST) Received: from laptop.ccl.net (laptop.ccl.net [129.74.52.62]) by webmail.nd.edu (IMP) with HTTP for ; Tue, 14 Dec 2004 17:56:50 -0500 Message-ID: <1103065010.41bf6fb2ea6f3-.at.-webmail.nd.edu> Date: Tue, 14 Dec 2004 17:56:50 -0500 From: Jan K Labanowski To: chemistry-.at.-ccl.net Cc: rbross-.at.-mmm.com, jlabanow-.at.-nd.edu Subject: Champions of 2nd Industrial Fluid Properties Simulation Challenge MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit User-Agent: Internet Messaging Program (IMP) 3.2.6 X-Originating-IP: 129.74.52.62 X-ND-MTA-Date: Tue, 14 Dec 2004 17:56:52 -0500 (EST) X-ND-Virus-Scan: engine v4.3.20; dat v4414 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 Dear Colleagues, The 2nd Industrial Fluid Properties Simulation Challenge has now been completed and the champions have been determined. Awards were presented in a special session at the Fall National AIChE meeting in Austin in November. Could you please find all the details in the attached Press Release. In behalf of the NIST and Industrial organizing committee, I would like to thank all who participated in this effort to further the development of simulation methods to predict industrially relevant properties. With kindest regards, Rick Ross 3M Company rbross-.at.-mmm.com ===================================================== CHAMPIONS ANNOUNCED IN THE SECOND INDUSTRIAL FLUID PROPERTIES SIMULATION CHALLENGE FOR IMMEDIATE RELEASE Contact: Fiona Case Phone: (802) 879-3684 Email: Fiona-.at.-casescientific.com Scientists and engineers from 3M, BP, Dow Chemical, DuPont, ExxonMobil, Mitsubishi Chemical, and NIST challenged the molecular modeling community to predict physical properties of industrially relevant fluid systems. Contest entrants presented their work, the champions were announced, and prizes awarded, during a special session at the AIChE Annual Meeting in Austin, TX. November 7, 2004 Academic groups, research laboratories, and scientific software companies from around the world were given just over a year to develop methods for predicting vapor pressures and heats of vaporization, gas solubility, and enthalpies of mixing for materials specified by the contest committee. Working in secret, scientists at NIST and Dow Chemical obtained accurate experimental measurements of these properties, which were used to judge the predictions made by the contest entrants. "The organizing committee managed to raise interest from around the globe," commented Philippe Ungerer, Institut Frangais du Pitrole (IFP), France, whose team won the overall "best in show" prize. "There were entries from almost every continent, including China, Japan, and from three countries in Europe," he observed. This second Industrial Fluid Properties Simulation Challenge, which was organized in conjunction with both the American Institute of Chemical Engineers (AIChE) Computational Molecular Science and Engineering Forum, and the Theoretical Subdivision of the American Chemical Society (ACS) Physical Chemistry Division, was held to obtain an in-depth and objective assessment of current capabilities for the prediction of fluid properties, and to promote the use of molecular modeling in this area. Molecular simulation has been identified as a promising technology for predicting materials properties in the Vision 2020 Roadmap for the Chemical Industry. The problems were closely focused on properties that are industrially relevant. There were three sections. The first section challenged entrants to predict vapor pressures and heats of vaporization for two different materials. "The heat of vaporization is an important property in the design of heat exchangers and other chemical process units," says Jim Olson of Dow Chemical, Midland, MI, USA "There are a growing number of chemicals whose vapor pressures and heats of vaporization need to be determined outside the range of ordinary apparatus. Molecular simulation could offer an attractive alternative to these difficult laboratory measurements." The second section challenged molecular modelers to predict the solubility of gases in liquids - dissolved gases are a key component of many industrial chemical processes. The last section involves the prediction of heats of mixing for an amine in both hydrocarbon oil, and in water, over a range of concentrations at different temperatures. "One of the premier challenges for modeling thermal separation processes (e.g. absorption, distillation, extraction) is the ability to describe activity coefficients over the whole concentration and temperature range with sufficient accuracy" says Martin Schiller of DuPont, Germany. "We were pleased with the level of entries this year," says Raymond Mountain, NIST, chairman of the organizing committee. "The contest provides a useful comparison between a number of different molecular modeling approaches, and some were clearly more successful than others," he noted. In the first two problem sets (the prediction of vapor pressures and heats of vaporization and the prediction of the solubility of gases in liquids) the various atomistic simulation methods did a fairly good job, and the best of the predictions were in reasonable agreement with the experimental data. The first problem set was won by Professor Richard Elliott and his students from the Department of Chemical Engineering at the University of Akron. The second problem set was won by Professor Jeffrey Errington and his students from the Department of Chemical and Biological Engineering, University of Buffalo, NY. The last section (prediction of enthalpies of mixing) was won by Professor Huai Sun and his students from the School of Chemistry and Chemical Technology at Shanghai Jiao Tong University, Shanghai, China. "This was certainly the most challenging of the problems, and we particularly appreciated the two groups that were brave enough to enter their results," commented Fiona Case, Case Scientific, a member of the IFPSC organizing committee. "The results showed that we have some way to go before atomistic simulation methods can be routinely used for predictions of miscibility, particularly for aqueous solutions." Sun's group was one of two who entered all three sections of the contest, using the same method and forcefields to predict all the different materials properties. "This is important, since it reflects the way that modeling methods are actually used in industry," commented Case. "These two groups really entered into the spirit of the contest, and it was encouraging to see them obtain reasonably good results across the different materials properties." The other group which entered all three sections was a European collaboration involving researchers from Institut Frangais du Pitrole (IFP), France; Universiti Paris-Sud, France; Universitat Rovira i Virgili, Tarragona, Spain; and the Commissariat a l'Energie Atomique in France. This group, headed by Philippe Ungerer, obtained the best overall score and was awarded the "best in show." "Normally you wouldn't see several different groups trying to predict the same physical properties," commented Anne Chaka, NIST. "But, this is important if we are to obtain an accurate assessment of the current capabilities of atomistic scale simulation." "One of the great things about this contest," commented Joe Golab, BP Chemicals "is that people were showing results that weren't particularly good. We wouldn't usually see those results, but it is important for industry to know what works and what doesn't." Further information: The entries will be published in a special edition of the journal Fluid Phase Equilibria, along with details of the evaluation of the "recommended values" for each materials property in the contest. The IFPSC web site: http://www.fluidproperties.org From chemistry-request@ccl.net Tue Dec 14 11:47:33 2004 Received: from mtaout-m.tc.umn.edu (mtaout-m.tc.umn.edu [160.94.23.21]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id iBEGlUhd019527 for ; Tue, 14 Dec 2004 11:47:32 -0500 Received: from pobox.com (abacavir.pharmacy.umn.edu [160.94.172.208] (may be forged)) by mtaout-m.tc.umn.edu with ESMTP; Tue, 14 Dec 2004 11:03:07 -0600 (CST) X-Umn-Remote-Mta: [N] abacavir.pharmacy.umn.edu [160.94.172.208] #+HF+LO+TS+AU Message-ID: <41BF1D9B.8060006[at]pobox.com> Date: Tue, 14 Dec 2004 11:06:35 -0600 From: Eric Bennett 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: Lily , chemistry[at]ccl.net Subject: Re: CCL:explicit connectivity for PDB structure in Gaussian References: <000101c4e175$c38d7f30$56cd6981@chunhui> In-Reply-To: <000101c4e175$c38d7f30$56cd6981@chunhui> Content-Type: text/plain; charset=ISO-8859-1; 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 Lily wrote: >I read a PDB structure into Gaussian and found that the bond order for >binding ligand is not right. I guess it is because the initial structure >is not good enough for proximity criteria in Gaussian. Then I wonder how >to make sure the bond order for both enzyme and substrate is right and >since it is a big system, it is hard to check manually. >I really appreciate if you could let me how to get the right >connectivity either changing parameter set up or using other package. >(Prefer free available) > >Thanks a lot, > >Lily > It appears that OpenBabel (free) will correctly assign bond orders to protein residues if you use it to convert your PDB file to mol2 format (which stores bond order information in the .mol2 file): babel -ipdb file.pdb -omol2 file.mol2 http://openbabel.sourceforge.net/ I don't use Gaussian but I presume it's smart enough to use the bond order information stored in a mol2 file. Commercial packages like Insight and Maestro can also assign protein bond orders, if you have access to either of those and don't feel like compiling OpenBabel... Maestro is nice because if it doesn't recognize a particular molecular fragment, it colors it differently from the rest of the molecule so you know to check the bond orders. But unless you are screening a large library of structures, it's best to always check your ligands manually, no matter how large they are and even if you are using a program which usually gets the bond orders right. You might be surprised at the number of ligands in the PDB that, upon close inspection (sometimes it doesn't even require close inspection!), appear to have been refined incorrectly because (a) they have obvious distortions from the expected geometry, (b) the x-ray resolution is low enough that such deviations should be assumed to be errors unless otherwise explained and (c) the authors don't bother to comment on the origin of the deviations in their paper. You'll probably want to manually inspect certain types of residues anyway, to make sure the protonation states make sense given available hydrogen bonding partners, and to correct for slip-ups like glutamines and asparagines that need to have their side chain ends flipped to make sensible h-bonds. Some commercial packages automate this task, but I would still check the active site area to make sure the results are sensible. -- Eric Bennett, Center for Drug Design, U of Minnesota