From chemistry-request@server.ccl.net Thu Mar 27 10:25:51 2003 Return-Path: Message-ID: <20030327022551.55873.qmail@web15210.mail.bjs.yahoo.com> Received: from [61.240.111.196] by web15210.mail.bjs.yahoo.com via HTTP; Thu, 27 Mar 2003 10:25:51 CST Date: Thu, 27 Mar 2003 10:25:51 +0800 (CST) From: =?gb2312?q?Jinsong=20Zhao?= Subject: How to calculate the molecular similarity To: CCL MIME-Version: 1.0 Content-Type: text/plain; charset=gb2312 Content-Transfer-Encoding: 8bit Dear cclers, Can someone here like to recommend me some methods to calculate the molecular quantum similarity, and to give me some suggestions on the molecular alignment of two or more molecules? Thank you very much in advance! Sincerely yours, Jinsong Zhao _________________________________________________________ Do You Yahoo!? QE;"M(MxBgKTV, KfJ1Kf5XCb7Q?(@-OK~~ http://rd.yahoo.com/mail_cn/tag/?http://cn.messenger.yahoo.com//chat/index.html From chemistry-request@server.ccl.net Thu Mar 27 01:34:09 2003 Received: from web15203.mail.bjs.yahoo.com ([61.135.128.133]) by server.ccl.net (8.11.6/8.11.0) with SMTP id h2R6Y8e11615 for ; Thu, 27 Mar 2003 01:34:09 -0500 Message-ID: <20030327063407.68582.qmail@web15203.mail.bjs.yahoo.com> Received: from [61.240.111.196] by web15203.mail.bjs.yahoo.com via HTTP; Thu, 27 Mar 2003 14:34:07 CST Date: Thu, 27 Mar 2003 14:34:07 +0800 (CST) From: =?gb2312?q?Jinsong=20Zhao?= Subject: How to calculate the bond energy To: CCL MIME-Version: 1.0 Content-Type: text/plain; charset=gb2312 Content-Transfer-Encoding: 8bit Dear all, I hope to calculate the energy of each bond in a organic compound. I am not familiar with quantum or computational chemistry. Would you like to give me some advice on this aspect? Thank you very much in advance! Sincerely yours, Jinsong Zhao _________________________________________________________ Do You Yahoo!? ÑÅ»¢Í¨ÍøÂçKTV, ËæʱËæµØÃâ·Ñ¿¨À­OK~~ http://rd.yahoo.com/mail_cn/tag/?http://cn.messenger.yahoo.com//chat/index.html From chemistry-request@server.ccl.net Thu Mar 27 03:38:45 2003 Received: from shiva.jussieu.fr ([134.157.0.129]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h2R8cie14000 for ; Thu, 27 Mar 2003 03:38:44 -0500 Received: from as2100.itodys.jussieu.fr (as2100.itodys.jussieu.fr [134.157.24.23]) by shiva.jussieu.fr (8.12.8/jtpda-5.4) with SMTP id h2R8cfZC011944 for ; Thu, 27 Mar 2003 09:38:42 +0100 (CET) Date: Thu, 27 Mar 2003 09:38:40 +0100 Message-Id: <03032709384090@itodys.jussieu.fr> From: petitjean@itodys.jussieu.fr To: chemistry@ccl.net Subject: CCL:Re: How to calculate the molecular similarity X-VMS-To: SMTP%"chemistry@ccl.net" X-Antivirus: scanned by sophie at shiva.jussieu.fr To: CCL Subject: CCL:Re: How to calculate the molecular similarity CSR, which is based on a geometric method, is downloadable from: http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html#CSR It performs a 3D alignment and extracts the common 3D motif. Michel Petitjean, Email: petitjean@itodys.jussieu.fr ITODYS (CNRS, UMR 7086) ptitjean@ccr.jussieu.fr 1 rue Guy de la Brosse Phone: +33 (0)1 44 27 48 57 75005 Paris, France. FAX : +33 (0)1 44 27 68 14 http://petitjeanmichel.free.fr/itoweb.petitjean.html >Dear cclers, > >Can someone here like to recommend me some methods to >calculate the molecular quantum similarity, and to >give me some suggestions on the molecular alignment of >two or more molecules? > >Thank you very much in advance! > >Sincerely yours, >Jinsong Zhao From chemistry-request@server.ccl.net Thu Mar 27 02:14:46 2003 Received: from century.fen.bilkent.edu.tr ([139.179.97.100]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h2R7Eie12404 for ; Thu, 27 Mar 2003 02:14:44 -0500 Received: from fen.bilkent.edu.tr (fenII-124.fen.bilkent.edu.tr [139.179.97.239]) by century.fen.bilkent.edu.tr (8.12.8/8.12.8) with ESMTP id h2R79Iga016074 for ; Thu, 27 Mar 2003 09:09:20 +0200 (EET) Message-ID: <3E82A5D1.4030605@fen.bilkent.edu.tr> Date: Thu, 27 Mar 2003 09:18:41 +0200 From: Ulrike Salzner Organization: Bilkent University User-Agent: Mozilla/5.0 (Windows; U; Win98; en-US; rv:0.9.4) Gecko/20011128 Netscape6/6.2.1 X-Accept-Language: en-us MIME-Version: 1.0 To: chemistry@ccl.net Subject: MPA in G98] Content-Type: multipart/mixed; boundary="------------070606070805050709010207" This is a multi-part message in MIME format. --------------070606070805050709010207 Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit Thanks to everyone who replied to my question. It seems that G98 can not perform this task. I received two links to programs, one commercial, one free of charge. The original answers are given below. I tried to install Reinaldo's program on a PC running Linux RedHat 7.2. Since the program requires gcc3, I tried to install this as well. Unfortunately, I ended up with tons of dependencies. So I tried to get the list of things which were shown to be missing. This resulted in more dependencies for every item I tried to install. Finally, I got lost and gave up. Is this the way it goes or am I doing something wrong? I am not very accomplished with Linux, just getting by. Regards, Uli Summary: Hello, is it possible to print individual summations of the Mulliken populations with G98 like in Mullikens 1955 paper? In particular, I would need the populations of basis functions in a given MO. Thanks, Uli Salzner Hi, I wrote a program to calculate the Mulliken pop analysis that gaussian doesn't. It needs a log file with the overlap matrix and all the coeffs in the mo-lcao expansion. You could have a try at it. It is available > from my web page at http://www.quimica.unlp.edu.ar/cequinor/rpd_en.htm under "software development". I called it MullPop. Let me know if it is useful for your purposes and/or if you have any problems during compilation/running. Hope this helps. Regards, Reinaldo Hello, you can do all this with the following program (it will "post-process" gaussian output files): http://www.obbligato.com/software/aomix/ With regards, Dr. S.I. Gorelsky Department of Chemistry, Stanford University Box 155, Mudd Bldg., 333 Campus Drive, Stanford, California 94305-5080 U.S.A. Brian Salter-Duke wrote: Hi Uli, I wrote a patch for G98 some years ago that does this in part. It sums the populations in each MO of all basis functions that have the same l value. I use it see if there is mixing between d and valence orbitals in 3rd row systems. I sent it to Gaussian but I do not think they want to put it in. If you want it, I can sort it out for you in a couple of days, but I'm pretty busy until Friday. Brian. --------------070606070805050709010207 Content-Type: message/rfc822; name="nsmail.eml" Content-Transfer-Encoding: 7bit Content-Disposition: inline; filename="nsmail.eml" Message-ID: <3E82A229.3040801@fen.bilkent.edu.tr> From: Ulrike Salzner To: chemistry@ccl.com Subject: MPA in G98 Date: Thu, 27 Mar 2003 02:03:05 -0500 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) X-MS-Embedded-Report: Content-Type: text/plain; charset="iso-8859-1" Thanks to everyone who replied to my question. It seems that G98 can not perform this task. I received two links to programs, one commercial, one free of charge. The original answers are given below. I tried to install Reinaldo's program on a PC running Linux RedHat 7.2. Since the program requires gcc3, I tried to install this as well. Unfortunately, I ended up with tons of dependencies. So I tried to get the list of things which were shown to be missing. This resulted in more dependencies for every item I tried to install. Finally, I got lost and gave up. Is this the way it goes or am I doing something wrong? I am not very accomplished with Linux, just getting by. Regards, Uli Summary: Hello, is it possible to print individual summations of the Mulliken populations with G98 like in Mullikens 1955 paper? In particular, I would need the populations of basis functions in a given MO. Thanks, Uli Salzner Hi, I wrote a program to calculate the Mulliken pop analysis that gaussian doesn't. It needs a log file with the overlap matrix and all the coeffs in the mo-lcao expansion. You could have a try at it. It is available > from my web page at http://www.quimica.unlp.edu.ar/cequinor/rpd_en.htm under "software development". I called it MullPop. Let me know if it is useful for your purposes and/or if you have any problems during compilation/running. Hope this helps. Regards, Reinaldo Hello, you can do all this with the following program (it will "post-process" gaussian output files): http://www.obbligato.com/software/aomix/ With regards, Dr. S.I. Gorelsky Department of Chemistry, Stanford University Box 155, Mudd Bldg., 333 Campus Drive, Stanford, California 94305-5080 U.S.A. Brian Salter-Duke wrote: Hi Uli, I wrote a patch for G98 some years ago that does this in part. It sums the populations in each MO of all basis functions that have the same l value. I use it see if there is mixing between d and valence orbitals in 3rd row systems. I sent it to Gaussian but I do not think they want to put it in. If you want it, I can sort it out for you in a couple of days, but I'm pretty busy until Friday. Brian. -= 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 --------------070606070805050709010207-- From chemistry-request@server.ccl.net Thu Mar 27 04:11:47 2003 Received: from techunix.technion.ac.il ([132.68.1.28]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h2R9Bke15810 for ; Thu, 27 Mar 2003 04:11:46 -0500 Received: from tx.technion.ac.il (unknown [132.68.86.41]) by techunix.technion.ac.il (Postfix) with ESMTP id 3FD6122383 for ; Thu, 27 Mar 2003 11:10:22 +0200 (IST) Message-ID: <3E82BF9A.48DE0431@tx.technion.ac.il> Date: Thu, 27 Mar 2003 11:08:42 +0200 From: Eric German X-Mailer: Mozilla 4.76 [en] (Win98; U) X-Accept-Language: en,ru MIME-Version: 1.0 To: chemistry@ccl.net Subject: frequency analysis Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear all, could you tell me more information or equations for the IR intensities calculated by the Gaussian98 Many thanks in advance Wishes E. German From chemistry-request@server.ccl.net Thu Mar 27 09:33:51 2003 Received: from srvus010.unitedcatalysts.com ([208.23.162.8]) by server.ccl.net (8.11.6/8.11.0) with SMTP id h2REXpe00627 for ; Thu, 27 Mar 2003 09:33:51 -0500 Received: by lvlxch02.unitedcatalysts.com with Internet Mail Service (5.5.2653.19) id ; Thu, 27 Mar 2003 09:32:17 -0500 Message-ID: <5CF08BBFE6DE97478C1E76E654CAF9089C25DA@lvlxch02.unitedcatalysts.com> From: "Shobe, Dave" To: "'Jinsong Zhao'" , "'CCL'" Subject: RE: How to calculate the bond energy Date: Thu, 27 Mar 2003 09:32:16 -0500 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-Type: multipart/mixed; boundary="----=_NextPartTM-000-e746a0d4-8e84-4912-873c-a8be994bd814" This message is in MIME format. Since your mail reader does not understand this format, some or all of this message may not be legible. ------=_NextPartTM-000-e746a0d4-8e84-4912-873c-a8be994bd814 Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01C2F46D.AA2C2E70" ------_=_NextPart_001_01C2F46D.AA2C2E70 Content-Type: text/plain; charset="gb2312" Content-Transfer-Encoding: quoted-printable The usual definition of a bond energy is the energy requirement to = break that particular, bond. Actually, people are more likely to use the = enthalpy than the energy itself, and the result is often abbreviated BDE =3D = bond dissociation enthalpy. Using methylamine as an example, we have: BDE(C-H) =3D delta H for CH3NH2 --> H + CH2NH2 BDE(N-H) =3D delta H for CH3NH2 --> H + CH3NH BDE(C-N) =3D delta H for CH3NH2 --> CH3 + NH2 However if you add up all these BDEs you will find that they do not add = up to the atomization enthalpy of the molecule!! (i.e. delta H for CH3NH2 = --> C + N + 5 H) Defining a particular bond's contribution to the total = binding energy of the molecule is difficult, and I'm not aware of any standard definition. --David Shobe S=FCd-Chemie Inc. phone (502) 634-7409 fax (502) 634-7724 email dshobe@sud-chemieinc.com Don't bother flaming me: I'm behind a firewall. =09 -----Original Message----- From: Jinsong Zhao [mailto:zh_jinsong@yahoo.com.cn] Sent: Thursday, March 27, 2003 1:34 AM To: CCL Subject: CCL:How to calculate the bond energy Dear all, I hope to calculate the energy of each bond in a organic compound. I am not familiar with quantum or computational chemistry. Would you like to give me some advice on this aspect? Thank you very much in advance! Sincerely yours, Jinsong Zhao _________________________________________________________ Do You Yahoo!?=20 =D1=C5=BB=A2=CD=A8=CD=F8=C2=E7KTV, = =CB=E6=CA=B1=CB=E6=B5=D8=C3=E2=B7=D1=BF=A8=C0=ADOK~~ http://rd.yahoo.com/mail_cn/tag/?http://cn.messenger.yahoo.com//chat/ind= ex.h tml -=3D This is automatically added to each message by mailing script =3D- 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 ------_=_NextPart_001_01C2F46D.AA2C2E70 Content-Type: text/html; charset="gb2312" Content-Transfer-Encoding: quoted-printable RE: How to calculate the bond energy

The usual definition of a bond energy is the energy = requirement to break that particular, bond.  Actually, people are = more likely to use the enthalpy than the energy itself, and the result = is often abbreviated BDE =3D bond dissociation enthalpy.  Using = methylamine as an example, we have:

BDE(C-H) =3D delta H for CH3NH2 --> H + = CH2NH2
BDE(N-H) =3D delta H for CH3NH2 --> H + = CH3NH
BDE(C-N) =3D delta H for CH3NH2 --> CH3 + = NH2

However if you add up all these BDEs you will find = that they do not add up to the atomization enthalpy of the molecule!! = (i.e. delta H for CH3NH2 --> C + N + 5 H)  Defining a = particular bond's contribution to the total binding energy of the = molecule is difficult, and I'm not aware of any standard = definition.

--David Shobe
S=FCd-Chemie Inc.
phone (502) 634-7409
fax     (502) 634-7724
email  dshobe@sud-chemieinc.com

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

       =20

-----Original Message-----
From: Jinsong Zhao [mailto:zh_jinsong@yahoo.com.cn]
Sent: Thursday, March 27, 2003 1:34 AM
To: CCL
Subject: CCL:How to calculate the bond energy


Dear all,

I hope to calculate the energy of each bond in = a
organic compound. I am not familiar with = quantum  or
computational chemistry. Would you like to give = me
some advice on this aspect? Thank you very much = in
advance!

Sincerely yours,
Jinsong Zhao


_________________________________________________________
Do You Yahoo!?
=D1=C5=BB=A2=CD=A8=CD=F8=C2=E7KTV, = =CB=E6=CA=B1=CB=E6=B5=D8=C3=E2=B7=D1=BF=A8=C0=ADOK~~
http://rd.yahoo.com/mail_cn/tag/?http://cn.messenger.y= ahoo.com//chat/index.html


-=3D This is automatically added to each message by = mailing script =3D-
CHEMISTRY@ccl.net -- To Everybody  | = CHEMISTRY-REQUEST@ccl.net -- To Admins
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------_=_NextPart_001_01C2F46D.AA2C2E70-- ------=_NextPartTM-000-e746a0d4-8e84-4912-873c-a8be994bd814-- From chemistry-request@server.ccl.net Thu Mar 27 04:54:22 2003 Received: from hpserv.imim.es ([193.144.6.104]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h2R9sMe28154 for ; Thu, 27 Mar 2003 04:54:22 -0500 Received: by hpserv.imim.es with Internet Mail Service (5.5.2656.59) id ; Thu, 27 Mar 2003 10:57:56 +0100 Received: from imim.es (diana.imim.es [193.146.190.154]) by hpserv.imim.es with SMTP (Microsoft Exchange Internet Mail Service Version 5.5.2656.59) id HJVBPQZF; Thu, 27 Mar 2003 10:57:51 +0100 From: "Barbany, Montse" To: chemistry@ccl.net Message-ID: <3E82CAFB.1050100@imim.es> Date: Thu, 27 Mar 2003 10:57:15 +0100 User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.0.1) Gecko/20020823 Netscape/7.0 X-Accept-Language: en-us, en MIME-Version: 1.0 Subject: CCL: How to calculate the bond energy Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 8bit Dear Jinsong Zhao, I am the developer of MIPSim package (http://genome.imim.es/modeling/mipsim/index.html) You can use mipline keyword implemented in MIPSim to calculate quantum energy along a bond of a molecule. Best wishes, Montse -- Montserrat Barbany Puig Computational Structural Biology Laboratory Research Group on Biomedical Informatics (GRIB) - IMIM/UPF Pg.Marítim de la Barceloneta, 37-49; 08003 Barcelona (Spain) Tel: +34 93 224 0893 // +34 93 224 0875 e-mail: mbarbany@imim.es http://www.imim.es/grib/ From chemistry-request@server.ccl.net Thu Mar 27 07:38:25 2003 Received: from luc.ac.be ([193.190.2.30]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h2RCcOe30968 for ; Thu, 27 Mar 2003 07:38:25 -0500 Received: from localhost (localhost [127.0.0.1]) by luc.ac.be (8.9.3/8.9.3) with ESMTP id NAA06968 for ; Thu, 27 Mar 2003 13:38:24 +0100 (MET) Received: from 50.250-136-217.adsl.skynet.be (50.250-136-217.adsl.skynet.be [217.136.250.50]) by webmail.luc.ac.be (IMP) with HTTP for ; Thu, 27 Mar 2003 13:38:51 +0100 Message-ID: <1048768731.3e82f0db7e7e3@webmail.luc.ac.be> Date: Thu, 27 Mar 2003 13:38:51 +0100 From: sergiusz.kwasniewski@luc.ac.be To: CCL Subject: question on resonance structures MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit User-Agent: Internet Messaging Program (IMP) 3.2.1 Hi, As you know, poly-acetylene has a doubly degenerate ground state structure, because of the Peierls distortion. The skelet structures can be seen in terms of bond alternations as struct1 = (=-=-=)n and struct2 = (-=-=-)n. They both consist of a linear combination of partial wavefunctions describing wave1 = (=-=-=)n and wave2 = (-=-=-)n (in VB theory). If I'm not mistaken wave1 and wave2 are resonance (canonics ?) structures and should therefore be written as wave1 <--> wave2. On the other hand, struct1 and struct2 are different molecular structures and they should therefore be written as struct1 <==> (i.e. as a chemical equilibrium). I believe these structures are called bondisomers. Each of these structures can thus be given by A*wave1+B*wave2. I would like your opinion on this and would like to get advise on the accurate nomenclature of structs and waves. I will summerize Thanks Serge From chemistry-request@server.ccl.net Thu Mar 27 05:27:41 2003 Received: from dobit2.rug.ac.be ([157.193.42.8]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h2RARee28601 for ; Thu, 27 Mar 2003 05:27:40 -0500 Received: from allserv.rug.ac.be (allserv.rug.ac.be [157.193.40.42]) by dobit2.rug.ac.be (8.12.8/8.12.8) with ESMTP id h2RAReUr029727 for ; Thu, 27 Mar 2003 11:27:40 +0100 (MET) Received: from hartree4.rug.ac.be (hartree4.rug.ac.be [157.193.91.12]) by allserv.rug.ac.be (8.12.8/8.12.8) with ESMTP id h2RARdQI020268 for ; Thu, 27 Mar 2003 11:27:39 +0100 (MET) Received: from inchem34 (inchem34.rug.ac.be [157.193.91.54]) by hartree4.rug.ac.be (AIX4.2/UCB 8.7/8.7) with SMTP id LAA07964 for ; Thu, 27 Mar 2003 11:29:49 +0100 (NFT) Message-Id: <4.1.20030327111900.00aacbc0@157.193.91.12> X-Sender: patrick@157.193.91.12 X-Mailer: QUALCOMM Windows Eudora Pro Version 4.1 Date: Thu, 27 Mar 2003 11:31:44 +0100 To: chemistry@ccl.net From: Patrick Bultinck Subject: Re: CCL:How to calculate the molecular similarity In-Reply-To: <03032709384090@itodys.jussieu.fr> Mime-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id h2RARfe28602 Dear, I would suggest you check the literature by Prof. Dr. Ramon Carbó-Dorca and my recent contributions in that field. Most commonly, the quantum similarity is calculated via : integral(rho_A(r).rho_B(r) dr), where rho_A is the electron density of molecule A smeared out over space. You could check the literature by Prof. Carbó-Dorca of the university of Girona. I could give a rather complete list. If interested, you can contact me directly (it seems this CCL message never reached me, so thanks Michel for replying) and I can send some recent results. In fact, we have very recently introduced a new quantum similarity based alignment scheme as well, which solves many problems associated with most often used techniques. Also, we have recently shown that several techniques involving reduced resolution quantum similarity methods contain mathematical inconsistencies in the mathematical space where they are defined. Best regards, Patrick Bultinck Ghent Quantum Chemistry Group Belgium >>Dear cclers, >> >>Can someone here like to recommend me some methods to >>calculate the molecular quantum similarity, and to >>give me some suggestions on the molecular alignment of >>two or more molecules? >> >>Thank you very much in advance! >> >>Sincerely yours, >>Jinsong Zhao > >-= 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 Thu Mar 27 10:43:23 2003 Received: from sims.csuohio.edu ([137.148.5.58]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h2RFhMe02544 for ; Thu, 27 Mar 2003 10:43:22 -0500 Received: from [137.148.208.57] (iridium.asic.csuohio.edu [137.148.208.57]) by sims.csuohio.edu (Sun Internet Mail Server sims.4.0.1999.09.28.17.31.p2) with ESMTP id <0HCE00CHRZQZAW@sims.csuohio.edu> for chemistry@ccl.net; Thu, 27 Mar 2003 10:44:59 -0500 (EST) Date: Thu, 27 Mar 2003 10:43:27 -0500 From: Mike Tallhammer Subject: Oniom problem in Gaussian 98 To: chemistry@ccl.net Message-id: MIME-version: 1.0 Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7BIT User-Agent: Microsoft-Entourage/10.0.0.1309 I am trying to run an Oniom calc on a large system and I have specified the calculation as follows in the header: Oniom(B3LYP/6-31G(d):UFF) SP First ONIOM calc on BH4 in NOS 1 2,0 1 I'm doing this for a few frames of a trajectory file and some are working but some are terminating with the following error: ONIOM: generating new system at layer 2 ONIOM: saving gridpoint 9 3405 basis functions 10218 primitive gaussians 1995 alpha electrons 1995 beta electrons nuclear repulsion energy 321931.9998387208 Hartrees. UFF calculation of energy. MO and density RWFs will be updated. Recover connectivity from rwf. EGHMM: NBAlg=1 ICut=1 CutNB= 1.43E+03 I= 907 IAn= 7 Valence= 4. JB= 1 J= 908 IAn= 6 IBT= 1 Dist= 1.47E+00 JB= 2 J= 926 IAn= 1 IBT= 1 Dist= 1.00E+00 JB= 3 J= 927 IAn= 1 IBT= 1 Dist= 1.00E+00 JB= 4 J= 928 IAn= 1 IBT= 1 Dist= 1.00E+00 I= 989 IAn= 8 Valence= 3. JB= 1 J= 934 IAn= 30 IBT= 1 Dist= 2.06E+00 JB= 2 J= 990 IAn= 1 IBT= 1 Dist= 1.00E+00 JB= 3 J= 991 IAn= 1 IBT= 1 Dist= 1.00E+00 I= 995 IAn= 8 Valence= 3. JB= 1 J= 934 IAn= 30 IBT= 1 Dist= 1.98E+00 JB= 2 J= 996 IAn= 1 IBT= 1 Dist= 1.00E+00 JB= 3 J= 997 IAn= 1 IBT= 1 Dist= 1.00E+00 I= 998 IAn= 8 Valence= 3. JB= 1 J= 934 IAn= 30 IBT= 1 Dist= 2.04E+00 JB= 2 J= 999 IAn= 1 IBT= 1 Dist= 1.00E+00 JB= 3 J= 1000 IAn= 1 IBT= 1 Dist= 1.00E+00 I= 1157 IAn= 8 Valence= 3. JB= 1 J= 934 IAn= 30 IBT= 1 Dist= 2.01E+00 JB= 2 J= 1158 IAn= 1 IBT= 1 Dist= 1.00E+00 JB= 3 J= 1159 IAn= 1 IBT= 1 Dist= 1.00E+00 I= 1169 IAn= 8 Valence= 3. JB= 1 J= 934 IAn= 30 IBT= 1 Dist= 2.02E+00 JB= 2 J= 1170 IAn= 1 IBT= 1 Dist= 1.00E+00 JB= 3 J= 1171 IAn= 1 IBT= 1 Dist= 9.99E-01 Energy= 23.337427580412 NIter= 0. Dipole moment= .000000 .000000 .000000 ONIOM: generating new system at layer 1 ONIOM: saving gridpoint 3 ONIOM: restoring gridpoint 9 285 basis functions 536 primitive gaussians 64 alpha electrons 63 beta electrons nuclear repulsion energy 1271.3742221023 Hartrees. RHF requested, but multiplicity is not 1. Error termination via Lnk1e in /software/g98/l401.exe. Job cpu time: 0 days 0 hours 0 minutes 22.0 seconds. File lengths (MBytes): RWF= 20 Int= 0 D2E= 0 Chk= 1 Scr= 1 I can't seem to figure out why some are working and some are not From chemistry-request@server.ccl.net Thu Mar 27 11:24:16 2003 Received: from shiva.jussieu.fr ([134.157.0.129]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h2RGOGe03696 for ; Thu, 27 Mar 2003 11:24:16 -0500 Received: from as2100.itodys.jussieu.fr (as2100.itodys.jussieu.fr [134.157.24.23]) by shiva.jussieu.fr (8.12.8/jtpda-5.4) with SMTP id h2RGOFZC022483 for ; Thu, 27 Mar 2003 17:24:15 +0100 (CET) Date: Thu, 27 Mar 2003 17:24:14 +0100 Message-Id: <03032717241479@itodys.jussieu.fr> From: petitjean@itodys.jussieu.fr To: chemistry@ccl.net Subject: CCL:Re[2]: How to calculate the molecular similarity X-VMS-To: SMTP%"chemistry@ccl.net" X-Antivirus: scanned by sophie at shiva.jussieu.fr To: chemistry@ccl.net Subject: CCL:Re[2]: How to calculate the molecular similarity I fully agree with Patrick Bultinck: there are inconsistencies in the mathematical space where most techniques are operating. E.g. the volumic integral of the product of two densities is NOT ensured to be finite, although the square root of the product exists indeed (I wrote that in 1996 in a paper in J.Chem.Inf.Comput.Sci.). The space of densities is not adequate. The space of distributions is better, and the space of probability laws much better. Probability metrics seems neglected by chemists, also this is an adequate approach for most similarity problems (see the definition of colored mixtures in J.Math.Phys. 2002,43,4147-4157, or look to my web site). Michel Petitjean, Email: petitjean@itodys.jussieu.fr ITODYS (CNRS, UMR 7086) ptitjean@ccr.jussieu.fr 1 rue Guy de la Brosse Phone: +33 (0)1 44 27 48 57 75005 Paris, France. FAX : +33 (0)1 44 27 68 14 http://petitjeanmichel.free.fr/itoweb.petitjean.html http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html > In fact, we have very recently introduced a new quantum similarity results. In fact, we have very recently introduced a new quantum similarity >based alignment scheme as well, which solves many problems associated with >most often used techniques. Also, we have recently shown that several >techniques involving reduced resolution quantum similarity methods contain >mathematical inconsistencies in the mathematical space where they are defined. > >Best regards, > >Patrick Bultinck >Ghent Quantum Chemistry Group >Belgium From chemistry-request@server.ccl.net Thu Mar 27 11:35:35 2003 Received: from smtp2.ruc.dk ([130.225.220.70]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h2RGZZe04070 for ; Thu, 27 Mar 2003 11:35:35 -0500 Received: by smtp2.ruc.dk (Postfix, from userid 504) id 585E1A1F6E9; Thu, 27 Mar 2003 17:35:34 +0100 (CET) Received: from virgil.ruc.dk (virgil.ruc.dk [130.225.220.110]) by smtp2.ruc.dk (Postfix) with ESMTP id 52FBDA1F6E5; Thu, 27 Mar 2003 17:35:32 +0100 (CET) Received: from VIRGIL/SpoolDir by virgil.ruc.dk (Mercury 1.47); 27 Mar 03 17:35:33 +0100 Received: from SpoolDir by VIRGIL (Mercury 1.47); 27 Mar 03 17:35:26 +0100 From: "Jens Spanget-Larsen" Organization: Roskilde Universitetscenter To: Eric German Date: Thu, 27 Mar 2003 17:35:01 +0100 Subject: Re: CCL:frequency analysis Reply-To: spanget@ruc.dk Cc: chemistry@ccl.net X-Confirm-Reading-To: spanget@ruc.dk X-pmrqc: 1 Priority: normal X-mailer: Pegasus Mail for Windows (v2.23) Message-ID: <7C34133E34@virgil.ruc.dk> X-Spam-Status: No, hits=0.0 required=5.0 tests=none version=2.50 X-Spam-Level: X-Spam-Checker-Version: SpamAssassin 2.50 (1.173-2003-02-20-exp) Eric German: > could you tell me more information or equations for the IR > intensities calculated by the Gaussian98 Dear Eric, I imagine that the review by Hess et al. contains much of what you need (particularly page 715): B.A. Hess, Jr., et al., Chem. Rev. 86, 709-730 (1986) Yours, Jens >--< =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= JENS SPANGET-LARSEN Office: +45 4674 2710 Department of Chemistry Fax: +45 4674 3011 Roskilde University (RUC) Mobile: +45 2320 6246 P.O.Box 260 E-Mail: spanget@ruc.dk DK-4000 Roskilde, Denmark http://virgil.ruc.dk/~spanget =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= From chemistry-request@server.ccl.net Thu Mar 27 11:30:03 2003 Received: from mail.ic.sunysb.edu ([129.49.1.4]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h2RGU3e03920 for ; Thu, 27 Mar 2003 11:30:03 -0500 Received: from postal.ic.sunysb.edu (mail [129.49.1.4]) by mail.ic.sunysb.edu (8.12.8/8.12.8) with SMTP id h2RGU2q7000682 for ; Thu, 27 Mar 2003 11:30:03 -0500 (EST) Received: from smtp.ic.sunysb.edu ([129.49.1.24]) by postal.ic.sunysb.edu (NAVGW 2.5.2.9) with SMTP id M2003032711300321341 for ; Thu, 27 Mar 2003 11:30:03 -0500 Received: from sparky.ic.sunysb.edu (sparky.ic.sunysb.edu [129.49.1.3]) by smtp.ic.sunysb.edu (8.12.8/8.12.8) with ESMTP id h2RGU3fo000697 for ; Thu, 27 Mar 2003 11:30:03 -0500 (EST) Received: from localhost (yonyang@localhost) by sparky.ic.sunysb.edu (8.12.8/8.12.8) with ESMTP id h2RGU2Jt009288 for ; Thu, 27 Mar 2003 11:30:02 -0500 (EST) Date: Thu, 27 Mar 2003 11:30:02 -0500 (EST) From: Yong Liang Yang To: chemistry@ccl.net Subject: Openbabel to convert .mmod files Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCL users: Currently I am using Openbabel to convert .mmod file which contain all the information for all the conformers(about 10 conformers per file) of one molecule to .dat file which is supposed to be the default file type for BatchMin job in MacroModel.But the output .dat file seems only containing the information for only one conformer of that molecule.Thus I want to know how can I get the .dat file containing all the conformers? Many thanks in advance to all the answers! cheers YL. Yang Dept of Chem. SUNY-Stony Brook From chemistry-request@server.ccl.net Thu Mar 27 10:59:01 2003 Received: from gate2.boehringer-ingelheim.de ([148.188.128.36]) by server.ccl.net (8.11.6/8.11.0) with SMTP id h2RFx0e03011 for ; Thu, 27 Mar 2003 10:59:00 -0500 Received: from bibex01.bc.de.bic by gate2.boehringer-ingelheim.de via smtpd (for [192.153.40.39]) with SMTP; 27 Mar 2003 15:52:57 UT Received: by bibex01.eu.boehringer.com with Internet Mail Service (5.5.2653.19) id ; Thu, 27 Mar 2003 16:58:58 +0100 Message-ID: <6C6304FC4E72D611A0EF00306E07C5CF0105AB21@bc0exch12.bc.de.bic> From: Thomas.Fox@bc.boehringer-ingelheim.com To: CHEMISTRY@ccl.net Subject: Calculation of chemical reactivity Date: Thu, 27 Mar 2003 16:58:56 +0100 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-Type: text/plain Hi ! I was asked to investigate the relative reactivities of various aniline derivatives in the following reaction: Ph-NH2 -> Ph-NHOH -> Ph-NO where Ph are differently substituted Phenyl or Azaphenyl (Pyridine, Pyrimidine...) rings. I have never dealt with this kind of problem, so I wonder if you have any idea how to tackle such a question, possible problems or pitfalls, pointers to literature etc... Thanks for any input; if there is enough interest Ill summarize. Th. > Dr. Thomas Fox > Dept. of Lead Discovery / Computer Aided Molecular Design > K91-00-10 > Boehringer Ingelheim Pharma GmbH & Co. KG > 88397 Biberach/Germany > Thomas.Fox@bc.boehringer-ingelheim.com > > From chemistry-request@server.ccl.net Thu Mar 27 11:26:41 2003 Received: from cirse.saclay.cea.fr ([132.166.192.127]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h2RGQfe03832 for ; Thu, 27 Mar 2003 11:26:41 -0500 Received: from argiope.saclay.cea.fr (argiope.saclay.cea.fr [132.166.192.108]) by cirse.saclay.cea.fr (8.12.8/CEAnet-Internet.1.0) with ESMTP id h2RGQeY5025785 for ; Thu, 27 Mar 2003 17:26:40 +0100 (MET) Received: from muguet.saclay.cea.fr (unverified) by argiope.saclay.cea.fr (Content Technologies SMTPRS 4.3.6) with ESMTP id for ; Thu, 27 Mar 2003 17:21:00 +0100 Received: from petunia.bruyeres.cea.fr (petunia.bruyeres.cea.fr [132.165.64.1]) by muguet.saclay.cea.fr (8.12.8/CEAnet-Interne.1.0) with ESMTP id h2RGQepX006458 for ; Thu, 27 Mar 2003 17:26:40 +0100 (MET) Received: from styx.bruyeres.cea.fr (styx-e76.bruyeres.cea.fr [132.165.76.3]) by petunia.bruyeres.cea.fr (8.9.3+Sun/jtpda-5.3.2) with ESMTP id RAA27448 for ; Thu, 27 Mar 2003 17:23:42 +0100 (MET) Received: by styx.bruyeres.cea.fr; id RAA04187; Thu, 27 Mar 2003 17:28:11 +0100 (MET) Message-Id: <200303271628.RAA04187@styx.bruyeres.cea.fr> Sender: Didier.MATHIEU@cea.fr Date: Thu, 27 Mar 2003 17:10:23 +0100 From: Didier MATHIEU X-Mailer: Mozilla 4.72 [fr] (X11; U; Linux 2.2.14-5.0 i686) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: unit cell primitiveness and symmetries Content-Type: multipart/alternative; boundary="------------9A2C89839CFFDE72924D927A" --------------9A2C89839CFFDE72924D927A Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hello, I have a model crystal structure given by a unit cell, i.e. as a set of cell vectors, atoms and their cartesian coordinates. I guess there are programs to check whether the unit cell is a primitive one, if not, provide a primitive unit cell and symmetry operations ? Thanks -- Didier Mathieu CEA - Le Ripault BP 16 37260 Monts Didier.Mathieu@cea.fr Tel +33 02 47 34 41 85 Fax +33 02 47 34 51 42 --------------9A2C89839CFFDE72924D927A Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit Hello,

I have a model crystal structure given by a unit cell, i.e. as a set of cell vectors, atoms and their cartesian coordinates. I guess there are programs to check whether the unit cell is a primitive one, if not, provide a primitive unit cell and symmetry operations ?

Thanks 

-- 
Didier Mathieu
CEA - Le Ripault
BP 16
37260 Monts
Didier.Mathieu@cea.fr
Tel +33 02 47 34 41 85
Fax +33 02 47 34 51 42
 

  --------------9A2C89839CFFDE72924D927A-- From chemistry-request@server.ccl.net Thu Mar 27 11:32:19 2003 Received: from evans.univer.kharkov.ua ([80.92.225.132]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h2RGW5e03982 for ; Thu, 27 Mar 2003 11:32:06 -0500 Received: from spin.univer.kharkov.ua (spin.univer.kharkov.ua [192.168.213.252]) by evans.univer.kharkov.ua (8.12.8/8.12.5) with SMTP id h2RGW2H5022578 for ; Thu, 27 Mar 2003 18:32:02 +0200 Received: by spin.univer.kharkov.ua with Microsoft Mail id <01C2F48E.8BF50820@spin.univer.kharkov.ua>; Thu, 27 Mar 2003 18:27:39 +0200 Message-ID: <01C2F48E.8BF50820@spin.univer.kharkov.ua> From: "sergey i. kotelevskii" To: "'CCL community'" Subject: Summary: MOLCAS manual Date: Thu, 27 Mar 2003 18:27:37 +0200 MIME-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id h2RGWJe03985 My very sincere thanks to all who responded to my request for MOLCAS manual. In short, the last updated release (5.4) is available for free download as zipped *.ps and *.html files from: http://www.teokem.lu.se/molcas/downloads/. Still, it is not completely suitable as an introduction for a novice like me who is about to get started with earlier version. My special gratitude is to Sorana Ionescu and Mihaly Mezei who kindly E-mailed attached files. Very best regards to all CCLers, SK. ********************************************************************************************* Serghey I. Kotelevskii, Department of Theoretical Chemistry and Astrochemistry, Research Institute for Chemistry, Kharkiv V.N.Karazin National University, Svobody Square 4, UA-61077 Kharkiv, UKRAINE E-mail: kotelevskiy@univer.kharkov.ua