From chemistry-request@ccl.net Sun Apr 24 23:21:41 2005 Received: from server.ccl.net (ccl [127.0.0.1]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j3P3Le0X002725 for ; Sun, 24 Apr 2005 23:21:40 -0400 Received: (from apache@localhost) by server.ccl.net (8.13.1/8.13.1/Submit) id j3P3Le7t002724 for chemistry!at!ccl.net; Sun, 24 Apr 2005 23:21:40 -0400 Date: Sun, 24 Apr 2005 23:21:40 -0400 Message-Id: <200504250321.j3P3Le7t002724!at!server.ccl.net> X-Authentication-Warning: server.ccl.net: apache set sender to chemistry-request!at!ccl.net using -f From: "Xi, , Chen" To: chemistry!at!ccl.net X-Web-Message-Number: 050424231818-2589 Subject: W:Seeking for methods for geometry optimization in solution X-Spam-Status: No, score=-2.8 required=5.0 tests=ALL_TRUSTED autolearn=failed version=3.0.1 X-Spam-Checker-Version: SpamAssassin 3.0.1 (2004-10-22) on server.ccl.net Hi, everyone I just encountered a diffcult problem which has to optimize the geometry of a organic anion molecules in aqueous solution. I've tested Gaussian03 and found the optimization can not get converged at all. Could you recommend a method or program to finish the job? Thank you. From chemistry-request@ccl.net Sun Apr 24 21:26:14 2005 Received: from relay00.uchicago.edu (relay00.uchicago.edu [128.135.12.75]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j3P1Q7rC030648 for ; Sun, 24 Apr 2005 21:26:07 -0400 Received: from uchicago.edu (bersuit.uchicago.edu [128.135.160.212]) by relay00.uchicago.edu (8.12.10/8.12.9) with ESMTP id j3P1Q64m020440; Sun, 24 Apr 2005 20:26:06 -0500 (CDT) Message-ID: <426C4723.2090608!at!uchicago.edu> Date: Sun, 24 Apr 2005 20:25:55 -0500 From: Andres Colubri User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.6) Gecko/20040115 X-Accept-Language: en-us, en MIME-Version: 1.0 To: forli!at!unisi.it CC: h.rzepa!at!imperial.ac.uk, chemistry!at!ccl.net Subject: Re: CCL:Molecule coordinates to .3ds, .dxf or .cad files References: <01LNECYIORSY91W3U5!at!mailsrv.unisi.it> In-Reply-To: <01LNECYIORSY91W3U5!at!mailsrv.unisi.it> Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit 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 You can use blender (an open source 3D modelling and animation tool): http://www.blender3d.org/cms/Home.2.0.html to import a VRML file and then to export it as DXF. Andres forli!at!unisi.it wrote: >There are different ways to make conversion. >You can do a PDB->VRML conversion using RasMol or other softwares, and >then VRML->3ds/dxf. >Depending on what chemical tool you use make first conversion, you can >get ribbons, cartoons, CPK and so on... >Second step will be the most difficult, I think, because at my knowledge >there are no free tools to do that. > >Here you can find few links: >http://www.pc.chemie.tu-darmstadt.de/research/vrml/pdb2vrml_right.shtml >http://www.sienahts.edu/~che/vrmlchem.html > >http://www.okino.com/conv/imp_pdb.htm Shareware tool to convert directly >PDB->3ds/dxf (some limiatations) > >If you find some free stuff to do everithing, please let me know. > >ciao, > >Stefano > > > >p.s. ...and you can post some snapshots of final product :) > > >--- > >*********************************** > Stefano Forli > Dip. Farmaco Chimico Tecnologico > Universita' degli Studi di Siena > Via Aldo Moro > I-53100 Siena, Italy > Phone: ++39 0577 234307 > Fax: ++39 0577 234333 > e-mail: forli!at!unisi.it >*********************************** > > >-= 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 Mon Apr 25 04:14:34 2005 Received: from ozone.few.vu.nl (ozone.few.vu.nl [130.37.20.6]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j3P8EQ4t015711 for ; Mon, 25 Apr 2005 04:14:27 -0400 Received: from [130.37.144.98] (europium.chem.vu.nl [130.37.144.98]) by ozone.few.vu.nl with esmtp (Smail #108) id m1DPxVi-00003UC; Mon, 25 Apr 2005 08:56 +0200 In-Reply-To: <200504250321.j3P3Le7t002724 +*+ server.ccl.net> References: <200504250321.j3P3Le7t002724 +*+ server.ccl.net> Mime-Version: 1.0 (Apple Message framework v622) Content-Type: multipart/alternative; boundary=Apple-Mail-1-813491636 Message-Id: <9ef72c9910eb2096461ef9451cabbbac +*+ few.vu.nl> Cc: CHEMISTRY +*+ ccl.net From: Marcel Swart Subject: Re: CCL:W:Seeking for methods for geometry optimization in solution Date: Mon, 25 Apr 2005 08:56:01 +0200 To: "Xi, , Chen" X-Mailer: Apple Mail (2.622) 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 --Apple-Mail-1-813491636 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=WINDOWS-1252; delsp=yes; format=flowed How do you treat the solution ? By a continuum model ? Then you should try ADF, which has COSMO as solvation model, and which in my experience converges the geometry of organic anions in aqueous solution perfectly; see J. Org. Chem. 70 (2005) 3542-3553 On Apr 25, 2005, at 5:21 AM, Xi, , Chen wrote: > Hi, everyone > I just encountered a diffcult problem which has to > optimize the geometry of a organic anion molecules in > aqueous solution. I've tested Gaussian03 and found the > optimization can not get converged at all. Could you > recommend a method or program to finish the job? Thank > you. > > > > -=3D This is automatically added to each message by the mailing script = =3D- > To send e-mail to subscribers of CCL put the string CCL: on your =20 > Subject: line > and send your message to: CHEMISTRY +*+ ccl.net > > Send your subscription/unsubscription requests to: =20 > CHEMISTRY-REQUEST +*+ 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, =20 > please > use the Web based form from CCL Home Page > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-=20= > +-+ > > > > > > =96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96= =96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96 dr. Marcel Swart Theoretische Chemie Vrije Universiteit Amsterdam Faculteit der Exacte Wetenschappen De Boelelaan 1083 1081 HV Amsterdam The Netherlands Tel +31-(0)20-5987619 Fax +31-(0)20-5987629 E-mail m.swart +*+ few.vu.nl Web http://www.few.vu.nl/~swart =96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96= =96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96 --Apple-Mail-1-813491636 Content-Transfer-Encoding: quoted-printable Content-Type: text/enriched; charset=WINDOWS-1252 How do you treat the solution ? By a continuum model ? Then you should try ADF, which has COSMO as solvation model, and which in my experience converges the geometry of organic anions in aqueous solution perfectly; see J. Org. Chem. 70 (2005) 3542-3553 On Apr 25, 2005, at 5:21 AM, Xi, , Chen wrote: Hi, everyone I just encountered a diffcult problem which has to optimize the geometry of a organic anion molecules in aqueous solution. I've tested Gaussian03 and found the optimization can not get converged at all. Could you recommend a method or program to finish the job? Thank you. -=3D This is automatically added to each message by the mailing script = =3D- To send e-mail to subscribers of CCL put the string CCL: on your Subject: line and send your message to: CHEMISTRY +*+ ccl.net Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST +*+ ccl.net=20 HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs=20 If your is mail bouncing from ccl.net domain due to spam filters, please use the Web based form from CCL Home Page=20 -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ = Helvetica=96=96=96=96=96= =96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96= =96=96=96=96=96=96=96=96=96=96=96=96=96=96 = Papyrusdr. Marcel Swart = Papyrus = OsakaTheoretische Chemie Vrije Universiteit Amsterdam Faculteit der Exacte Wetenschappen De Boelelaan 1083 1081 HV Amsterdam The Netherlands Tel +31-(0)20-5987619 Fax +31-(0)20-5987629 E-mail m.swart +*+ few.vu.nl Web http://www.few.vu.nl/~swart = Helvetica=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96= =96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96 --Apple-Mail-1-813491636-- From chemistry-request@ccl.net Mon Apr 25 07:50:20 2005 Received: from distrib3.mail.u-psud.fr (distrib3.mail.u-psud.fr [129.175.34.155]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j3PBoBrH025623 for ; Mon, 25 Apr 2005 07:50:12 -0400 Received: from intfiltre3.mail.u-psud.fr (intfiltre3.mail.u-psud.fr [129.175.34.151]) by distrib3.mail.u-psud.fr (8.12.10/8.12.0.Beta10) with ESMTP id j3P8V4mP016487 for ; Mon, 25 Apr 2005 10:31:04 +0200 Received: from post1.mail.u-psud.fr (post1.mail.u-psud.fr [129.175.34.87]) by intfiltre3.mail.u-psud.fr (8.12.10/8.12.0.Beta10) with ESMTP id j3P8SkaC014216 for ; Mon, 25 Apr 2005 10:30:50 +0200 Received: from ext.lcp.u-psud.fr (ext.lcp.u-psud.fr [129.175.100.5]) by post1.mail.u-psud.fr (8.12.10/8.12.0.Beta10) with ESMTP id j3P8Qnhx032523 for ; Mon, 25 Apr 2005 10:26:53 +0200 Received: from lcp.u-psud.fr (pc7.lcp.u-psud.fr [129.175.101.37]) by ext.lcp.u-psud.fr (8.13.1/8.13.1) with ESMTP id j3P8QpwB012673 for ; Mon, 25 Apr 2005 10:26:52 +0200 Message-ID: <426CA9CB.6080404 %x% lcp.u-psud.fr> Date: Mon, 25 Apr 2005 10:26:51 +0200 From: Pierre Archirel User-Agent: Mozilla/5.0 (X11; U; Linux i686; fr; rv:1.4.1) Gecko/20031114 X-Accept-Language: fr, en MIME-Version: 1.0 To: CHEMISTRY %x% ccl.net Subject: CCL: PCM optimisation with G03 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 8bit X-Scanned: by amavis 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 Dear collegue, The B version of Gaussian 03 has a bug in the energy gradients of the PCM method, if core pseudo potentials are used, with d components and higher. This bug is fixed in the C version. This implies that the B version cannot optimise geometries of molecules in solution, if they contain heavy metals and if you absolutely need a core pseudo for them. Is it your case? Bes wishes, PA. __________________________________________________________ Pierre Archirel Groupe de Chimie Thiorique Laboratoire de Chimie Physique Tel: 01 69 15 63 86 Bat 349 Fax: 01 69 15 61 88 91405 Orsay Cedex France pierre.archirel %x% lcp.u-psud.fr __________________________________________________________ From chemistry-request@ccl.net Sun Apr 24 10:38:52 2005 Date: Sun, 24 Apr 2005 18:02:34 +0530 (IST) Message-ID: <59553.10.103.1.1.1114345954.squirrel (a) www.chem.iitb.ac.in> Subject: CCL: Re: Help to obtain orbital diagram using CACAO From: "Raji Stephen" To: "Tamas E. Gunda" Cc: "Raji Stephen" , chemistry (a) ccl.net Thank you very much for responding to my query. I had given only some part of our molecule just to show how our input file look like. The molecule is a bigger one. We would like to get an orbital diagram like the one I attached here. It is also found that when I put coordinate values from Gaussian log output as the input for CACAO, I am getting very higher difference in MO energy values between those software outputs. Hope you can help us in this regard. With regards, Raji Stephen > The molecule contains less hydrogens than necessary. Is it surely correct? > > > Dr. Tamas E. Gunda > Dept. of Pharmaceutical Chemistry > University of Debrecen > POBox 36 > H-4010 Debrecen, Hungary > > tgunda (AT) puma.unideb.hu > *********************************************************** / Junior Research Fellow / / Organometallic Synthesis and Homogeneous Catalysis Lab / / Dept. of Chemistry / / IIT Bombay 400076 / / URL: http://www.chem.iitb.ac.in/~pghosh/RS.htm / / Tel. No:(Lab) 022-25764129 / / (Mbl) 9820078895 / *********************************************************** From chemistry-request@ccl.net Mon Apr 25 12:41:28 2005 Received: from hal.ahpcrc.org (hal.ahpcrc.org [144.34.2.1]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j3PGfN6G009771 for < ccl.net>; Mon, 25 Apr 2005 12:41:24 -0400 Received: from localhost (localhost [127.0.0.1]) by hal.ahpcrc.org (Postfix) with ESMTP id BF331E4F6 for < ccl.net>; Mon, 25 Apr 2005 10:39:35 -0500 (CDT) Received: from hal.ahpcrc.org ([127.0.0.1]) by localhost (hal.ahpcrc.org [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id 14367-10 for < ccl.net>; Mon, 25 Apr 2005 10:39:35 -0500 (CDT) Received: from [144.34.131.150] (ace501.famu.ahpcrc.org [144.34.131.150]) by hal.ahpcrc.org (Postfix) with ESMTP id 74CCCE4F1 for < ccl.net>; Mon, 25 Apr 2005 10:39:35 -0500 (CDT) Message-ID: <426D0F37.4030008 >< ahpcrc.org> Date: Mon, 25 Apr 2005 10:39:35 -0500 From: Genzo Tanaka < ahpcrc.org> User-Agent: Mozilla Thunderbird 1.0.2 (Macintosh/20050317) X-Accept-Language: en-us, en MIME-Version: 1.0 To: chemistry >< ccl.net Subject: coordinates output Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit X-Virus-Scanned: by amavisd-new-20030616-p10 (Debian) at hal.ahpcrc.org 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, Could you advise me how to get a coordinate set (cartesian or Z-matrix) for a relaxed PES scan? Gaussian 98 prints optimized parameters after a stationary point is found, but I want to extract an optimized structure at each point. Thanks, Genzo ----------------------------------------------------------------------- This message (including any attachments) may contain proprietary or privileged information, the use and disclosure of which is legally restricted. If you have received this message in error please notify the sender by reply message, do not otherwise distribute it, and delete this message, with all of its contents, from your files. ----------------------------------------------------------------------- From chemistry-request@ccl.net Mon Apr 25 11:13:02 2005 Received: from server.ccl.net (ccl [127.0.0.1]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j3PFD1v9004390 for < ccl.net>; Mon, 25 Apr 2005 11:13:01 -0400 Received: (from apache@localhost) by server.ccl.net (8.13.1/8.13.1/Submit) id j3PFD1ab004389 for chemistry >< ccl.net; Mon, 25 Apr 2005 11:13:01 -0400 Date: Mon, 25 Apr 2005 11:13:01 -0400 Message-Id: <200504251513.j3PFD1ab004389 >< server.ccl.net> X-Authentication-Warning: server.ccl.net: apache set sender to chemistry-request >< ccl.net using -f From: "Paul, , Momoh" < vcu.edu> To: chemistry >< ccl.net X-Web-Message-Number: 050425110411-3507 Subject: W:Viewing IRC calculation X-Spam-Status: No, score=-2.8 required=5.0 tests=ALL_TRUSTED autolearn=failed version=3.0.1 X-Spam-Checker-Version: SpamAssassin 3.0.1 (2004-10-22) on server.ccl.net Good morning, Is anybody familiar with a program (other than gaussview) for viewing IRC calculations-a program I can download over the WWW. Thanks Paul Momoh momohpo >< vcu.edu From chemistry-request@ccl.net Mon Apr 25 15:44:15 2005 Received: from webshield-01.med.umich.edu (host-16.subnet-17.med.umich.edu [141.214.17.16]) by server.ccl.net (8.13.1/8.13.1) with SMTP id j3PJiBeL018230 for ; Mon, 25 Apr 2005 15:44:11 -0400 Received: from (141.214.93.150) by webshield-01.med.umich.edu via smtp id 2b54_b83a1064_b594_11d9_87e7_0002b3c90089; Mon, 25 Apr 2005 10:17:13 -0400 (EDT) Received: from gwia-02-MTA by med-gwia-02a.med.umich.edu with Novell_GroupWise; Mon, 25 Apr 2005 10:02:11 -0400 Message-Id: X-Mailer: Novell GroupWise Internet Agent 6.5.2 Date: Mon, 25 Apr 2005 10:01:54 -0400 From: "Renxiao Wang" To: Subject: The PDBbind database version 2003 is being released Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Disposition: inline X-NAIMIME-Disclaimer: 1 X-NAIMIME-Modified: 1 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 Dear researchers, We would like to announce the release of an update to the PDBbind database, i.e. version 2003. The PDBbind database, publicly accessible at http://www.pdbbind.org/, is constructed to provide a collection of binding affinity data for the protein-ligand complexes in the Protein Data Bank (PDB). This updated version has binding affinity data (Kd, Ki, & IC50) for over 1,700 protein-ligand complexes released by PDB before 01/01/2004. Its "refined set", which is compiled particularly for docking/scoring studies, has a total of 900 protein-ligand complexes. The PDBbind database is developed in Dr. Shaomeng Wang's group at the University of Michigan. All of the current enrolled users may still access this database through their existing accounts. Other researchers who are interested in this database are welcome to explore it through a demo account on our web site. This version has not been released until now mainly due to the delay in paper preparation/reviewing. Our plan is to update this database annualy to keep up with the growth of PDB, and we are working very hard on version 2004 right now. We expect to release version 2004 later this year. Best regards, Renxiao -------------------------------------------------------------------------------------------------- Renxiao Wang, Ph.D. Research Investigator Department of Internal Medicine, Hematology/Oncology Division University of Michigan Medical School Ann Arbor, MI 48109, U.S.A. Tel: (734) 764-2449; Fax: (734) 764-2532 E-mail: renxiao = = = med.umich.edu Web: http://sw8.im.med.umich.edu/~arthur/ -------------------------------------------------------------------------------------------------- ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues. From chemistry-request@ccl.net Mon Apr 25 11:35:17 2005 Received: from webshield-01.med.umich.edu (host-16.subnet-17.med.umich.edu [141.214.17.16]) by server.ccl.net (8.13.1/8.13.1) with SMTP id j3PFZBhJ005790 for ; Mon, 25 Apr 2005 11:35:11 -0400 Received: from (141.214.93.150) by webshield-01.med.umich.edu via smtp id 6c6c_dd9a68ce_b2d6_11d9_886b_0002b3c90089; Thu, 21 Apr 2005 22:33:09 -0400 (EDT) Received: from gwia-02-MTA by med-gwia-02a.med.umich.edu with Novell_GroupWise; Thu, 21 Apr 2005 22:18:33 -0400 Message-Id: X-Mailer: Novell GroupWise Internet Agent 6.5.2 Date: Thu, 21 Apr 2005 22:18:22 -0400 From: "Renxiao Wang" To: Subject: The PDBbind database (version 2003) is being released Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Disposition: inline X-NAIMIME-Disclaimer: 1 X-NAIMIME-Modified: 1 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 Dear researchers, We would like to announce the release of an update to the PDBbind database, i.e. version 2003. The PDBbind database, publicly accessible at http://www.pdbbind.org/, is constructed to provide a collection of binding affinity data for the protein-ligand complexes in the Protein Data Bank (PDB). This updated version has binding affinity data (Kd, Ki, & IC50) for over 1,700 protein-ligand complexes released by PDB before 01/01/2004. Its "refined set", which is compiled particularly for docking/scoring studies, has a total of 900 protein-ligand complexes. The PDBbind database is developed in Dr. Shaomeng Wang's group at the University of Michigan. All of the current enrolled users may still access this database through their existing accounts. Other researchers who are interested in this database are welcome to explore it through a demo account on our web site. This version has not been released until now mainly due to the delay in paper preparation/reviewing. Our plan is to update this database annualy to keep up with the growth of PDB, and we are working very hard on version 2004 right now. We expect to release version 2004 later this year. Best regards, Renxiao Wang -------------------------------------------------------------------------------------------------- Renxiao Wang, Ph.D. Research Investigator Department of Internal Medicine, Hematology/Oncology Division University of Michigan Medical School Ann Arbor, MI 48109, U.S.A. Tel: (734) 764-2449; Fax: (734) 764-2532 E-mail: renxiao = = = med.umich.edu Web: http://sw8.im.med.umich.edu/~arthur/ -------------------------------------------------------------------------------------------------- ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.