From chemistry-request@ccl.net Tue May 11 03:24:07 2004 Received: from hawk.dcu.ie (mail.dcu.ie [136.206.1.5]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i4B8O5kh013512 for ; Tue, 11 May 2004 03:24:05 -0500 Received: from [136.206.1.18] by hawk.dcu.ie with HTTP; Tue, 11 May 2004 09:26:11 +0100 Date: Tue, 11 May 2004 09:26:11 +0100 Message-ID: <406A6C3900042751.-at-.hawk.dcu.ie> In-Reply-To: <004601c4368c$8ed1c510$6401a8c0@goofy> From: "Noel O'Boyle" Subject: RE: CCL:Computing absorbtion and emission spectral band shapes To: "John McKelvey" Cc: chemistry.-at-.ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" X-Spam-Status: No, hits=1.0 required=7.5 tests=IMPRONONCABLE_1 autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id i4B8O7kh013518 Hello John, My own program (GaussSum) or another program by Gorelsky (Swizard) may help. http://gausssum.sourceforge.net http://www.stanford.edu/~gorelsky/software/swizard/ If you have any questions about my program, or would like any feature added, please let me know. Noel >-- Original Message -- >From: "John McKelvey" >To: >Subject: CCL:Computing absorbtion and emission spectral band shapes >Date: Mon, 10 May 2004 07:44:37 -0500 > > >Hello.. > >I am interested in computing UV-VIS absorbtion and emission band shapes. > I can optimize geometries in the ground and excited states and can compute >the respective vibrational frequencies and normal modes. I would like to >locate a paper or two, or even some code, that provides enough detailed information >so that the remaining steps can be coded. > >Any assistance would most appreciated. > >Best regards, > >John McKelvey > From chemistry-request@ccl.net Tue May 11 07:32:59 2004 Received: from hawk.dcu.ie (mail.dcu.ie [136.206.1.5]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i4BCWxkh024750 for ; Tue, 11 May 2004 07:32:59 -0500 Received: from [136.206.1.18] by hawk.dcu.ie with HTTP; Tue, 11 May 2004 13:35:09 +0100 Date: Tue, 11 May 2004 13:35:09 +0100 Message-ID: <406A6C390004323C/at/hawk.dcu.ie> From: "Noel O'Boyle" Subject: Hirshfeld partitioning for Gaussian To: chemistry/at/ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" X-Spam-Status: No, hits=0.0 required=7.5 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id i4BCWxkh024756 Dear CCLers, Does anyone have some code to perform Hirshfeld population analysis on Gaussian03 output? Or know where I can get it? Noel O'Boyle From chemistry-request@ccl.net Tue May 11 07:37:16 2004 Received: from mailhub1.shef.ac.uk (mailhub1.shef.ac.uk [143.167.1.9]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i4BCbFkh024891 for ; Tue, 11 May 2004 07:37:16 -0500 Received: from titania.shef.ac.uk ([143.167.3.1]) by mailhub1.shef.ac.uk with esmtp (Exim 3.22 #12) id 1BNWXY-0006OO-00 for chemistry!at!ccl.net; Tue, 11 May 2004 13:39:20 +0100 Received: from localhost (li1vg@localhost) by titania.shef.ac.uk (8.11.7p1+Sun/8.11.7) with ESMTP id i4BCdQ318167 for ; Tue, 11 May 2004 13:39:26 +0100 (BST) Date: Tue, 11 May 2004 13:39:26 +0100 (BST) From: Val Gillet To: chemistry!at!ccl.net Subject: CCL: Workshop: Practical Introduction to Chemoinformatics Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Spam-Status: No, hits=1.0 required=7.5 tests=NO_RDNS2 autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net "A Practical Introduction to Chemoinformatics" June 15th-June 18th 2004 The University of Sheffield, UK, will hosting the above short course which is supported by the Chemical Structure Association Trust and the Molecular Graphics and Modelling Society. This intensive short course provides an introduction to the major aspects of Chemoinformatics, with particular emphasis on applications in modern drug discovery. The course will comprise a mixture of hands-on workshops, lectures, and informal discussions. Please note that places on the course are limited. For further details see: http://cisrg.shef.ac.uk/ci_course or contact Val Gillet (v.gillet!at!sheffield.ac.uk) From chemistry-request@ccl.net Tue May 11 00:46:30 2004 Received: from gveu50.emea.givaudan.com (mail-external3.givaudan.com [57.66.141.4]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i4B5kSkh008069; Tue, 11 May 2004 00:46:29 -0500 To: m.mackey..at..cresset-bmd.com Cc: chemistry..at..ccl.net, "Computational Chemistry List" Subject: Re: CCL:Enumeration / SMILES handling software MIME-Version: 1.0 X-Mailer: Lotus Notes Release 5.0.11 July 24, 2002 Message-ID: From: Andras.Borosy..at..givaudan.com Date: Tue, 11 May 2004 07:48:34 +0200 X-MIMETrack: Serialize by Router on gvedoh01/H/Givaudan(Release 5.0.12 |February 13, 2003) at 11/05/2004 07:48:39, Serialize complete at 11/05/2004 07:48:39 Content-Type: text/plain; charset="iso-8859-1" X-Spam-Status: No, hits=1.0 required=7.5 tests=IMPRONONCABLE_1,NO_REAL_NAME, SMILEY autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id i4B5kUkh008073 Dear Colleague, Try Jchem! http://www.chemaxon.com/ Regards, Andras Borosy PhD Computational Chemist Givaudan Schweiz AG Fragrance Research Ueberlandstr. 138 8600 D|bendorf Switzerland tel: + 41-1-8242164 fax: +41-1-8242926 e-mail: andras.borosy..at..givaudan.com "Mark Mackey" Sent by: "Computational Chemistry List" 10.05.2004 16:20 To: cc: Subject: CCL:Enumeration / SMILES handling software Hi all. Ib re looking at quickb nb dirty ways to enumerate some libraries for a database. There seem to be hundreds of commercial library enumeration tools out there, most of which are horribly overpriced for what they do :). All we want is to enumerate a couple of libraries reasonably quickly and get the resulting molecules either as OKish 3D structures or as reasonable 2D structures. Enumerating libraries in SMILES space is trivial, but thereb s a lack of tools available to do the coordinate generation. So, does anyone know of a free/cheap tool that will either (a) enumerate simple libraries into, say, SDF files, or (b) generate 2D or 3D coordinates for SMILES strings. I know that Corina et al. do (b), but we don't really need very good 3D coordinates (the molecules are going to be subjected to conformational searches and minimisation) so it's overkill and overexpensive for what we want. Mark. -= This is automatically added to each message by the mailing script =- To send e-mail to subscribers of CCL put the string CCL: on your Subject: line and send your message to: CHEMISTRY..at..ccl.net Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST..at..ccl.net HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs If your mail is bouncing from CCL.NET domain send it to the maintainer: Jan Labanowski, jlabanow..at..nd.edu (read about it on CCL Home Page) -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ From chemistry-request@ccl.net Tue May 11 01:20:17 2004 Received: from mx5.informatik.uni-tuebingen.de (mx5.Informatik.Uni-Tuebingen.De [134.2.12.32]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i4B6KFkh009188 for >ccl.net>; Tue, 11 May 2004 01:20:15 -0500 Received: from localhost (loopback [127.0.0.1]) by mx5.informatik.uni-tuebingen.de (Postfix) with ESMTP id 2124C10E; Tue, 11 May 2004 08:22:25 +0200 (MST) Received: from mx3.informatik.uni-tuebingen.de ([134.2.12.26]) by localhost (mx5 [134.2.12.32]) (amavisd-new, port 10024) with ESMTP id 14996-01; Tue, 11 May 2004 08:22:23 +0200 (DFT) Received: from informatik.uni-tuebingen.de (rapc90 [134.2.10.190]) by mx3.informatik.uni-tuebingen.de (Postfix) with ESMTP id 0604E134; Tue, 11 May 2004 08:22:23 +0200 (MST) Message-ID: <40A071C1.4010305<>informatik.uni-tuebingen.de> Date: Tue, 11 May 2004 08:25:05 +0200 From: "Joerg K. Wegner" >informatik.uni-tuebingen.de> Organization: Department of Computer Architecture User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.0; en-US; rv:1.6) Gecko/20040113 X-Accept-Language: en-us, en MIME-Version: 1.0 To: Mark Mackey >cresset-bmd.com> Cc: chemistry<>ccl.net Subject: Re: CCL:Enumeration / SMILES handling software References: <000601c43699$ef9d5be0$0207a8c0@cresset23> In-Reply-To: <000601c43699$ef9d5be0$0207a8c0@cresset23> Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit X-Virus-Scanned: by amavisd-new (McAfee AntiVirus) at informatik.uni-tuebingen.de X-Spam-Status: No, hits=2.2 required=7.5 tests=COMBINED_FROM,MY_BAD_DOT, NO_RDNS2 autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Hi Mark, i know only three 'usable' free appraoches: 1. CACTVS from W.D.Ihlenfeld (tcl, no source code for a low price), but maybe the best free tool out there. http://www2.ccc.uni-erlangen.de/software/cactvs/ 2. CDK: SMILES with 2D generation http://sourceforge.net/projects/cdk/ 3. JOELib: SMILES and interface to CDK (2D) and Ghemical (3D, simple all atom force field) joelib.sf.net Interesting commercial approaches are: - 2D: a new tool of Rarey et al. http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/ci049958u - 3D: OMEGA with OEChem as chemistry kernel (formerly called OELib) http://www.eyesopen.com/ So they have a good and advanced chemistry and computer science design (C++, object oriented, source code available, if you pay for their work). - 2D: http://www.chemaxon.com/marvin/ (good programming interface) - 3D: MOE for energy minimization (MMFF94 all-atom pair force field) in batch mode http://www.chemcomp.com/ Kind regards, Joerg -- Dipl. Chem. Joerg K. Wegner Center of Bioinformatics Tuebingen (ZBIT) Department of Computer Architecture Univ. Tuebingen, Sand 1, D-72076 Tuebingen, Germany Phone: (+49/0) 7071 29 78970 Fax: (+49/0) 7071 29 5091 E-Mail: mailto:wegnerj<>informatik.uni-tuebingen.de WWW: http://www-ra.informatik.uni-tuebingen.de -- Never mistake motion for action. (E. Hemingway) Never mistake action for meaningful action. (Hugo Kubinyi,2004) From chemistry-request@ccl.net Tue May 11 13:36:20 2004 Received: from mx5.net.nih.gov (mailfwd.nih.gov [165.112.130.36]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i4BIaHkh012013 for ; Tue, 11 May 2004 13:36:18 -0500 Received: from mx5.net.nih.gov (localhost [127.0.0.1]) by mx5.net.nih.gov (8.12.10/8.12.8p1) with ESMTP id i4BIcSqB005539 for ; Tue, 11 May 2004 14:38:28 -0400 Received: from pollux.cber.nih.gov (pollux.cber.nih.gov [128.231.52.5]) by mx5.net.nih.gov (8.12.10/8.12.8p1) with ESMTP id i4BIcPd3005514; Tue, 11 May 2004 14:38:25 -0400 Date: Tue, 11 May 2004 14:33:27 -0400 From: Rick Venable To: wei cc: chemistry..at..ccl.net Subject: Re: CCL:NMA parameters in charmm In-Reply-To: <200405100959.41374.wzhuang..at..uci.edu> Message-ID: References: <200405100959.41374.wzhuang..at..uci.edu> ReplyTo: Rick_Venable..at..nih.gov MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Spam-Status: No, hits=0.0 required=7.5 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net On Mon, 10 May 2004, wei wrote: > I want to do a simulation of NMA in charmm,but the parameters > (especially the partial charges) of the amino acids can't be used > directly. can anyone give me some help about this The NMA* residue can be found in the distributed top_all22_model.inp, in the toppar subdir * assuming NMA = N-methyl acetamide =+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+= Rick Venable 29/500 FDA/CBER/OVRR Biophysics Lab 1401 Rockville Pike HFM-419 Rockville, MD 20852-1448 U.S.A. (301) 496-1905 Rick_Venable..at..nih.gov ALT email: rvenable..at..speakeasy.org ------------------------------------- "Don't blame me, I voted for Kang." Homer =+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+= From chemistry-request@ccl.net Tue May 11 11:45:48 2004 Received: from mxout5.cac.washington.edu (mxout5.cac.washington.edu [140.142.32.135]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i4BGjlkh007321 for ; Tue, 11 May 2004 11:45:48 -0500 Received: from smtp.washington.edu (smtp.washington.edu [140.142.33.9]) by mxout5.cac.washington.edu (8.12.11+UW04.02/8.12.11+UW04.03) with ESMTP id i4BGlmH3030473 for ; Tue, 11 May 2004 09:47:54 -0700 Received: from u.washington.edu (konga.chem.washington.edu [128.95.128.222]) (authenticated bits=0) by smtp.washington.edu (8.12.11+UW04.02/8.12.11+UW04.03) with ESMTP id i4BGlh7H008767 (version=TLSv1/SSLv3 cipher=RC4-MD5 bits=128 verify=NOT) for ; Tue, 11 May 2004 09:47:48 -0700 Message-ID: <40A103A4.5000601/at/u.washington.edu> Date: Tue, 11 May 2004 09:47:32 -0700 From: Carsten Detering 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 To: chemistry/at/ccl.net Subject: PES scan + solvent Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=1.0 required=7.5 tests=IMPRONONCABLE_1 autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Thanks to all who replied to my previous message about the PES scan using SCRF and the opt key word. I seem to have gotten a little further by making my hydrogens explicit with radii=UFF and placing a sphere on the proton that I scan the surface with (using sphereonh=n). THis time however, Gassian concludes with an error like this: radii=UFF sphereonh=41 --- end of non-standard input. ------------------------------------------------------------------------------ Polarizable Continuum Model (PCM) ================================= Model : PCM. Atomic radii : UFF (Universal Force Field). Polarization charges : Total charges. Charge compensation : None. Solution method : Matrix inversion. Cavity : GePol (RMin=0.200 OFac=0.890). Default sphere list used, NSphG= 39. Tesserae with average area of 0.200 Ang**2. 1st derivatives : Analytical V*U(x)*V algorithm (CHGder, D1EAlg=0). Cavity 1st derivative terms included. Solvent : Chloroform, Eps= 4.900000. ------------------------------------------------------------------------------ One-electron integrals computed using PRISM. NBasis= 351 RedAO= T NBF= 351 NBsUse= 351 1.00D-06 NBFU= 351 Harris functional with IExCor= 205 diagonalized for initial guess. ExpMin= 1.61D-01 ExpMax= 7.00D+03 ExpMxC= 1.05D+03 IAcc=1 IRadAn= 1 AccDes= 1.00D-06 HarFok: IExCor= 205 AccDes= 1.00D-06 IRadAn= 1 IDoV=1 ScaDFX= 1.000000 1.000000 1.000000 1.000000 Requested convergence on RMS density matrix=1.00D-08 within 128 cycles. Requested convergence on MAX density matrix=1.00D-06. Requested convergence on energy=1.00D-06. No special actions if energy rises. PCMQM-DMIVC allocation failure: iend,mxcore= 19448991 5979574 Error termination via Lnk1e in /software/gaussian/g03_B.4/g03/l502.exe at Tue May 11 04:32:33 2004. Job cpu time: 0 days 0 hours 1 minutes 33.3 seconds. File lengths (MBytes): RWF= 550 Int= 0 D2E= 0 Chk= 1 Scr= 1 What could the PCMQM-DMIVC allocation failure be due to, and what can I do to avoid this error? THanks again in advance for any helpful suggestions, Carsten -- Carsten Detering University of Washington Seattle, WA 98195 Fon 206.543.5081 Fax 206.685.8665 From chemistry-request@ccl.net Tue May 11 10:57:40 2004 Received: from gveu50.emea.givaudan.com (mail-external3.givaudan.com [57.66.141.4]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i4BFvdkh004410; Tue, 11 May 2004 10:57:39 -0500 To: nadtanet..at..atc.atccu.chula.ac.th Cc: chemistry..at..ccl.net, "Computational Chemistry List" Subject: Re: CCL:field fit in SYBYL MIME-Version: 1.0 X-Mailer: Lotus Notes Release 5.0.11 July 24, 2002 Message-ID: From: Andras.Borosy..at..givaudan.com Date: Tue, 11 May 2004 17:59:47 +0200 X-MIMETrack: Serialize by Router on gvedoh01/H/Givaudan(Release 5.0.12 |February 13, 2003) at 11/05/2004 17:59:51, Serialize complete at 11/05/2004 17:59:51 Content-Type: text/plain; charset="iso-8859-1" X-Spam-Status: No, hits=1.5 required=7.5 tests=IMPRONONCABLE_1,NO_REAL_NAME autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id i4BFvekh004414 Dear Colleague, I tried to use Field Fit once, but I could not succed. I built several CoMFA modell, and I used DISCO and DISTILL as alignment tools. Regards, Andras Borosy PhD Computational Chemist Givaudan Schweiz AG Fragrance Research Ueberlandstr. 138 8600 D|bendorf Switzerland tel: + 41-1-8242164 fax: +41-1-8242926 e-mail: andras.borosy..at..givaudan.com "Nadtanet Nunthaboot" Sent by: "Computational Chemistry List" 10.05.2004 20:51 To: chemistry..at..ccl.net cc: Subject: CCL:field fit in SYBYL -- NeoMail - Webmail that doesn't suck... as much. http://neomail.sourceforge.net Dear Cclers, I try to use CoMFA in SYBYL6.8. I got the poor q2 (0.3)value . I want to know the alignment method especiallly " Field Fit " alignment. I try to use field fit in SYBYL follow the manual but not success. I can not align my compounds by field fit method. Any body known about these procedure or method to use field fit alignment in SYBYL? Pleaes tell me about informations or datails about how to align compounds by field fit method. I will appreciate for your help. Thank you very much. Best Wishes, Nadtanet -= This is automatically added to each message by the mailing script =- To send e-mail to subscribers of CCL put the string CCL: on your Subject: line and send your message to: CHEMISTRY..at..ccl.net Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST..at..ccl.net HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs If your mail is bouncing from CCL.NET domain send it to the maintainer: Jan Labanowski, jlabanow..at..nd.edu (read about it on CCL Home Page) -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ From chemistry-request@ccl.net Tue May 11 10:53:38 2004 Received: from web1.ulb.ac.be (st.ulb.ac.be [164.15.59.200]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i4BFrakh004206 for ; Tue, 11 May 2004 10:53:37 -0500 Received: from wwwdev.ulb.ac.be (resu1 [164.15.59.200]) by web1.ulb.ac.be (8.8.8/3.17.1.ap (resu)) id RAA26063; Tue, 11 May 2004 17:55:48 +0200 (MEST) for chemistry(at)ccl.net Date: Tue, 11 May 2004 17:55:48 +0200 (MEST) Message-Id: <200405111555.RAA26063(at)web1.ulb.ac.be> From: Goedele Roos To: chemistry(at)ccl.net X-sender-IP: 81.83.81.96 Subject: calculating polarizabilities X-Mailer: Webmail ULB v2.1 X-Spam-Status: No, hits=0.9 required=7.5 tests=MY_BAD_DOT autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Dear all, Calculating the polarizability for a perfect tetrahedral dianion, gives for the three diagonal elements of the polarizability tensor: (XX)=(YY)=(ZZ). But, when I calculate the polarizability of the mono-anion (of the same system) on the optimized geometry of the dianion (thus on the perfect tetrahedral geometry), the polarizabilitytensor gives (XX)=(YY), but the (ZZ) component is different. Has anyone also had this problems? What can I do to solve this? Can anyone give me some advise? Thanks in advance for your help, Sincerely Yours, Goedele Roos Drs. Goedele Roos Dienst Algemene Chemie (ALGC) Vrije Universiteit Brussel (VUB) Pleinlaan 2 B-1050 Brussels Tel: 0032-2-629 35 16 Fax: 0032-2-629 33 17 From chemistry-request@ccl.net Tue May 11 10:13:27 2004 Received: from mail-h12-03.cc.ksu.edu (mail-h12-03.cc.ksu.edu [129.130.12.152]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i4BFDQkh001592 for ; Tue, 11 May 2004 10:13:26 -0500 Received: from kansasiaui2z79 ([129.130.170.132]) by mail-h12-03.cc.ksu.edu (8.12.9/8.12.9) with SMTP id i4BFFc4P000692 for ; Tue, 11 May 2004 10:15:38 -0500 (CDT) Message-ID: <004801c4376a$d0c15a10$84aa8281@kansasiaui2z79> From: "Gustavo Seabra" To: Subject: XPS program Date: Tue, 11 May 2004 10:15:37 -0500 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0045_01C43740.E7AE4910" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2800.1409 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1409 X-Spam-Status: No, hits=3.0 required=7.5 tests=HTML_30_40,HTML_MESSAGE, HTML_TAG_EXISTS_TBODY,NO_RDNS2 autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net This is a multi-part message in MIME format. ------=_NextPart_000_0045_01C43740.E7AE4910 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hi, I wonder if anyone here would know of a (free) program capable of: 1. Read some experimental spectra 2. Read a list of (calculated) peak positions and respective areas 3. Fit the calculated to the experimental spectra using a = Gaussian-Lorentzian shape. The output of the program would probably be the G-L parameters that = provide the best total fit to the experimental points. I am looking particularly in the area of photoelectron spectra, but such = a program would probably be general enough to other spectroscopies too, = and I'd believe someone has already implement something like this = before. If not, suggestions of a nice starting point would also be = appreciated. Thank you very much, -------------------------------------------------------------------------= ------- Gustavo Seabra - Graduate Student=20 E-Mail: seabra-.at.-ksu.edu=20 Phone: (785) 532-6072 Chemistry Department=20 Kansas State University=20 Manhattan, KS 66506-3701=20 =20 ------=_NextPart_000_0045_01C43740.E7AE4910 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Hi,
 
I wonder if anyone here would know of a = (free)=20 program capable of:
 
    1. Read some = experimental=20 spectra
    2. Read a list of = (calculated)=20 peak positions and respective areas
    3. Fit the = calculated to the=20 experimental spectra using a Gaussian-Lorentzian shape.
 
The output of the program would = probably be the G-L=20 parameters that provide the best total fit to the experimental=20 points.
 
I am looking particularly in the area = of=20 photoelectron spectra, but such a program would probably be general = enough to=20 other spectroscopies too, and I'd believe someone has already = implement=20 something like this before. If not, suggestions of a nice starting point = would=20 also be appreciated.
 
Thank you very much,
Gustavo=20 Seabra - Graduate Student
E-Mail: seabra-.at.-ksu.edu
Phone: = (785) 532-6072=20 		Chemistry Department =
Kansas State University =
Manhattan, KS=20 66506-3701
------=_NextPart_000_0045_01C43740.E7AE4910-- From chemistry-request@ccl.net Tue May 11 09:36:14 2004 Received: from chemaxon.hu ([195.228.156.90]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i4BEaBkh031504 for ; Tue, 11 May 2004 09:36:12 -0500 Received: from chemaxon.com (99.122-182-adsl-pool.axelero.hu [81.182.122.99]) by chemaxon.hu (8.12.8/8.12.8) with ESMTP id i4BEcMqG030461; Tue, 11 May 2004 16:38:22 +0200 Message-ID: <40A0E558.2040701)at(chemaxon.com> Date: Tue, 11 May 2004 16:38:16 +0200 From: Ferenc Csizmadia User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.6) Gecko/20040113 X-Accept-Language: en-us, en, hu, zh-cn MIME-Version: 1.0 To: chemistry)at(ccl.net CC: Mark Mackey Subject: Re: CCL:Enumeration / SMILES handling software References: In-Reply-To: Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=4.5 required=7.5 tests=MY_DSL,NO_RDNS2, RCVD_IN_DYNABLOCK,RCVD_IN_SORBS autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Mark, I suggest to check out our tools MolCoverter and Reactor. Using MolConverter you can interconvert between file formats (like from SMILES to SDF) and generate 2D or 3D coordinates. http://www.chemaxon.com/marvin/doc/user/molconvert.html MolConverter is free if you don't build it into custom applications. It is available in the Marvin Beans and the JChem package. (Marvin Beans is easier to install) You can use Reactor to enumerate virtual libraries using reaction modelling. http://www.jchem.com/doc/user/Reactor.html Movie: http://www.chemaxon.com/demos/flash/reactor.html Reactor is included in the JChem package. You can download these packages from our web site. http://www.chemaxon.com/products.html Best regards, Ferenc >Hi all. > >Ib re looking at quickb nb dirty ways to enumerate some libraries for >a database. There seem to be hundreds of commercial library enumeration >tools out there, most of which are horribly overpriced for what they do >:). All we want is to enumerate a couple of libraries reasonably quickly >and get the resulting molecules either as OKish 3D structures or as >reasonable 2D structures. Enumerating libraries in SMILES space is >trivial, but thereb s a lack of tools available to do the coordinate >generation. > >So, does anyone know of a free/cheap tool that will either >(a) enumerate simple libraries into, say, SDF files, or >(b) generate 2D or 3D coordinates for SMILES strings. > >I know that Corina et al. do (b), but we don't really need very good 3D >coordinates (the molecules are going to be subjected to conformational >searches and minimisation) so it's overkill and overexpensive for what we >want. > >Mark. > > > > > From chemistry-request@ccl.net Tue May 11 11:00:20 2004 Received: from gveu50.emea.givaudan.com (mail-external3.givaudan.com [57.66.141.4]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i4BG0Jkh004608; Tue, 11 May 2004 11:00:19 -0500 To: chemistry..at..ccl.net, "Computational Chemistry List" Subject: Modelling Tools in Material Science MIME-Version: 1.0 X-Mailer: Lotus Notes Release 5.0.11 July 24, 2002 Message-ID: From: Andras.Borosy..at..givaudan.com Date: Tue, 11 May 2004 18:02:28 +0200 X-MIMETrack: Serialize by Router on gvedoh01/H/Givaudan(Release 5.0.12 |February 13, 2003) at 11/05/2004 18:02:31, Serialize complete at 11/05/2004 18:02:31 Content-Type: text/plain; charset="iso-8859-1" X-Spam-Status: No, hits=1.5 required=7.5 tests=IMPRONONCABLE_1,NO_REAL_NAME autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id i4BG0Kkh004612 Dear Colleagues, Do you know an alternative tool of Material Studio? Many thank, Andras Borosy PhD Computational Chemist Givaudan Schweiz AG Fragrance Research Ueberlandstr. 138 8600 D|bendorf Switzerland tel: + 41-1-8242164 fax: +41-1-8242926 e-mail: andras.borosy..at..givaudan.com