From chemistry-request@ccl.net Tue Apr 20 00:46:39 2004 Received: from mehl.gfz-potsdam.de (mehl.gfz-potsdam.de [139.17.1.100]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i3K5kXuR004487 for ; Tue, 20 Apr 2004 00:46:34 -0500 Received: from nfw1.gfz-potsdam.de (virscan [139.17.1.10]) by mehl.gfz-potsdam.de (8.12.10/8.12.10) with SMTP id i3K5lNnV013878 for ; Tue, 20 Apr 2004 07:47:24 +0200 (MET DST) Received: from exp17.gfz-potsdam.de ([139.17.140.117]) by nfw1; Tue, 20 Apr 2004 07:47:21 +0200 (CEST) Mime-Version: 1.0 (Apple Message framework v613) To: Computational Chemistry List Message-Id: <31F4320C-928E-11D8-B93C-000A95BA19DA=at=gfz-potsdam.de> Content-Type: multipart/alternative; boundary=Apple-Mail-2-1053627796 From: Matthias Gottschalk Subject: CCL:Heat capacities with g03 Date: Tue, 20 Apr 2004 07:47:22 +0200 X-Mailer: Apple Mail (2.613) X-Spam-Status: No, hits=4.5 required=7.5 tests=HTML_MESSAGE,IMPRONONCABLE_1, IMPRONONCABLE_2,MK_BAD_HTML_04,MY_BAD_DOT,MY_HTML_OBFU,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 --Apple-Mail-2-1053627796 Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; format=flowed Dear CCL, as a naive geoscientist I try to calculate the heat capacities of specific single molecules using g03 with something like that for Si2O7H6: %chk=si2ooh6.chk %mem=2048MB %nproc=1 # opt=(restart, verytight) Int=UltraFine freq pbepbe/6-311++g(3d,2p) geom=connectivity temperature=298.15 pressure=0.9869233 . . . . Everything runs fine. At the end I do get the following warnings within my results: ------------------- - Thermochemistry - ------------------- Temperature 298.150 Kelvin. Pressure .98700 Atm. Molecular mass: 173.96521 amu. Principal axes and moments of inertia in atomic units: 1 2 3 EIGENVALUES -- 890.447432428.485422488.20921 X -.63183 .74944 .19780 Y -.05907 -.30101 .95179 Z .77285 .58968 .23446 This molecule is an asymmetric top. Rotational symmetry number 1. Warning -- assumption of classical behavior for rotation may cause significant error Rotational temperatures (Kelvin) .09727 .03567 .03481 Rotational constants (GHZ): 2.02678 .74316 .72532 Zero-point vibrational energy 237943.2 (Joules/Mol) 56.86979 (Kcal/Mol) Warning -- explicit consideration of 20 degrees of freedom as vibrations may cause significant error Vibrational temperatures: 22.32 47.39 164.92 198.54 252.18 (Kelvin) 274.49 292.94 351.57 352.45 378.41 424.27 433.89 483.89 496.09 507.09 529.63 559.68 590.08 792.66 885.13 1071.96 1143.85 1168.05 1211.52 1224.45 1259.83 1274.99 1281.78 1340.88 1371.30 1389.84 1430.93 1501.79 5248.42 5427.26 5454.86 5462.94 5466.36 5467.29 Zero-point correction= .090628 (Hartree/Particle) Thermal correction to Energy= .103807 Thermal correction to Enthalpy= .104751 Thermal correction to Gibbs Free Energy= .050334 E (Thermal) CV S KCal/Mol Cal/Mol-Kelvin Cal/Mol-Kelvin Total 65.140 46.134 114.529 Electronic .000 .000 .000 Translational .889 2.981 41.394 Rotational .889 2.981 30.066 Vibrational 63.362 40.173 43.069 Vibration 1 .593 1.986 7.139 Vibration 2 .594 1.983 5.644 Vibration 3 .608 1.937 3.189 Vibration 4 .614 1.915 2.832 Vibration 5 .627 1.873 2.378 Vibration 6 .634 1.853 2.220 Vibration 7 .639 1.835 2.100 Vibration 8 .660 1.772 1.771 Vibration 9 .660 1.771 1.767 Vibration 10 .670 1.741 1.642 Vibration 11 .689 1.683 1.446 Vibration 12 .694 1.671 1.408 Vibration 13 .717 1.603 1.230 Vibration 14 .723 1.586 1.190 Vibration 15 .729 1.570 1.155 Vibration 16 .741 1.538 1.088 Vibration 17 .757 1.494 1.004 Vibration 18 .774 1.448 .926 Vibration 19 .906 1.138 .542 Vibration 20 .975 1.000 .424 In this regard I do have the following questions: 1. Some rotations might be frozen at low temperatures, but the rotational temperatures are here so low that I can ignore the first warning at ambient temperatures and above. Right? 2. Most if not all of the vibrational temperatures are significant. The calculated total heat capacity is too high because not all vibrations are active at the chosen temperature. Right? What can I do to get reliable heat capacities. Are there other options in g03? How to choose the right vibrational contributions to cv? Can I reduce the explicit consideration of 20 degrees of freedom? Where can I learn more how to deal with the problem practically? Any help is welcome. Matthias -- PD Dr. Matthias Gottschalk GeoForschungsZentrum Projektbereich 4.1 Telegrafenberg 14473 Potsdam Germany tel/fax +49 (0) 331 288-1418/1402 --Apple-Mail-2-1053627796 Content-Transfer-Encoding: 7bit Content-Type: text/enriched; charset=US-ASCII Dear CCL, as a naive geoscientist I try to calculate the heat capacities of specific single molecules using g03 with something like that for Si2O7H6: Courier%chk=si2ooh6.chk %mem=2048MB %nproc=1 # opt=(restart, verytight) Int=UltraFine freq pbepbe/6-311++g(3d,2p) geom=connectivity temperature=298.15 pressure=0.9869233 . . . . Everything runs fine. At the end I do get the following warnings within my results: Courier------------------- - Thermochemistry - ------------------- Temperature 298.150 Kelvin. Pressure .98700 Atm. Molecular mass: 173.96521 amu. Principal axes and moments of inertia in atomic units: 1 2 3 EIGENVALUES -- 890.447432428.485422488.20921 X -.63183 .74944 .19780 Y -.05907 -.30101 .95179 Z .77285 .58968 .23446 This molecule is an asymmetric top. Rotational symmetry number 1. Warning -- assumption of classical behavior for rotation may cause significant error Rotational temperatures (Kelvin) .09727 .03567 .03481 Rotational constants (GHZ): 2.02678 .74316 .72532 Zero-point vibrational energy 237943.2 (Joules/Mol) 56.86979 (Kcal/Mol) Warning -- explicit consideration of 20 degrees of freedom as vibrations may cause significant error Vibrational temperatures: 22.32 47.39 164.92 198.54 252.18 (Kelvin) 274.49 292.94 351.57 352.45 378.41 424.27 433.89 483.89 496.09 507.09 529.63 559.68 590.08 792.66 885.13 1071.96 1143.85 1168.05 1211.52 1224.45 1259.83 1274.99 1281.78 1340.88 1371.30 1389.84 1430.93 1501.79 5248.42 5427.26 5454.86 5462.94 5466.36 5467.29 Zero-point correction= .090628 (Hartree/Particle) Thermal correction to Energy= .103807 Thermal correction to Enthalpy= .104751 Thermal correction to Gibbs Free Energy= .050334 E (Thermal) CV S KCal/Mol Cal/Mol-Kelvin Cal/Mol-Kelvin Total 65.140 46.134 114.529 Electronic .000 .000 .000 Translational .889 2.981 41.394 Rotational .889 2.981 30.066 Vibrational 63.362 40.173 43.069 Vibration 1 .593 1.986 7.139 Vibration 2 .594 1.983 5.644 Vibration 3 .608 1.937 3.189 Vibration 4 .614 1.915 2.832 Vibration 5 .627 1.873 2.378 Vibration 6 .634 1.853 2.220 Vibration 7 .639 1.835 2.100 Vibration 8 .660 1.772 1.771 Vibration 9 .660 1.771 1.767 Vibration 10 .670 1.741 1.642 Vibration 11 .689 1.683 1.446 Vibration 12 .694 1.671 1.408 Vibration 13 .717 1.603 1.230 Vibration 14 .723 1.586 1.190 Vibration 15 .729 1.570 1.155 Vibration 16 .741 1.538 1.088 Vibration 17 .757 1.494 1.004 Vibration 18 .774 1.448 .926 Vibration 19 .906 1.138 .542 Vibration 20 .975 1.000 .424 In this regard I do have the following questions: 1. Some rotations might be frozen at low temperatures, but the rotational temperatures are here so low that I can ignore the first warning at ambient temperatures and above. Right? 2. Most if not all of the vibrational temperatures are significant. The calculated total heat capacity is too high because not all vibrations are active at the chosen temperature. Right? What can I do to get reliable heat capacities. Are there other options in g03? How to choose the right vibrational contributions to cv? Can I reduce the explicit consideration of 20 degrees of freedom? Where can I learn more how to deal with the problem practically? Any help is welcome. Matthias -- PD Dr. Matthias Gottschalk GeoForschungsZentrum Projektbereich 4.1 Telegrafenberg 14473 Potsdam Germany tel/fax +49 (0) 331 288-1418/1402 --Apple-Mail-2-1053627796-- From chemistry-request@ccl.net Mon Apr 19 19:30:53 2004 Received: from uncle-oscar.newcastle.edu.au (uncle-oscar.newcastle.edu.au [134.148.24.51]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i3K0UpuR020246 for ; Mon, 19 Apr 2004 19:30:52 -0500 Received: from conversion-daemon.uncle-oscar.newcastle.edu.au by uncle-oscar.newcastle.edu.au (Sun ONE Messaging Server 6.0 Patch 1 (built Jan 28 2004)) id <0HWG004010X5DT00(at)uncle-oscar.newcastle.edu.au> (original mail from Renate.Griffith(at)newcastle.edu.au) for CHEMISTRY(at)ccl.net; Tue, 20 Apr 2004 10:31:21 +1000 (EST) Received: from MC-GWDOM2.newcastle.edu.au ([134.148.4.94]) by uncle-oscar.newcastle.edu.au (Sun ONE Messaging Server 6.0 Patch 1 (built Jan 28 2004)) with ESMTP id <0HWG00EN91G9LG00(at)uncle-oscar.newcastle.edu.au> for CHEMISTRY(at)ccl.net; Tue, 20 Apr 2004 10:31:21 +1000 (EST) Received: from Sec-Dom1-MTA by MC-GWDOM2.newcastle.edu.au with Novell_GroupWise; Tue, 20 Apr 2004 10:31:38 +1000 Date: Tue, 20 Apr 2004 10:31:32 +1000 From: Renate Griffith Subject: CCL: MM2004 - Register Now!!! To: CHEMISTRY(at)ccl.net Message-id: MIME-version: 1.0 X-Mailer: Novell GroupWise Internet Agent 6.0.4 Beta Content-type: text/plain; charset=ISO-8859-1 Content-disposition: inline X-Spam-Status: No, hits=3.3 required=7.5 tests=ALUSSINAN_5,NO_RDNS2, PLING_PLING 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 i3K0UruR020252 Closing Dates: Abstract Submission: 23 Apr 04 Early Bird Registration: 30 Apr 04 The 9th Australian Molecular Modelling Workshop, MM2004, will be held in Sydney, Australia DATES: Wed 30th June till Sat 3rd July 2004 VENUE: InterContinental Hotel, Central Sydney Full details available at http://www.pco.com.au/mm2004 The workshop is a joint conference of the Molecular Graphics and Modelling Society (MGMS), the Royal Australian Chemical Institute (RACI), and the Modellers of Australia. The workshop will cover a broad range of topics spanning biological, chemical, and physical applications including: Bioinformatics StructureBased Drug Design LigandBased Drug Design Protein Modelling 1st Principles Techniques Teaching Molecular Modelling Material Science Confirmed Speakers include: Prof. Peter Boyd, University of Auckland Prof. Tim Clark, University of ErlangenN|rnberg Dr David Edwards, Accelrys San Diego Prof. Marcus Elstner, University of Paderborn Dr Michael Frisch, Gaussian Inc. Dr Valerie Gillet, University of Sheffield Dr Jill Gready, Australian National University Prof. David Jones, University College London Dr Ricardo Mancera, De Novo Pharmaceuticals Prof. Leo Radom, University of Sydney Prof. Gustavo Scuseria, Rice University Dr Mark Smythe, Institute for Molecular Bioscience Prof. Catherine Stampfl, University of Sydney Prof. David Winkler, CSIRO Molecular Science Dr Irene Yarovsky, RMIT University Dr Brian Yates, University of Tasmania MM2004 will start with a joint session on Wednesday afternoon, with the 6th Australia / Japan Symposium on Drug Design and Development (6DDD). 6DDD starts 27th June, also in Sydney. http://www.usyd.edu.au/pharmacology/aalab/6DDD/ MM2004 will also be preceded in Sydney by a workshop sponsored by Gaussian Inc. on ab initio, density functional, solid-state, and biological molecular computational methods, running from Monday 28th June till Thursday 1st July. http://www.gaussian.com/g_workshops/ws_sydney.htm MM2004 will finish in time for attendees to travel on to Cairns, Queensland, Australia, for the meeting of the Organic Chemistry Division of the RACI, which starts 4th July, 2004. http://www.cairnsconferences.com.au/ISMCORG2004 For more information contact: Dr Renate Griffith, School of Environmental and Life Sciences, University of Newcastle Email: Renate.Griffith(at)newcastle.edu.au Dr. Renate Griffith Lecturer in Medicinal Chemistry and Molecular Design School of Environmental and Life Sciences Life Sciences Building (Mail to: Biology Building) The University of Newcastle Callaghan, NSW 2308, Australia Email: Renate.Griffith(at)newcastle.edu.au Phone: +61 2 4921 6990 Fax: +61 2 4921 6923 From chemistry-request@ccl.net Tue Apr 20 08:01:02 2004 Received: from postoffice7.mail.cornell.edu (postoffice7.mail.cornell.edu [132.236.56.22]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i3KD10uR021642 for ; Tue, 20 Apr 2004 08:01:01 -0500 Received: from cornell.edu (67-42-23-149.slkc.qwest.net [67.42.23.149]) by postoffice7.mail.cornell.edu (8.12.10/8.12.6) with ESMTP id i3KD17YU021092; Tue, 20 Apr 2004 09:01:48 -0400 (EDT) Message-ID: <40851F13.7010108)at(cornell.edu> Date: Tue, 20 Apr 2004 07:01:07 -0600 From: Richard Wood User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.4) Gecko/20030624 Netscape/7.1 (ax) X-Accept-Language: en-us, en MIME-Version: 1.0 To: "chemistry)at(ccl.net" Subject: Re: CCL:converting an sdf database into a chemfinder database References: <4316.129.123.250.158.1082407282.squirrel)at(webmail.cornell.edu> In-Reply-To: <4316.129.123.250.158.1082407282.squirrel)at(webmail.cornell.edu> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit X-PMX-Version: 4.5.0.92886, Antispam-Core: 4.0.4.93542, Antispam-Data: 2004.4.19.97922 X-Spam-Status: No, hits=1.1 required=7.5 tests=FROM_ENDS_IN_NUMS, TO_ADDRESS_EQ_REAL 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 all I should note that the file that I am trying to open and convert, CANS03.sdf, is a file that I obtained from the NCI database (I don't have the url with me, it's at work), and it originally couldn't be opened with CACTVS, until someone at the NCI "fixed" it. CACTVS now reads it, but won't write it out, at least not the whole file. The part that CACTVS does write out, can be read by Chemfinder, however. CACTVS will currently write out the first 37 structures I believe and then not write anymore, but only if I write the first 15 and then append the next 15 and so on. SO it writes two sets of 15 structures and then 7 of the next 15 and then stops. I'm doing this using the CACTVS browser, btw. I hope this helps all of those that responded with questions/suggestions. TIA, Richard Richard L. Wood wrote: >Hi all > >I'm wondering if there is anyway to convert an sdf database into something >that Chemfinder can read easily. > >Chemfinder is supposed to be able to import sdf databases, but the file I >have must not be formatted correctly, because chemfinder can't read it. > >Thanks in advance, >Richard > > >-= 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) >-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > -- Richard L. Wood, Ph. D. Computational Chemist SynVax, Inc. N. Logan, UT 84341 From chemistry-request@ccl.net Tue Apr 20 06:12:00 2004 Received: from oulu.fi (ousrvr.oulu.fi [130.231.240.1]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i3KBBwuR017471 for ; Tue, 20 Apr 2004 06:11:59 -0500 Received: from cc.oulu.fi (sun3.oulu.fi [130.231.240.13]) by oulu.fi (8.12.10/8.12.10) with ESMTP id i3KBCor3004141 for ; Tue, 20 Apr 2004 14:12:50 +0300 (EEST) Received: from sun3.oulu.fi (sun3.oulu.fi [130.231.240.13]) by cc.oulu.fi (8.12.10/8.12.10) with ESMTP id i3KBCmuF016948 for ; Tue, 20 Apr 2004 14:12:48 +0300 (EEST) Date: Tue, 20 Apr 2004 14:12:48 +0300 (EEST) From: Satyan Sharma X-X-Sender: satyan..at..sun3.oulu.fi To: chemistry..at..ccl.net Subject: G03 Error Message-ID: 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 Dear CCLers: I am trying do study enzyme reaction. The system has active site residues with substrate bound. I want to treat the species involved in reaction at higher level and rest at PM3 level. For this I am using ONIOM Calculation in G03. But I get following Error. -------------------------------------------------- dumping /fiocom/, unit = 2 NFiles = 1 SizExt = 0 WInBlk = 1024 defal = F LstWrd = 66560 FType=2 FMxFil=10000 Number 0 Base 40960 End 66560 End1 66560 Wr Pntr 40960 Rd Pntr 40960 Length 25600 dumping /fiocom/, unit = 3 NFiles = 1 SizExt = 524288 WInBlk = 512 defal = T LstWrd = 66048 FType=2 FMxFil=10000 Number 0 Base 40448 End 66048 End1 66048 Wr Pntr 40448 Rd Pntr 40448 Length 25600 Error termination in NtrErr: NtrErr Called from FileIO. -------------------------------------------------------- Any clues anybody, With best regards, Satyan From chemistry-request@ccl.net Tue Apr 20 11:11:32 2004 Received: from smtpgw.sud-chemieinc.com (smtpgw.sud-chemieinc.com [208.23.162.5]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i3KGBTuR027574 for ; Tue, 20 Apr 2004 11:11:30 -0500 Received: from localhost (smtpgw.sud-chemieinc.com [127.0.0.1]) by localhost.sud-chemieinc.com (Postfix) with ESMTP id CF15848C7A; Tue, 20 Apr 2004 12:11:40 -0400 (EDT) Received: from smtpgw.sud-chemieinc.com ([127.0.0.1]) by localhost (smtpgw.sud-chemieinc.com [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id 03897-10; Tue, 20 Apr 2004 12:11:39 -0400 (EDT) Received: from srvkyem1.americas.sc-world.com (srvkyem1.americas.sc-world.com [10.16.100.68]) by smtpgw.sud-chemieinc.com (Postfix) with ESMTP id C8B52480D2; Tue, 20 Apr 2004 12:11:39 -0400 (EDT) X-MimeOLE: Produced By Microsoft Exchange V6.0.6487.1 content-class: urn:content-classes:message MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01C426F2.2997CF80" Subject: RE: Heat capacities with g03 Date: Tue, 20 Apr 2004 12:11:39 -0400 Message-ID: <9DD56492790889439F731F5BD6DACA0047FD34=at=srvkyem1.americas.sc-world.com> X-MS-Has-Attach: X-MS-TNEF-Correlator: Thread-Topic: Heat capacities with g03 Thread-Index: AcQmoSOioR6LoS9XSjapR/6vW4KJeQATRpUQ From: "Shobe, David" To: "Matthias Gottschalk" , "CCL computational chemistry list (E-mail)" X-Spam-Status: No, hits=4.5 required=7.5 tests=HTML_20_30,HTML_FONTCOLOR_BLUE, HTML_MESSAGE,HTML_TITLE_EMPTY,IMPRONONCABLE_1,IMPRONONCABLE_2, 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_001_01C426F2.2997CF80 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable As far as the warning goes: Warning -- assumption of classical behavior for rotation=20 may cause significant error=20 there is an option freq=3Dhindrot that recognizes internal rotations and = treats them accordingly. Not that I've had the need to use it in my own = calculations. The algorithm was I'm sure designed with organic = molecules in mind, and perhaps it won't handle the ~180=B0 Si-O-H and = Si-O-Si angles found in siloxanes well, but it's one option. =20 =20 If you have some independent way to calculate the internal rotational = enthalpy and entropy, you can: take Gaussian's total enthalpy and entropy, and=20 subtract the contribution of the suspect "vibrations"=20 (That's what the lines beginning "Vibration 1", etc. are for), = and=20 add in the independently calculated internal rotational enthalpy and = entropy. =20 As for the vibrational temperatures: I wouldn't worry about these. AFAIK = Gaussian correctly determines the thermodynamic contributions of each = vibration, regardless of the vibration temperature, subject only to the = assumption that the vibrational modes are harmonic oscillators and = independent of other molecular motions. I *hope* this is correct, = anyway! =20 --David Shobe, Ph.D., M.L.S.=20 S=FCd-Chemie, Inc.=20 phone (502) 634-7409=20 fax (502) 634-7724=20 Don't bother flaming me: I'm behind a firewall.=20 -----Original Message----- From: Computational Chemistry List [mailto:chemistry-request=at=ccl.net]On = Behalf Of Matthias Gottschalk Sent: Tuesday, April 20, 2004 1:47 AM To: Computational Chemistry List Subject: CCL:Heat capacities with g03 Dear CCL,=20 as a naive geoscientist I try to calculate the heat capacities of = specific single=20 molecules using g03 with something like that for Si2O7H6:=20 %chk=3Dsi2ooh6.chk=20 %mem=3D2048MB=20 %nproc=3D1=20 # opt=3D(restart, verytight) Int=3DUltraFine freq pbepbe/6-311++g(3d,2p) = geom=3Dconnectivity temperature=3D298.15 pressure=3D0.9869233=20 >.=20 >.=20 >.=20 >.=20 Everything runs fine. At the end I do get the following warnings within = my results:=20 -------------------=20 - Thermochemistry -=20 -------------------=20 Temperature 298.150 Kelvin. Pressure .98700 Atm.=20 Molecular mass: 173.96521 amu.=20 Principal axes and moments of inertia in atomic units:=20 1 2 3=20 EIGENVALUES -- 890.447432428.485422488.20921=20 X -.63183 .74944 .19780=20 Y -.05907 -.30101 .95179=20 Z .77285 .58968 .23446=20 This molecule is an asymmetric top.=20 Rotational symmetry number 1.=20 Warning -- assumption of classical behavior for rotation=20 may cause significant error=20 Rotational temperatures (Kelvin) .09727 .03567 .03481=20 Rotational constants (GHZ): 2.02678 .74316 .72532=20 Zero-point vibrational energy 237943.2 (Joules/Mol)=20 56.86979 (Kcal/Mol)=20 Warning -- explicit consideration of 20 degrees of freedom as=20 vibrations may cause significant error=20 Vibrational temperatures: 22.32 47.39 164.92 198.54 252.18=20 (Kelvin) 274.49 292.94 351.57 352.45 378.41=20 424.27 433.89 483.89 496.09 507.09=20 529.63 559.68 590.08 792.66 885.13=20 1071.96 1143.85 1168.05 1211.52 1224.45=20 1259.83 1274.99 1281.78 1340.88 1371.30=20 1389.84 1430.93 1501.79 5248.42 5427.26=20 5454.86 5462.94 5466.36 5467.29=20 Zero-point correction=3D .090628 (Hartree/Particle)=20 Thermal correction to Energy=3D .103807=20 Thermal correction to Enthalpy=3D .104751=20 Thermal correction to Gibbs Free Energy=3D .050334=20 E (Thermal) CV S=20 KCal/Mol Cal/Mol-Kelvin Cal/Mol-Kelvin=20 Total 65.140 46.134 114.529=20 Electronic .000 .000 .000=20 Translational .889 2.981 41.394=20 Rotational .889 2.981 30.066=20 Vibrational 63.362 40.173 43.069=20 Vibration 1 .593 1.986 7.139=20 Vibration 2 .594 1.983 5.644=20 Vibration 3 .608 1.937 3.189=20 Vibration 4 .614 1.915 2.832=20 Vibration 5 .627 1.873 2.378=20 Vibration 6 .634 1.853 2.220=20 Vibration 7 .639 1.835 2.100=20 Vibration 8 .660 1.772 1.771=20 Vibration 9 .660 1.771 1.767=20 Vibration 10 .670 1.741 1.642=20 Vibration 11 .689 1.683 1.446=20 Vibration 12 .694 1.671 1.408=20 Vibration 13 .717 1.603 1.230=20 Vibration 14 .723 1.586 1.190=20 Vibration 15 .729 1.570 1.155=20 Vibration 16 .741 1.538 1.088=20 Vibration 17 .757 1.494 1.004=20 Vibration 18 .774 1.448 .926=20 Vibration 19 .906 1.138 .542=20 Vibration 20 .975 1.000 .424=20 In this regard I do have the following questions:=20 1. Some rotations might be frozen at low temperatures, but the = rotational temperatures are here=20 so low that I can ignore the first warning at ambient temperatures and = above. Right?=20 2. Most if not all of the vibrational temperatures are significant. The = calculated total heat capacity=20 is too high because not all vibrations are active at the chosen = temperature. Right? What can I do=20 to get reliable heat capacities.=20 Are there other options in g03?=20 How to choose the right vibrational contributions to cv?=20 Can I reduce the explicit consideration of 20 degrees of freedom?=20 Where can I learn more how to deal with the problem practically?=20 Any help is welcome.=20 Matthias=20 --=20 PD Dr. Matthias Gottschalk=20 GeoForschungsZentrum=20 Projektbereich 4.1=20 Telegrafenberg=20 14473 Potsdam=20 Germany=20 tel/fax +49 (0) 331 288-1418/1402=20 ------_=_NextPart_001_01C426F2.2997CF80 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
As far=20 as the warning goes:
Warning -- = assumption of=20 classical behavior for rotation
may cause = significant error=20
there=20 is an option freq=3Dhindrot that recognizes internal rotations and = treats them=20 accordingly.  Not that I've had the need to use it in my own=20 calculations.  The algorithm was I'm sure designed with organic = molecules=20 in mind, and perhaps it won't handle the ~180=B0 Si-O-H and Si-O-Si = angles found=20 in siloxanes well, but it's one option. 
 
If you=20 have some independent way to calculate the internal rotational enthalpy = and=20 entropy, you can:
    take Gaussian's total enthalpy and entropy, = and=20
    subtract the contribution of the suspect = "vibrations"=20
        (That's what the = lines=20 beginning "Vibration 1", etc. are for), and
    add in the independently calculated internal = rotational enthalpy and entropy.
 
As for=20 the vibrational temperatures: I wouldn't worry about these. = AFAIK Gaussian=20 correctly determines the thermodynamic contributions of each vibration,=20 regardless of the vibration temperature, subject only to the assumption = that the=20 vibrational modes are harmonic oscillators and independent of other = molecular=20 motions.  I *hope* this is correct, anyway!
 

--David Shobe, Ph.D., M.L.S. =
S=FCd-Chemie, Inc.
phone=20 (502) 634-7409
fax (502) = 634-7724

Don't bother flaming me: I'm behind a=20 firewall.

-----Original Message-----
From: Computational = Chemistry List=20 [mailto:chemistry-request=at=ccl.net]On Behalf Of Matthias=20 Gottschalk
Sent: Tuesday, April 20, 2004 1:47 = AM
To:=20 Computational Chemistry List
Subject: CCL:Heat capacities = with=20 g03

Dear CCL,

as a naive geoscientist I try to calculate the heat capacities of = specific single
molecules using g03 with something like that for Si2O7H6: =

%chk=3Dsi2ooh6.chk
%mem=3D2048MB
%nproc=3D1
# opt=3D(restart, verytight) Int=3DUltraFine freq = pbepbe/6-311++g(3d,2p)=20
geom=3Dconnectivity temperature=3D298.15 pressure=3D0.9869233 =
>.
>.
>.
>.


Everything runs fine. At the end I do get the following warnings = within=20 my results:

-------------------
- Thermochemistry -
-------------------
Temperature 298.150 Kelvin. Pressure .98700 Atm.
Molecular mass: 173.96521 amu.
Principal axes and moments of inertia in atomic units:
1 2 3
EIGENVALUES -- 890.447432428.485422488.20921
X -.63183 .74944 .19780
Y -.05907 -.30101 .95179
Z .77285 .58968 .23446
This molecule is an asymmetric top.
Rotational symmetry number 1.
Warning -- assumption of classical behavior for rotation
may cause significant error
Rotational temperatures (Kelvin) .09727 .03567 .03481
Rotational constants (GHZ): 2.02678 .74316 .72532
Zero-point vibrational energy 237943.2 (Joules/Mol)
56.86979 (Kcal/Mol)
Warning -- explicit consideration of 20 degrees of freedom as =
vibrations may cause significant error
Vibrational temperatures: 22.32 47.39 164.92 198.54 252.18
(Kelvin) 274.49 292.94 351.57 352.45 378.41
424.27 433.89 483.89 496.09 507.09
529.63 559.68 590.08 792.66 885.13
1071.96 1143.85 1168.05 1211.52 1224.45
1259.83 1274.99 1281.78 1340.88 1371.30
1389.84 1430.93 1501.79 5248.42 5427.26
5454.86 5462.94 5466.36 5467.29
Zero-point correction=3D .090628 (Hartree/Particle)
Thermal correction to Energy=3D .103807
Thermal correction to Enthalpy=3D .104751
Thermal correction to Gibbs Free Energy=3D .050334
E (Thermal) CV S
KCal/Mol Cal/Mol-Kelvin Cal/Mol-Kelvin
Total 65.140 46.134 114.529
Electronic .000 .000 .000
Translational .889 2.981 41.394
Rotational .889 2.981 30.066
Vibrational 63.362 40.173 43.069
Vibration 1 .593 1.986 7.139
Vibration 2 .594 1.983 5.644
Vibration 3 .608 1.937 3.189
Vibration 4 .614 1.915 2.832
Vibration 5 .627 1.873 2.378
Vibration 6 .634 1.853 2.220
Vibration 7 .639 1.835 2.100
Vibration 8 .660 1.772 1.771
Vibration 9 .660 1.771 1.767
Vibration 10 .670 1.741 1.642
Vibration 11 .689 1.683 1.446
Vibration 12 .694 1.671 1.408
Vibration 13 .717 1.603 1.230
Vibration 14 .723 1.586 1.190
Vibration 15 .729 1.570 1.155
Vibration 16 .741 1.538 1.088
Vibration 17 .757 1.494 1.004
Vibration 18 .774 1.448 .926
Vibration 19 .906 1.138 .542
Vibration 20 .975 1.000 .424

In this regard I do have the following questions:

1. Some rotations might be frozen at low temperatures, but the = rotational=20 temperatures are here
so low that I can ignore the first warning at ambient = temperatures and=20 above. Right?

2. Most if not all of the vibrational temperatures are = significant. The=20 calculated total heat capacity
is too high because not all vibrations are active at the chosen=20 temperature. Right? What can I do
to get reliable heat capacities.

Are there other options in g03?
How to choose the right vibrational contributions to cv?
Can I reduce the explicit consideration of 20 degrees of freedom? =
Where can I learn more how to deal with the problem practically?=20

Any help is welcome.

Matthias

--

PD Dr. Matthias Gottschalk
GeoForschungsZentrum
Projektbereich 4.1
Telegrafenberg
14473 Potsdam
Germany

tel/fax +49 (0) 331 288-1418/1402 =
------_=_NextPart_001_01C426F2.2997CF80-- From chemistry-request@ccl.net Tue Apr 20 07:36:48 2004 Received: from grassmarket.ucs.ed.ac.uk (grassmarket.ucs.ed.ac.uk [129.215.166.64]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i3KCaluR020613 for ; Tue, 20 Apr 2004 07:36:47 -0500 Received: from grassmarket.ucs.ed.ac.uk (localhost [127.0.0.1]) by grassmarket.ucs.ed.ac.uk (8.12.10/8.12.10) with ESMTP id i3KCbdla028727 for ; Tue, 20 Apr 2004 13:37:40 +0100 (BST) Received: (from nobody@localhost) by grassmarket.ucs.ed.ac.uk (8.12.10/8.12.9/Submit) id i3KCbddM028711 for chemistry|at|ccl.net; Tue, 20 Apr 2004 13:37:39 +0100 (BST) X-Authentication-Warning: grassmarket.ucs.ed.ac.uk: nobody set sender to P.Lozano-Casal|at|ed.ac.uk using -f Received: from parsons-res11.chem.ed.ac.uk (parsons-res11.chem.ed.ac.uk [129.215.220.249]) by sms.ed.ac.uk (IMP) with HTTP for ; Tue, 20 Apr 2004 13:37:39 +0100 Message-ID: <1082464659.408519939afbf|at|sms.ed.ac.uk> Date: Tue, 20 Apr 2004 13:37:39 +0100 From: Patricia Lozano-Casal To: chemistry|at|ccl.net Subject: QUESTION ABOUT COULOMBIC POTENTIAL MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-15 Content-Transfer-Encoding: 8bit User-Agent: Internet Messaging Program (IMP) 3.2.3 X-Spam-Status: No, hits=1.6 required=7.5 tests=LINES_OF_YELLING, LINES_OF_YELLING_2,SUBJ_ALL_CAPS autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net SUBJECT: QUESTION ABOUT COULOMBIC POTENTIAL Dear all, I am trying to write a program to calculate the electrostatic contribution of the lattice energy for molecular crystals. I have run plane-wave DFT calculations (using the CASTEP package) to calculate the total lattice energy and using Mulliken charges I hoped to estimate the electrostatic contribution by coding a simple Coulombic potential. But, I get really weird results!! I am overestimating my lattice energy by many orders of magnitude. I know that Mulliken charges are not the ideal point charge to use for this but I had not expected my numbers to be that wrong. Could anybody help or if not, could anybody recommend and existing program to use instead (preferably free)? Many thanks, Patricia Lozano-Casal (p.lozano-casal|at|ed.ac.uk) -- Room 85, School of Chemistry, Joseph Black Building, Kings Buildings, West Mains Road, Edinburgh, EH9 3JJ United Kingdom Tel: +441316504804 From chemistry-request@ccl.net Tue Apr 20 15:21:16 2004 Received: from helix.nih.gov (helix.nih.gov [128.231.2.3]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i3KKLFuR005029 for ; Tue, 20 Apr 2004 15:21:15 -0500 Received: (from igorf@localhost) by helix.nih.gov (8.11.7-8.359.2.8/8.11.6) id i3KKEF615794890; Tue, 20 Apr 2004 16:14:15 -0400 (EDT) Date: Tue, 20 Apr 2004 16:14:15 -0400 From: "Igor Filippov [Contr]" To: Richard Wood cc: "chemistry..at..ccl.net" Subject: Re: CCL:converting an sdf database into a chemfinder database In-Reply-To: <40851F13.7010108..at..cornell.edu> Message-ID: References: <4316.129.123.250.158.1082407282.squirrel..at..webmail.cornell.edu> <40851F13.7010108..at..cornell.edu> MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Spam-Status: No, hits=0.3 required=7.5 tests=FCS_URI_NODOTS autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Richard, Is it possible that you're talking about NCI database processed by our group (CADD @ LMC @ NCI-Frederick) ? The website is http://cactus.nci.nih.gov where you can download public portion of NCI database (processed). As the whole processing was done in CACTVS it is hard to imagine that one is not able to read/write the structures anymore. If you downloaded NCI database somewhere else then it is, of course, impossible to tell what did you get and what the problem with it might be. Regards, Igor Filippov Contractor - SAIC-Frederick Computer Aided Drug Design group Laboratory of Medicinal Chemistry National Cancer Institute On Tue, 20 Apr 2004, Richard Wood wrote: > Hi all > > I should note that the file that I am trying to open and convert, > CANS03.sdf, is a file that I obtained from the NCI database (I don't > have the url with me, it's at work), and it originally couldn't be > opened with CACTVS, until someone at the NCI "fixed" it. CACTVS now > reads it, but won't write it out, at least not the whole file. The part > that CACTVS does write out, can be read by Chemfinder, however. CACTVS > will currently write out the first 37 structures I believe and then not > write anymore, but only if I write the first 15 and then append the next > 15 and so on. SO it writes two sets of 15 structures and then 7 of the > next 15 and then stops. I'm doing this using the CACTVS browser, btw. > > I hope this helps all of those that responded with questions/suggestions. > > TIA, > Richard > > Richard L. Wood wrote: > > >Hi all > > > >I'm wondering if there is anyway to convert an sdf database into something > >that Chemfinder can read easily. > > > >Chemfinder is supposed to be able to import sdf databases, but the file I > >have must not be formatted correctly, because chemfinder can't read it. > > > >Thanks in advance, > >Richard > > > > > > > > > > > > > > > > -- > Richard L. Wood, Ph. D. > Computational Chemist > SynVax, Inc. > N. Logan, UT 84341 > > > > > > -= 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 Apr 20 20:55:14 2004 Received: from web15407.mail.cnb.yahoo.com (web15407.mail.cnb.yahoo.com [202.43.216.210]) by server.ccl.net (8.12.8/8.12.8) with SMTP id i3L1t9uR018262 for >ccl.net>; Tue, 20 Apr 2004 20:55:11 -0500 Message-ID: <20040421015603.88629.qmail<>web15407.mail.cnb.yahoo.com> Received: from [202.106.124.167] by web15407.mail.cnb.yahoo.com via HTTP; Wed, 21 Apr 2004 09:56:03 CST Date: Wed, 21 Apr 2004 09:56:03 +0800 (CST) From: =?gb2312?q?Jinsong=20Zhao?= >yahoo.com.cn> Subject: How to change the molecular view in gOpenMol To: CCL >ccl.net> MIME-Version: 1.0 Content-Type: text/plain; charset=gb2312 Content-Transfer-Encoding: 8bit X-Spam-Status: No, hits=6.1 required=7.5 tests=DATE_IN_PAST_12_24, IMPRONONCABLE_2,MK_YAHOO_REDIR_01,RCVD_IN_DSBL,RCVD_IN_NJABL, RCVD_IN_NJABL_RELAY,WLS_URI_OPT_150 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, I have some difficult to view two molecular structure in ONE window with licorice model. I set the "Cyl.rad" to 0.1, one molecule will change to the correct view, however, the other also display in licorice model but with "Cyl.rad" at 0.3. In one word, the change of "Cyl.rad" and/or "Sph.rad" just change one molecule. Can anyone here give me some help? Any suggestions will be really appreciated. Best wishes, Jinsong ===== (Mr.) Jinsong Zhao Ph.D. Candidate School of the Environment Nanjing University No.22 Hankou Road, Najing 210093 P.R. China E-mail: zh_jinsong<>yahoo.com.cn _________________________________________________________ Do You Yahoo!? ;]FUTTSNO7>g#,MfSNO7#,VP4s=1#! http://cn.rd.yahoo.com/mail_cn/tag/SIG=1402c0to2/**http%3A%2F%2Fhp.allyes.com%2Flaserjet%2Fgamestory%2Findex.html%3Fjumpid%3Dex_hphqapcn_MongooseLJ1010%2F201073CN407016%2FYahoo From chemistry-request@ccl.net Tue Apr 20 20:35:00 2004 Received: from hotmail.com ([207.68.164.207]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i3L1YwuR017830 for ; Tue, 20 Apr 2004 20:34:59 -0500 Received: from mail pickup service by hotmail.com with Microsoft SMTPSVC; Tue, 20 Apr 2004 18:35:43 -0700 Received: from 210.83.210.9 by sea2-dav72.sea2.hotmail.com with DAV; Wed, 21 Apr 2004 01:35:42 +0000 X-Originating-IP: [210.83.210.9] X-Originating-Email: [liuxin_dut=at=hotmail.com] X-Sender: liuxin_dut=at=hotmail.com From: "li" To: Subject: CCL: Basis sets for transitional metals Date: Wed, 21 Apr 2004 09:35:38 +0800 MIME-Version: 1.0 Content-Type: text/plain; charset="gb2312" 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 Message-ID: X-OriginalArrivalTime: 21 Apr 2004 01:35:43.0683 (UTC) FILETIME=[F64CB930:01C42740] X-Spam-Status: No, hits=1.5 required=7.5 tests=MIME_BASE64_TEXT,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 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from base64 to 8bit by server.ccl.net id i3L1Z0uR017834 Hi! I am using G98 now, and I am trying to get the electronic structure of CO molecule. By using all the methods implemented in G98, I found that all the result give a similar result - O gets charges from C and has a negative charge. This is quite different from the description I found in books, C should get charge from O and has a negative charge. This makes me confused. What should I do to make a correct calculation of CO? I hope that you would not mind giving me some detailed instruction on the calculation. Sincerely yours Xin, Liu