From chemistry-request@server.ccl.net Mon Feb 3 18:18:02 2003 Received: from postoffice.mail.cornell.edu ([132.236.56.7]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h13NI1I29909 for ; Mon, 3 Feb 2003 18:18:01 -0500 Received: from cornell.edu ([128.84.182.122]) by postoffice.mail.cornell.edu (8.9.3/8.9.3) with ESMTP id SAA28692; Mon, 3 Feb 2003 18:17:58 -0500 (EST) Message-ID: <3E3EF835.3080003@cornell.edu> Date: Mon, 03 Feb 2003 18:16:05 -0500 From: Richard Gillilan User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.0.1) Gecko/20020830 X-Accept-Language: en-us, en MIME-Version: 1.0 To: Chris Arthur CC: CHEMISTRY Subject: Re: CCL:Protein PDB to Mol2 References: <003c01c2cb63$e3165e50$3b2ade89@chm.bris.ac.uk> Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit Chris Arthur wrote: > Hi > > I was wondering if anyone knows how o convert Protein PDB files to > MOL2. I've tried using Babel howver it has problems when it comes to > recognising the CE, NZ, CZ and SG (and varients of) atom codes instead > calling them Du when it gets confused (I assume that...CE - epsilon C > , NZ....zeta nitrogen , CZ .....zeta carbon and SG....gamma Sulfur) > > Anyone know of a GPL or GNU program that'll do this happily ? > > Chris > > I recently got OpenBabel to correctly protonate a pdb file for use in molecular simulation (including a GDP group). The code is still really beta for this purpose and I had to make some modifications, but it does seem to work now for polypeptides and is actually quite fast. Check http://sourceforge.net/projects/openbabel/ You are welcome to my modified version of the code. Some mods are checked in to the official version but not all. Richard Gillilan MacCHESS, Cornell From chemistry-request@server.ccl.net Tue Feb 4 06:22:50 2003 Received: from puga.vdu.lt ([193.219.38.32]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h14BMnI24159 for ; Tue, 4 Feb 2003 06:22:49 -0500 Received: from amavis by puga.vdu.lt with scanned-ok for chemistry@ccl.net id 18g1A3-0006yO-00; Tue, 04 Feb 2003 13:22:43 +0200 Received: from vaidila.vdu.lt ([193.219.38.52] ident=mail) by puga.vdu.lt with esmtp for chemistry@ccl.net id 18g1A3-0006yF-00; Tue, 04 Feb 2003 13:22:43 +0200 Received: from vejas.vdu.lt ([193.219.38.82] helo=localhost) by vaidila.vdu.lt with esmtp for chemistry@ccl.net id 18g1OW-0004zI-00; Tue, 04 Feb 2003 13:37:40 +0200 Date: Tue, 4 Feb 2003 13:22:48 +0200 From: Arturas X-Mailer: The Bat! (v1.44) UNREG / CD5BF9353B3B7091 Reply-To: Arturas Organization: SemteX X-Priority: 3 (Normal) Message-ID: <46171316660.20030204132248@vaidila.vdu.lt> To: CCL Subject: transition metals Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Virus-Scanned: by AMaViS snapshot-20020300 Hello CCL'ers, Could anybody point me to overview of electronic structure of transition metals by itself and thier complexes ? Would be nice that the source would be written not only for QM/quantum chemistry guru. Thaks in advance Arturas Z From chemistry-request@server.ccl.net Tue Feb 4 03:11:40 2003 Received: from mailstudenti.unimi.it ([159.149.10.4]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h148BdI18403 for ; Tue, 4 Feb 2003 03:11:39 -0500 Received: from smtp.unimi.it (smtp.unimi.it [159.149.10.3]) by mailstudenti.unimi.it (iPlanet Messaging Server 5.1 (built May 7 2001)) with ESMTP id <0H9R00IEVYR9HX@mailstudenti.unimi.it> for chemistry@ccl.net; Tue, 04 Feb 2003 09:11:33 +0100 (MET) Received: from Villa (villa.farma.unimi.it [159.149.79.66]) by smtp.unimi.it (iPlanet Messaging Server 5.1 (built May 7 2001)) with SMTP id <0H9R00KMWYR8L2@smtp.unimi.it> for chemistry@ccl.net; Tue, 04 Feb 2003 09:11:33 +0100 (MET) Date: Tue, 04 Feb 2003 09:15:59 +0100 From: Giulio Vistoli Subject: Protein PDB to Mol2 To: chris.arthur@bristol.ac.uk, CCL Message-id: <003901c2cc25$a68697d0$424f959f@farma.unimi.it> Organization: =?iso-8859-1?Q?Universit=E0_di_Milano?= MIME-version: 1.0 X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2800.1106 X-Mailer: Microsoft Outlook Express 6.00.2800.1106 Content-type: multipart/alternative; boundary="Boundary_(ID_PylaKO03C/n8B/3GsKk/dQ)" X-Priority: 3 X-MSMail-priority: Normal This is a multi-part message in MIME format. --Boundary_(ID_PylaKO03C/n8B/3GsKk/dQ) Content-type: text/plain; charset=iso-8859-1 Content-transfer-encoding: 7BIT Dear Chris, you can use VEGA (http://www.ddl.unimi.it). It is able to convert pdb files in mol2 format assigning the correct atom types (and, if you want, also the atomic charges). Giulio --------- Giulio Vistoli Istituto di Chimica Farmaceutica e Tossicologica Viale Abruzzi, 42 I-20131 Milano Italia Tel. +39-02-50317545 Fax +39-02-50317565 giulio.vistoli@unimi.it http://www.ddl.unimi.it --Boundary_(ID_PylaKO03C/n8B/3GsKk/dQ) Content-type: text/html; charset=iso-8859-1 Content-transfer-encoding: 7BIT
Dear Chris,
 
you can use VEGA (http://www.ddl.unimi.it). It is able to convert pdb files in mol2 format assigning the correct atom types (and, if you want, also the atomic charges).
 
Giulio
 
---------
Giulio Vistoli
Istituto di Chimica Farmaceutica e Tossicologica
Viale Abruzzi, 42
I-20131 Milano
Italia
Tel. +39-02-50317545
Fax +39-02-50317565
giulio.vistoli@unimi.it
http://www.ddl.unimi.it
--Boundary_(ID_PylaKO03C/n8B/3GsKk/dQ)-- From chemistry-request@server.ccl.net Tue Feb 4 05:05:02 2003 Received: from camdmail01.cam.accelrys.com ([192.190.183.254]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h14A51I13304 for ; Tue, 4 Feb 2003 05:05:01 -0500 To: "Coussens, Betty" Cc: CHEMISTRY@ccl.net Subject: Re: CCL:calculating NMR spectra for crystal structures MIME-Version: 1.0 X-Mailer: Lotus Notes Release 5.0.11 July 24, 2002 Message-ID: From: vmilman@accelrys.com Date: Tue, 4 Feb 2003 10:04:58 +0000 X-MIMETrack: Serialize by Router on camdmail01/Server/Accelrys(Release 5.0.9 |November 16, 2001) at 02/04/2003 10:05:02 AM, Serialize complete at 02/04/2003 10:05:02 AM Content-Type: text/plain; charset="us-ascii" Dear Betty, The state-of-the-art solid state NMR is implemented by Francesco Mauri and Chris Pickard in Mauri's code PARATEC [this is currently being incorporated in CASTEP]. I think Chris is in the best position to tell you about the computational cost: cjp20@phy.cam.ac.uk He would also explain why their approach is more complete and accurate than the one in CPMD. Here is a brief list of current publications from this group (PRB paper has the details of the implementation and comparisons to quantum-chemistry formalisms as in Gaussian): http://ojps.aip.org/getabs/servlet/GetabsServlet?prog=normal&id=PRLTAO000088000008086403000001&idtype=cvips&gifs=yes First-principles theory of the EPR g tensor in solids: Defects in quartz Pickard CJ, Mauri F PHYSICAL REVIEW LETTERS 88 (8): art. no. 086403 FEB 25 2002 A theory for the reliable prediction of the EPR g tensor for paramagnetic defects in solids is presented. It is based on density functional theory and on the gauge including projector augmented wave approach to the calculation of all-electron magnetic response. The method is validated by comparison with existing quantum chemical and experimental data for a selection of diatomic radicals. We then perform the first prediction of EPR g tensors in the solid state and find the results to be in excellent agreement with experiment for the E-1' and substitutional phosphorus defect centers in quartz. http://ojps.aip.org/getabs/servlet/GetabsServlet?prog=normal&id=PRLTAO000087000008085506000001&idtype=cvips&gifs=yes Atomic structure of icosahedral B4C boron carbide from a first principles analysis of NMR spectra Mauri F, Vast N, Pickard CJ PHYSICAL REVIEW LETTERS 87 (8): art. no. 085506 AUG 20 2001 Density functional theory is demonstrated to reproduce the C-13 and B-11 NMR chemical shifts of icosahedral boron carbides with sufficient accuracy to extract previously unresolved structural information from experimental NMR spectra. B4C can be viewed as an arrangement of 3-atom linear chains and 12-atom icosahedra. According to our results, all the chains have a CBC structure. Most of the icosahedra have a B11C structure with the C atom placed in a polar site, and a few percent have a B-12 structure or a B10C2 structure with the two C atoms placed in two antipodal polar sites. http://ojps.aip.org/getabs/servlet/GetabsServlet?prog=normal&id=PRBMDO000063000024245101000001&idtype=cvips&gifs=yes All-electron magnetic response with pseudopotentials: NMR chemical shifts Pickard CJ, Mauri F PHYSICAL REVIEW B 63 (24): art. no. 245101 JUN 15 2001 A theory for the ab initio calculation of all-electron NMR chemical shifts in insulators using pseudopotentials is presented. It is formulated for both finite and infinitely periodic systems and is based on an extension to the projector augmented-wave approach of Blochl [P. E. Blochl, Phys. Rev. B 50, 17 953 (1994)] and the method of Mauri et al. [F. Mauri, B. G. Pfrommer, and S. G. Louie, Phys. Rev. Lett. 77, 5300 (1996)]. The theory is successfully validated for molecules by comparison with a selection of quantum chemical results, and in periodic systems by comparison with plane-wave all-electron results for diamond. http://www.iop.org/EJ/S/UNREG/ks17LhBicNsPpD6NufvXEA/abstract/0953-8984/14/11/310 Applications of ab initio atomistic simulations to biology Segall MD JOURNAL OF PHYSICS-CONDENSED MATTER 14 (11): 2957-2973 MAR 25 2002 Biological systems provide a particularly challenging set of problems for the application of ab initio quantum mechanical simulations. Despite this, these methods are providing insights into biological structures and processes at an atomistic level. This paper outlines current methods for first-principles modelling of biological systems. Example applications to the cytochrome P450 family of metabolic enzymes, photoreactive rhodopsin proteins and the calculation of NMR chemical shifts are described. Finally, trends in the development of new algorithms and the biological problems to which they will be applied are discussed. ============================================================= Victor Milman * Fellow Accelrys Inc * tel: (01223) 228500/228619 334 Science Park * fax: (01223) 228501 Cambridge CB4 0WN * tel. from abroad: +44 1223 228500 UK * e-mail: vmilman@accelrys.com ============================================================= "Coussens, Betty" Sent by: "Computational Chemistry List" 03/02/2003 13:22 To: "'chemistry@ccl.net'" cc: Subject: CCL:calculating NMR spectra for crystal structures Dear all, I would like to calculate NMR chemical shifts for a number of crystal structures containing H, C, N, O and P atoms. I know that this is possible using e.g. plane wave codes like CPMD but I would like to hear the opinion of you who have a lot of experience with this type of computations. Can anybody tell me what type of codes are most suitable for my purpose and give me an idea about typical CPU timings for these type of calculations? Thanks a lot! Betty Disclaimer 1. This e-mail is for the intended recipient only. If you have received it by mistake please let us know by reply and then delete it from your system; access, disclosure, copying, distribution or reliance on any of it by anyone else is prohibited. 2. If you as intended recipient have received this e-mail incorrectly, please notify the sender (via e-mail) immediately. This e-mail is confidential and may be legally privileged. DSM does not guarantee that the information sent and/or received by or with this e-mail is correct and does not accept any liability for damages related thereto. -= This is automatically added to each message by mailing script =- CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net From chemistry-request@server.ccl.net Tue Feb 4 04:03:25 2003 Received: from cirse.saclay.cea.fr ([132.166.192.127]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h1493OI24783 for ; Tue, 4 Feb 2003 04:03:25 -0500 Received: from argiope.saclay.cea.fr (argiope.saclay.cea.fr [132.166.192.108]) by cirse.saclay.cea.fr (8.12.2/8.12.2/CEAnet-Internet.1.0) with ESMTP id h1493OiF005238 for ; Tue, 4 Feb 2003 10:03:24 +0100 (MET) Received: from muguet.saclay.cea.fr (unverified) by argiope.saclay.cea.fr (Content Technologies SMTPRS 4.3.6) with ESMTP id for ; Tue, 4 Feb 2003 09:59:21 +0100 Received: from penelope.saclay.cea.fr (penelope.saclay.cea.fr [132.166.189.102]) by muguet.saclay.cea.fr (8.12.2/8.12.2/CEAnet-Interne.1.0) with ESMTP id h1493NUH013371 for ; Tue, 4 Feb 2003 10:03:23 +0100 (MET) Received: by penelope.saclay.cea.fr with Internet Mail Service (5.5.2653.19) id <1BG8KS0G>; Tue, 4 Feb 2003 10:06:13 +0100 Message-ID: <3808A7D2DCEAD6118B630090272872650145D6@azurite.saclay.cea.fr> From: VITORGE Pierre 094605 To: "'chemistry@ccl.net'" Subject: Summary: SDD for La+++ iin Gaussian 98 Date: Tue, 4 Feb 2003 10:03:21 +0100 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-Type: text/plain; charset="iso-8859-1" I received the following information (also, see below the copy of the e-mails), The Net was bloked just after I sent my question, I hope I received all the answers (please re-send it, if you are not in the summary). Discussing with F.-Y. Dupradeau, I got Publication. Cao & Dolg J. Chem. Phys. (2001) 115, 7348-7355 and downlooaded ref.25 of this publication from http://www.aip.org/pubservs/epaps.html ECP are in MOLPRO format, however I should get them in Gaussian94 format > from http://www.emsl.pnl.gov:2080/forms/basisform.html These ECP have been slightly corrected in Publication Cao & Dolg J. Chem. Phys.118, 2, 487-496 (2003) _________ SUMMARY _____ 25 jan. 2003 09:01, F.-Y. Dupradeau ECP/basis set par default dans g98: - Stuttgart group: Basis set: SDDAll; ECP: SDD - Stevens group: Basis set: CEP-31; ECP: CEP web http://www.emsl.pnl.gov:2080/forms/basisform.html - Ross group (CRENBL ECP @ http://www.emsl.pnl.gov:2080/forms/basisform.html ) - Stuttgart (+ rescent) ______ 25 jan. 2003 13:02 Sean Hughes "the Stutgart Pseudopotential [...](SDD) [...] predefined in Gaussian is the Small Core ECP... the Small Core ECP is at times problematic whereas the Large Core ECPs converge rather nicely. A list of ECPs for La can be found on the EMSL website at: http://www.emsl.pnl.gov:2080/forms/basisform.html There you can find other ECPS or basis sets for La ______ 25 jan. 2003 13:02 Mark Russell Lanl2DZ, should be the best for Ln3+. Lanl2MB is a large core, while lanl2dz is a small core. _____________________________________________ a typical Gaussian98 input for SDD ECP/basis set is #p rhf SDDAll pseudo=read opt=readFC optcyc=100 freq test La(H2O)+++ RHF/SDD SDDAll FREQ 3 1 La O,1,r1 H,2,r2,1,a1 H,2,r2,1,a1,3,180.,0 Variables: r1=2.38106816 r2=0.97698107 a1=127.56767073 La 0 SDD O 0 SDD ______ For seeing more details on these SDD ECP/basis set in the output file, you can use the command line #p rhf SDDAll pseudo=read GFInput GFPrint ______ For your own ECP/basis sets a typical input should be #p rhf gen pseudo=read opt=readFC optcyc=100 freq test after the geometry (before line "La 0" in the above input) La 0 S 3 1.00 0.5087399000D+01 -0.4172430000D+00 0.4270978000D+01 0.8860100000D+00 0.1915458000D+01 -0.1419752000D+01 S 1 1.00 0.5255960000D+00 0.1000000000D+01 S 1 1.00 0.2634740000D+00 0.1000000000D+01 S 1 1.00 0.4882000000D-01 0.1000000000D+01 S 1 1.00 0.2283600000D-01 0.1000000000D+01 P 3 1.00 0.3025161000D+01 0.5381960000D+00 0.2382095000D+01 -0.9816400000D+00 0.5844260000D+00 0.1239590000D+01 P 1 1.00 0.2603600000D+00 0.1000000000D+01 P 1 1.00 0.8333400000D-01 0.1000000000D+01 P 1 1.00 0.3027500000D-01 0.1000000000D+01 D 3 1.00 0.1576824000D+01 -0.9694400000D-01 0.5923900000D+00 0.4074660000D+00 0.2495000000D+00 0.7043630000D+00 D 1 1.00 0.1065130000D+00 0.1000000000D+01 D 1 1.00 0.4583100000D-01 0.1000000000D+01 **** O 0 S 3 1.00 0.1307093214D+03 0.1543289673D+00 0.2380886605D+02 0.5353281423D+00 0.6443608313D+01 0.4446345422D+00 SP 3 1.00 0.5033151319D+01 -0.9996722919D-01 0.1559162750D+00 0.1169596125D+01 0.3995128261D+00 0.6076837186D+00 0.3803889600D+00 0.7001154689D+00 0.3919573931D+00 **** H 0 S 3 1.00 0.3425250914D+01 0.1543289673D+00 0.6239137298D+00 0.5353281423D+00 0.1688554040D+00 0.4446345422D+00 **** La 0 SDD O 0 SDD _____________________________________________ ORIGINAL E-MAILS > > > De: FyD [mailto:fyd@u-picardie.fr] > Date: samedi 25 janvier 2003 09:01 > > > Gaussian 98 include predefined Pseudopotentials. Are they OK for > > calculating Lanthanum? > > Which one can be used? SDD? > > Are they special options for chosing large or small core? > > With which basis set? > > plusieurs ECP/basis set par default dans g98: > - Stuttgart group: Basis set: SDDAll; ECP: SDD > - Stevens group: Basis set: CEP-31; ECP: CEP > cf page 34 of g98 user'ref. and ref 235-264 > > d'autre st disponibles sur le web > http://www.emsl.pnl.gov:2080/forms/basisform.html mais ne sont pas present > par > default dans g98: il faut donc utiliser le keyword "gen" pour le Basis > set... > - Ross group (CRENBL ECP @ > http://www.emsl.pnl.gov:2080/forms/basisform.html ) > - Stuttgart (+ rescent) > > F.-Y. Dupradeau > http://www.u-picardie.fr/labo/lbpd/fyd.htm > > ________________________________________________ > De: Mark Russell [mailto:M.L.Russell@bath.ac.uk] > Date: samedi 25 janvier 2003 13:02 > > > Gaussian 98 include predefined Pseudopotentials. Are they OK for > calculating > > Lanthanum? > > Should be fine. > > > Which one can be used? SDD? > > Try Lanl2DZ, should be the best for Ln3+. > > > Are they special options for chosing large or small core? > > With which basis set? > > Yes, Lanl2MB is a large core, while lanl2dz is a small core. > > Mark Russell > > -----Message d'origine----- > De: VITORGE Pierre 094605 > Date: vendredi 24 janvier 2003 18:03 > À: 'chemistry@ccl.net' > Objet: SDD for La+++ iin Gaussian 98 > > Gaussian 98 include predefined Pseudopotentials. Are they OK for > calculating Lanthanum? > Which one can be used? SDD? > Are they special options for chosing large or small core? > With which basis set? > > > Pierre Vitorge > DEN Saclay DPC/SCPA/LCRE & UMR 8587 (Universite d'Evry-CNRS-CEA) > CEA Saclay Bat.450 pce 157D > 91191 Gif sur Yvette cedex > France > tel.(+33) 169-08-32-65, secr.: (+33)169-08-32-50, fax:(+33)169-08-32-42 > pierre.vitorge@cea.fr > http://perso.club-internet.fr/vitorgen/pierre/pierre.html From chemistry-request@server.ccl.net Tue Feb 4 07:50:56 2003 Received: from dove2.cf.ac.uk ([131.251.1.170]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h14CosI04932 for ; Tue, 4 Feb 2003 07:50:54 -0500 Received: from maincf2p.cf.ac.uk ([131.251.4.71] helo=MAINCF2P) by dove2.cf.ac.uk with esmtp (Exim 4.05) id 18g2XK-0006ES-00 for chemistry@ccl.net; Tue, 04 Feb 2003 12:50:50 +0000 Received: from cardiff.ac.uk (m114.phrm.cf.ac.uk [131.251.35.246]) by MAINCF2P; Tue, 04 Feb 2003 12:50:43 +0000 Date: Tue, 4 Feb 2003 12:49:45 +0000 Subject: Re: CCL:Protein PDB to Mol2 Content-Type: multipart/alternative; boundary=Apple-Mail-2--516207747 Mime-Version: 1.0 (Apple Message framework v546) From: Dimitrios Vlachakis To: chemistry@ccl.net In-Reply-To: <003c01c2cb63$e3165e50$3b2ade89@chm.bris.ac.uk> Message-Id: <23106F61-383F-11D7-A66B-0030656D04F2@cardiff.ac.uk> X-Mailer: Apple Mail (2.546) --Apple-Mail-2--516207747 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-1; format=flowed Dear Chris, Babel does not seem to work fine when it is doing the MOL2 conversion=20 of the PDB files. The best way to convert PDB files to MOL2 is to use=20 one of the demo molecular modelling software that is available such as=20= HyperChem (you can download the demo from www.hyper.com)... hope that helps Dimitrios Vlachakis Cardiff Univeristy On Monday, February 3, 2003, at 09:08 am, Chris Arthur wrote: > Hi > =A0 > I was wondering if anyone knows how o convert Protein PDB files to=20 > MOL2. I've tried using Babel howver it has problems when it comes to=20= > recognising the CE, NZ, CZ and SG (and varients of) atom codes instead=20= > calling them Du when it gets confused (I assume that...CE - epsilon C=20= > , NZ....zeta nitrogen , CZ .....zeta carbon and SG....gamma Sulfur) > =A0 > Anyone=A0know of a GPL or GNU program that'll do this happily=A0? > =A0 > Chris=A0 > =A0 > =A0 --Apple-Mail-2--516207747 Content-Transfer-Encoding: quoted-printable Content-Type: text/enriched; charset=ISO-8859-1 Dear Chris, Babel does not seem to work fine when it is doing the MOL2 conversion of the PDB files. The best way to convert PDB files to MOL2 is to use one of the demo molecular modelling software that is available such as HyperChem (you can download the demo from www.hyper.com)... hope that helps Dimitrios Vlachakis Cardiff Univeristy On Monday, February 3, 2003, at 09:08 am, Chris Arthur wrote: = ArialHi =A0 ArialI was wondering if anyone knows how o convert Protein PDB files to MOL2. I've tried using Babel howver it has problems when it comes to recognising the CE, NZ, CZ and SG (and varients of) atom codes instead calling them Du when it gets confused (I assume that...CE - epsilon C , NZ....zeta nitrogen , CZ ....zeta carbon and SG....gamma Sulfur) =A0 ArialAnyone=A0know of a GPL or GNU program that'll do this happily=A0? =A0 ArialChris=A0 =A0 =A0 = --Apple-Mail-2--516207747-- From chemistry-request@server.ccl.net Tue Feb 4 08:46:44 2003 Received: from vscan1-eur.ext.dsm.com ([163.175.162.4]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h14DkhI14505 for ; Tue, 4 Feb 2003 08:46:44 -0500 Received: from nlgln00ntms910.GLN00.DSM-GROUP.COM (localhost [127.0.0.1]) by vscan1-eur.ext.dsm.com (8.9.3/8.8.5-1.2.2m-19990317) with ESMTP id OAA16533 for ; Tue, 4 Feb 2003 14:46:42 +0100 (MET) Received: by nlgln00ntms910.gln00.dsm-group.com with Internet Mail Service (5.5.2653.19) id <1B36C2B8>; Tue, 4 Feb 2003 14:46:05 +0100 Message-ID: <6D47A7D05774D411959200508BDF739A024386F4@nlgln50ntms001.gln51.dsm-group.com> From: "Coussens, Betty" To: "'chemistry@ccl.net'" Subject: convergence problem with AM1 calculation using Gaussian98 Date: Tue, 4 Feb 2003 14:45:56 +0100 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-Type: text/plain; charset="iso-8859-1" Dear all, I am trying to perform an AM1 calculation on a system containing H, C, Si, O, Mg and Cl atoms using the Gaussian98 package. Previous calculations on this system using Vamp were succesful; however, due to cost reductions, this package is no longer available to me. With Gaussian98, severe convergence problems are encountered. Suprisingly, the same system converges without problems at the PM3 level. Does anybody has an idea what's going on in the AM1 computation? Thanks in advance! Bety Disclaimer 1. This e-mail is for the intended recipient only. If you have received it by mistake please let us know by reply and then delete it from your system; access, disclosure, copying, distribution or reliance on any of it by anyone else is prohibited. 2. If you as intended recipient have received this e-mail incorrectly, please notify the sender (via e-mail) immediately. This e-mail is confidential and may be legally privileged. DSM does not guarantee that the information sent and/or received by or with this e-mail is correct and does not accept any liability for damages related thereto. From chemistry-request@server.ccl.net Tue Feb 4 16:18:51 2003 Received: from prserv.net ([32.97.166.52]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h14LIpI23222 for ; Tue, 4 Feb 2003 16:18:51 -0500 Received: from attglobal.net (dhcp065-029-080-040.indy.rr.com[65.29.80.40]) by prserv.net (asmtp2) with SMTP id <2003020421184925200e3gpce> (Authid: jmmckel); Tue, 4 Feb 2003 21:18:49 +0000 Message-ID: <3E3FE960.964380C1@attglobal.net> Date: Tue, 04 Feb 2003 16:25:05 +0000 From: jmmckel@attglobal.net Reply-To: jmmckel@attglobal.net X-Mailer: Mozilla 4.79 [en] (WinNT; U) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: Benchmarks Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Folks, Once upon a time there was used a piece of cde from Gaussian70, I believe, for cpu benchmarks. I believe the code was part of the two electron integral code. Does anyone remember any of this and/or could point me to it? Suggestions for other useful scientific cpu tests are also welcome, particularly if public domain, and would stress the cpu and cpu-memory communication. Thanks! John McKelvey Return-Path: Message-ID: <000901c2ccb3$739d5be0$cf03103f@anick000> From: "David J Anick" To: chemistry@ccl.net Subject: Summary: Program to decompose spectrum into individual Gaussians Date: Tue, 4 Feb 2003 17:11:00 -0800 Dear CCL-ers, I recently submitted a query seeking any programs which, given a 1-D complex spectrum or line shape, can decompose it into a sum of overlapping Gaussians. Several of you responded, and I am grateful. Responses are listed below. Where I did some additional research, my comments are included preceded by 4 #s. Sincerely, David Anick David.Anick@gte.net ============================================================== There is an excellent program for this.... It has lots of choices for functions, and excellent statistics and graphics... PEAKFIT it's called... from SAS, I believe. John McKelvey jmmckel@attglobal.net #### Web search led inexorably to this product: #### http://www.systat.com/products/PeakFit/ ============================================================== Excel will work, with a little bit of luck... Use the Solver Add-in. Solver can be used to make a non-linear least-squares fitting routine -- which is what you want. It also conveniently plots your results. If you provide me with a fax number, I can fax you some pages out of a lab manual that explain how to do this. Roy Jensen royj@uvic.ca #### The reference provided in the fax was: M. Iannone, "Using Excel Solver: An addendum to the HCl Infrared Spectrum Experiment", J. Chem. Educ. 75 #9 (1998), p. 1188. ============================================================== Hello, Here is one program to do exactly what you want: http://www.obbligato.com/software/swizard/ You can model your spectrum as a sum of Gaussians, a sum of Lorentzian functions, or their mixture. With regards, S. Gorelsky Department of Chemistry, Stanford University, 333 Campus Drive, Stanford, CA 94305-5080 Fax: (650) 723-0553 Phone: (650) 723-0041 http://www.stanford.edu/~gorelsky/ #### This program appears to do the reverse: given a set of #### transition frequencies and intensities, it generates #### the spectrum. ============================================================== Dear David, An alternative with a nice GUI interface is GRAMS, a commercial product by Thermo-Galactic which runs in Windows. If you have a lot spectra and want an easy-to-use curve-fitting routine, this may be worth the asking price (~$600, last I checked), especially if you can use the other routines included (file IO, FT, peak finding/integration, etc.) Steve Steve Cabaniss Department of Chemistry University of New Mexico Albuquerque, NM 87131 (505) 277-4445 www.unm.edu/~cabaniss ============================================================== From chemistry-request@server.ccl.net Tue Feb 4 20:10:08 2003 Received: from freyr.chem.washington.edu ([128.95.128.138]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h151A6I10246 for ; Tue, 4 Feb 2003 20:10:07 -0500 Received: from localhost (fer@localhost) by freyr.chem.washington.edu (8.11.6/8.11.6) with ESMTP id h150HZM31465 for ; Tue, 4 Feb 2003 16:17:35 -0800 Date: Tue, 4 Feb 2003 16:17:34 -0800 (PST) From: "Fernando D. Vila" To: Computational Chemistry List Subject: EPR hyperfine coupling Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello people.. A graduate student in our lab (not a member of CCL) is doing some calculations of hyperfine coupling constants for some quartz clusters. I have very little experience in this area and was wondering if anybody here could point her to some references. Anything would probably do: tutorials, papers, books, personal experience, etc. She is using Gaussian and is specially interested in knowing about the most commonly used basis sets and methods. I'll make a summary of the responses on her behalf.. Best regards to everybody and thanks in advance. ******************************************************************************* Fernando D. Vila Voice (206)616-3207 Department of Chemistry Fax (206)685-8665 University of Washington E-mail fdv@u.washington.edu Seattle, WA 98195, USA WWW http://faculty.washington.edu/fdv *******************************************************************************