From chemistry-request@server.ccl.net Thu Jul 20 02:47:53 2000 Received: from hydra.chem.rug.nl (hydra.chem.rug.nl [129.125.35.229]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id CAA04478 for ; Thu, 20 Jul 2000 02:47:52 -0400 Received: from [129.125.7.13] (theochem1.chem.rug.nl [129.125.7.13]) by hydra.chem.rug.nl (AIX4.2/UCB 8.7/8.7) with ESMTP id IAA40420 for ; Thu, 20 Jul 2000 08:47:48 +0200 (MET DST) Mime-Version: 1.0 X-Sender: swart@hydra.chem.rug.nl Message-Id: In-Reply-To: References: Date: Thu, 20 Jul 2000 08:50:20 +0200 To: CHEMISTRY@ccl.net From: Marcel Swart Subject: Re: CCL:DFT & metal metal bonds Content-Type: text/plain; charset="us-ascii" ; format="flowed" >Sorry, > >for wasting bandwidth, but in my last post to CCL. I forgot to mention, >that if the metal-metal bond distance was fixed to the experimentally >observed shorter distance, the energy was found to be ca. 5 kcal/mol >higher than the geometry optimized structure with the longer M-M >distance. Also, I forgot to mention that I tried polarisation functions >as well (also numerical basis sets i.e. Dmol). I have not tried STO's >yet. Perhaps I should give ADF a try? The answer is a definite YES. Furthermore, did you also include relativistic effects ? I guess when you look at Tungsten/Molybdenum, these can be quite significant. Again this is a YES to ADF, since in this program these effects are easily taken into account. Marcel. From chemistry-request@server.ccl.net Thu Jul 20 03:40:38 2000 Received: from pdchfi.chfi.unipd.it (root@pdchfi.chfi.unipd.it [147.162.53.1]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id DAA04705 for ; Thu, 20 Jul 2000 03:40:36 -0400 Received: from chfi.unipd.it (gtw2.chfi.unipd.it [147.162.53.202]) by pdchfi.chfi.unipd.it (8.8.8/8.8.8) with ESMTP id JAA14861 for ; Thu, 20 Jul 2000 09:42:51 +0200 Posted-Date: Thu, 20 Jul 2000 09:42:51 +0200 Message-ID: <3976ABE7.B81D2B80@chfi.unipd.it> Date: Thu, 20 Jul 2000 09:36:07 +0200 From: Gabriella Severin X-Mailer: Mozilla 4.6 [en] (Win98; I) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: Problem with scipcm in gaussian Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCLers, I am having a problem with either SCIPCM and/or DFT in Gaussian98 (I don't know which one). I was running a job on a rather large open shell system (82 atoms) with the following input: " #P B3LYP/6-31G(d) SCRF=scipcm Pop=Reg Opt Nosymm Test .... " and the job ends after a while with the messages: " Total "Solvent Accessible Surface Area" of solute cavity = 2.032972E+03 au Volume of solute cavity = 6.819984E+03 au Total number of cavity surface points = 6632 Polarization charges will be scaled so the total potential on the cavity surface equals zero in a conducting medium Close points will be merged for conductor scaling The A matrix elements will be calculated on the fly (1/(4*pi)) * flux of nuclear E-field thru cavity surface = 0.42244484D+03 (1/(4*pi)) * flux of solute E-field thru cavity surface = -0.92210354D+00 (1/(1-1/epsi)) * unscaled total surface polarization charge = -0.92210113D+00 (1/(1-1/epsi)) * scaled total surface polarization charge = 0.20804499D+03 (1/2) * solvent-solute interaction energy = 0.78285963D+01 WARNING! Serious error in surface integrals. It is probable that some of the solute is outside the cavity and/or parts of the cavity surface cannot be reached from the origin. Try more integration points or a different set of integration origins. Surface Problems in SciFoc Error termination via Lnk1e in /usr/local/g98/l502.exe. " I don't know how I can increase the number of integration points (in the SCIPCM calculation? o in the DFT?). I think that other people had similar problems, in fact I found a question on this subject on the CCL archive, but I didn't find any answer. I hope that somebody can help me in any way and give any suggestion. Thank you very much in advance Gabriella Maria Gabriella Severin Dipartimento di Chimica Fisica University of Padua 35131 Padova- Italy From chemistry-request@server.ccl.net Thu Jul 20 04:19:22 2000 Received: from hydra.chem.rug.nl (hydra.chem.rug.nl [129.125.35.229]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id EAA05097 for ; Thu, 20 Jul 2000 04:19:21 -0400 Received: from [129.125.7.13] (theochem1.chem.rug.nl [129.125.7.13]) by hydra.chem.rug.nl (AIX4.2/UCB 8.7/8.7) with ESMTP id KAA17422 for ; Thu, 20 Jul 2000 10:19:16 +0200 (MET DST) Mime-Version: 1.0 X-Sender: swart@hydra.chem.rug.nl Message-Id: In-Reply-To: <200007200722.JAA66801@zisgi.unizh.ch> References: <200007200722.JAA66801@zisgi.unizh.ch> Date: Thu, 20 Jul 2000 10:21:48 +0200 To: CHEMISTRY@ccl.net From: Marcel Swart Subject: Re: CCL:DFT & metal metal bonds Content-Type: text/plain; charset="us-ascii" ; format="flowed" >You want to elaborate on this? Is it because of the STOs? As to GTO's I >use TZVP/P basis sets, which are not too bad usually. Yes, the STO's are always much better. But not only that. It is a very clever program, making the calculations very efficient when looking at CPU-time, parallellization, those kind of things. > > Furthermore, did you also include relativistic effects ? > >yes, scalar relativistic via the ECP. Well, that's not really what I meant. You assume that the ECP's mimic the relativistic effects you are after, but it is not the same as including the relativistic effects themselves !!! > > I guess when you look at Tungsten/Molybdenum, these can be quite >significant. >> Again this is a YES to ADF, since in this program these effects are > > easily taken into account. Also, I know from work from my Professor (yet unpublished I think), who is an expert in Relativistic Quantum Chemistry (J.G. Snijders), that these relativistic effects are needed for heavy atom dimers. If you don't include them (properly), the calculations are not performing very well. Marcel. From chemistry-request@server.ccl.net Thu Jul 20 05:49:20 2000 Received: from mail-c.bcc.ac.uk (mail-c.bcc.ac.uk [144.82.100.23]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id FAA05456 for ; Thu, 20 Jul 2000 05:49:20 -0400 Received: from ri.ac.uk (actually host davy.ri.ac.uk) by mail-c.bcc.ac.uk with SMTP (Mailer); Thu, 20 Jul 2000 10:48:41 +0100 Received: from landlord (nb-davidc) by ri.ac.uk (5.x/SMI-SVR4) id AA00967; Thu, 20 Jul 2000 10:47:57 +0100 Message-Id: <001401bff230$813eed00$c6503fc1@ri.ac.uk> From: David S Coombes To: Oscar Rey , CHEMISTRY References: <00a701bff16b$ccbe4700$0c5691c1@iqs.url.es> Subject: Re: CCL:porphyrin/porphycene Date: Thu, 20 Jul 2000 10:54:22 +0100 Organization: Royal Institution of Great Britain Mime-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 8bit X-Priority: 3 X-Msmail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.00.2919.6600 Disposition-Notification-To: "David S Coombes" X-Mimeole: Produced By Microsoft MimeOLE V5.00.2919.6600 Dear Oscar The following URL's may be useful-they contain references and background on commonly used forcefields. http://bmbiris.bmb.uga.edu/BMB8200/using-ff/mmrefs.html http://pollux.chem.umn.edu/~sullivan/8003/handouts/forcefield.html David ******************************************************************************** Phone: 0207 409 2992 (Work) Dr. D.S. Coombes 0207 670 2934 (Voicemail) The Royal Institution of Great Britain 07958 677156 (Mobile) 21 Albemarle Street Fax: 0207 629 3569 London W1S 4BS Email davidc@ri.ac.uk Mobile email: davecoombes@sms.genie.co.uk (Less than 160 characters) ****************Registered Charity No. 227938**************************** ----- Original Message ----- From: "Oscar Rey" To: "CHEMISTRY" Sent: 19 July 2000 11:26 Subject: CCL:porphyrin/porphycene Dear CCL members I'd like to obtein some information (bibliography, previous works) about atom types and force file parameters related to porphyrin and porfycene, specially about Weiner et al. and Cornell et al. force fields. Thanks in advance Oscar Rey Puiggrrs Computational Chemistry Group (Section of Synthesis), Organic Chemistry Departament Institut Qummic de Sarri` (URL) e-mail: orey@iqs.edu telf: 932 038 900 Ext.:2361 Via Augusta 390, 08017 Barcelona_CATALUNYA (Spain) _____________________________________________________________ -= This is automatically added to each message by mailing script =- CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net From chemistry-request@server.ccl.net Thu Jul 20 06:39:03 2000 Received: from mum.mans.eun.eg (mum.mans.eun.eg [193.227.50.2]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id GAA05684 for ; Thu, 20 Jul 2000 06:33:06 -0400 Received: by mum.mans.eun.eg with Internet Mail Service (5.5.2650.21) id ; Thu, 20 Jul 2000 13:34:35 +0300 Message-ID: <4EF2E03A9B67D2119E2E0000F805349942741E@mum.mans.eun.eg> From: Tarek Mamoun El-Gogary To: "'CHEMISTRY@ccl.net'" Subject: QSAR QUESTIONS Date: Thu, 20 Jul 2000 13:34:27 +0300 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2650.21) Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01BFF236.18C0D3FF" 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. ------_=_NextPart_001_01BFF236.18C0D3FF Content-Type: text/plain Dear netters, I am some how begginer in QSAR. I have got some basic questions. 1- is there a limit of N , the number of drugs used in qsar analysis, ? 2- how small is the correlation coeffient to be acceptable? 3- how much simillar the drugs should be? 4- Are there known drugs developed by qsar? I appreciate any response Regards Tarek El-gogary Chem. Dept. Fac. of Sci. Mans.Univ. Egypt ------_=_NextPart_001_01BFF236.18C0D3FF Content-Type: text/html QSAR QUESTIONS

Dear netters,
I am some how begginer in QSAR. I have got some basic questions.
1- is there a limit of N , the number of drugs used in qsar analysis, ?
2- how small is the correlation coeffient to be acceptable?
3- how much simillar the drugs should be?
4- Are there known drugs developed by qsar?
I appreciate any response
Regards
Tarek El-gogary
Chem. Dept.
Fac. of Sci.
Mans.Univ.
Egypt

------_=_NextPart_001_01BFF236.18C0D3FF-- From chemistry-request@server.ccl.net Thu Jul 20 11:19:18 2000 Received: from mail-nord.nord.univ-mrs.fr (mail-nord.nord.univ-mrs.fr [194.214.97.11]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA07645 for ; Thu, 20 Jul 2000 11:19:17 -0400 Received: from [194.214.94.10] ([194.214.94.10]) by mail-nord.nord.univ-mrs.fr (8.9.3/8.9.3) with ESMTP id QAA07756 for ; Thu, 20 Jul 2000 16:25:03 +0200 Mime-Version: 1.0 X-Sender: sampieri@mail-nord.nord.univ-mrs.fr Message-Id: Date: Thu, 20 Jul 2000 17:19:03 +0200 To: CHEMISTRY@server.ccl.net From: Francois Sampieri Subject: Building complex multimeric models Content-Type: text/plain; charset="us-ascii" ; format="flowed" Hi all, I had to construct a model of a protein complex derived from experimental 3D structures. I believed that it could be obtained without special skills. The templates were: 1- A protein P made up of two well separated domains covalently attached: A and B, such: A-B 2- A non-covalent complex between 3 protein subunits C, D, and E: C==D==E My purpose was to split the protein P into its two domains and to covalently attach each domain to the C and E units with a polypetidyl arm: A and B / \ C E to eventually obtain, in the presence of D, a new complex: A=B / \ C==D==E with A=B bound non-covalently. I worked with InsightII-Biopolymer from MSI, and I succeded in splitting the starting protein model into its two separate domains, then building the arms (I'm so proud of that ;-), but a problem arose when I attempted to bind these arms to their respective C/E unit, since when creating the covalent bond between, say the A-arm and C, the whole C==D==E complex went into a very embarrassing orientation in the space, due to the rigid geometry of the bond created. Seems as if there is only one way to make a new bond in InsightII. I tried lots of methods without success and now I wonder if this could be possible with this program. Unless I missed some hidden tricks in InsightII, my question is: is there any other program (running on a SGI O2; IRIX 6.5) capable of building bonds with 'soft' (not rigid) geometry? Thus, it would de possible to build the complex with the actual conformations and orientations of A-B and of C==D==E bound to the polypeptide arms, then energy-minimize the arms to make them to conform to the standard geometry. A program with only building capabilities would be satisfactory, provided that it should be able to create pdb files and handle more than 15.000 atoms. I hope I'have not been too obscure. Thanks and best wishes to all! Francois Francois Sampieri sampieri.f@jean-roche.univ-mrs.fr Laboratoire de Biochimie IFR Jean Roche Faculte de Medecine Nord MARSEILLE FRANCE From chemistry-request@server.ccl.net Thu Jul 20 04:52:27 2000 Received: from smtprelay.ruc.dk (smtprelay.ruc.dk [130.225.220.22]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id EAA05250 for ; Thu, 20 Jul 2000 04:52:26 -0400 Received: from virgil.ruc.dk (virgil.ruc.dk [130.225.220.110]) by smtprelay.ruc.dk (8.9.3/8.9.3) with ESMTP id KAA24738 for ; Thu, 20 Jul 2000 10:44:51 +0200 (MET DST) Received: from VIRGIL/SpoolDir by virgil.ruc.dk (Mercury 1.44); 20 Jul 00 10:43:18 +0100 Received: from SpoolDir by VIRGIL (Mercury 1.44); 20 Jul 00 10:43:12 +0100 From: "Jens Spanget-Larsen" Organization: Roskilde Universitetscenter To: CHEMISTRY@ccl.net Date: Thu, 20 Jul 2000 10:43:01 +0100 Subject: CCL: Seeing molecular orbitals? Priority: normal X-mailer: Pegasus Mail for Windows (v2.23) Message-ID: <92CE6BB1672@virgil.ruc.dk> Dear CCL: In a recent, most interesting publication ('Seeing molecular orbitals', Chem.Phys.Letters 321, 78-82 [2000]) scanning tunneling microscopy is used to observe the shapes of single molecular orbitals of the fullerene C60: "..the scanning tunneling microscope (STM) is probing a single molecular orbital (MO)." However, this reminds me of previous statements in the literature some time ago, associated with the advent of molecular photoelectron spectroscopy, f.i. "Chemists can see the orbital structure of even fairly large molecules and no longer have to rely on the predictions of theoreticians" "Photoelectron spectroscopy has demonstrated experimentally to chemists, physicists and other sceptics that molecular orbitals really do exist" I wonder whether this is acceptable terminology, considering the fact that molecular orbitals are model constructs; they are not physical observables. By using approximations, such as Koopmans' approximation, many experimental observations can be conveniently interpreted in terms of theoretical MO data. But strictly speaking, this does not turn MOs into observable quantities; MOs have no physical existence. Any comments? Yours, Jens >--< =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= JENS SPANGET-LARSEN Phone: +45 4674 2000 (RUC) Department of Chemistry +45 4674 2710 (direct) Roskilde University (RUC) Fax: +45 4674 3011 P.O.Box 260 E-Mail: JSL@virgil.ruc.dk DK-4000 Roskilde, Denmark http://www.rub.ruc.dk/dis/chem/psos/ =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= From chemistry-request@server.ccl.net Thu Jul 20 09:46:56 2000 Received: from mailhost.msi.com (fire.msi.com [146.202.0.242]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id JAA07310 for ; Thu, 20 Jul 2000 09:46:55 -0400 Received: (from daemon@localhost) by mailhost.msi.com (980427.SGI.8.8.8/970903.SGI.AUTOCF) id GAA22993; Thu, 20 Jul 2000 06:43:06 -0700 (PDT) Received: from unknown(146.202.85.72) by mailhost.msi.com via smap (V2.0) id xma022976; Thu, 20 Jul 00 06:42:41 -0700 Message-ID: <003101bff250$45f7b3b0$4855ca92@msi.com> From: "Amit Kulkarni (UIC)" To: "Tarek Mamoun El-Gogary" , References: <4EF2E03A9B67D2119E2E0000F805349942741E@mum.mans.eun.eg> Subject: Re: CCL:QSAR QUESTIONS Date: Thu, 20 Jul 2000 09:41:49 -0400 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_002C_01BFF22E.BA5FC840" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.00.2014.211 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2014.211 This is a multi-part message in MIME format. ------=_NextPart_000_002C_01BFF22E.BA5FC840 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable QSAR QUESTIONSHi In order to get a good QSAR model the number of compounds in the dataset = should be > 20 and also there should be considerable difference in the = range of activities. Ideally the acceptable r2 value is > 0.80 but again = it depends on lot of other factors. If the main objective of your QSAR = analysis is make perfect predictions then you should go in for a model = with r2 >0.9, but if your main objective is just to cluster the = molecules in activity ranges then r2 > 0.8 can be used. It is good to = have structurally diversity while building the QSAR model.=20 Cheers Amit ----------------------------------------------------------------- Amit Kulkarni, Ph.D. Applications Scientist Life Science Molecular Simulations Inc. Burlington, MA 01803 (781) 359 1217 Fax: (781) 229 989 Email: amit@msi.com ----------------------------------------------------------------- ----- Original Message -----=20 From: Tarek Mamoun El-Gogary=20 To: 'CHEMISTRY@ccl.net'=20 Sent: Thursday, July 20, 2000 6:34 AM Subject: CCL:QSAR QUESTIONS Dear netters,=20 I am some how begginer in QSAR. I have got some basic questions.=20 1- is there a limit of N , the number of drugs used in qsar analysis, = ?=20 2- how small is the correlation coeffient to be acceptable?=20 3- how much simillar the drugs should be?=20 4- Are there known drugs developed by qsar?=20 I appreciate any response=20 Regards=20 Tarek El-gogary=20 Chem. Dept.=20 Fac. of Sci.=20 Mans.Univ.=20 Egypt=20 ------=_NextPart_000_002C_01BFF22E.BA5FC840 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable QSAR QUESTIONS
Hi
In order to get a good QSAR model the = number of=20 compounds in the dataset should be > 20 and also there should be = considerable=20 difference in the range of activities. Ideally the acceptable r2 value = is >=20 0.80 but again it depends on lot of other factors. If the main objective = of your=20 QSAR analysis is make perfect predictions then you should go in for a = model with=20 r2 >0.9, but if your main objective is just to cluster the molecules = in=20 activity ranges then r2 > 0.8 can be used. It is good to have = structurally=20 diversity while building the QSAR model.
Cheers
Amit
-------------------------------------------------------------= ----
Amit=20 Kulkarni, Ph.D.
Applications Scientist
Life Science
Molecular=20 Simulations Inc.
Burlington, MA 01803
(781) 359 1217 Fax: (781) = 229=20 989
Email: amit@msi.com
------------------------= -----------------------------------------
----- Original Message -----
From:=20 Tarek=20 Mamoun El-Gogary
Sent: Thursday, July 20, 2000 = 6:34=20 AM
Subject: CCL:QSAR = QUESTIONS

Dear netters,
I=20 am some how begginer in QSAR. I have got some basic questions.=20
1- is there a limit of N , the number = of drugs=20 used in qsar analysis, ?
2- how = small is=20 the correlation coeffient to be acceptable?
3- how much simillar the drugs should be?
4- Are there known drugs developed by qsar?
I appreciate any response
Regards
Tarek = El-gogary=20
Chem. Dept.
Fac. of Sci.
Mans.Univ.=20
Egypt =

------=_NextPart_000_002C_01BFF22E.BA5FC840-- From chemistry-request@server.ccl.net Wed Jul 19 17:14:49 2000 Received: from lrz.uni-muenchen.de (lsanca1-ar99-078-106.biz.dsl.gtei.net [4.3.78.106]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id RAA02164 for ; Wed, 19 Jul 2000 17:14:49 -0400 Received: (from eugene.leitl@localhost) by lrz.uni-muenchen.de (8.8.8/8.8.8) id NAA26174; Wed, 19 Jul 2000 13:14:08 -0700 From: Eugene Leitl MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Message-ID: <14710.3088.329870.233343@lrz.uni-muenchen.de> Date: Wed, 19 Jul 2000 13:14:08 -0700 (PDT) Cc: Subject: Chemoinformatics conf: Sheffield, 2001 (fwd) X-Mailer: VM 6.71 under 21.1 (patch 4) "Arches" XEmacs Lucid From: Val Gillet Sender: Molecular Diversity for Basic Research & Drug discovery To: MOL-DIVERSITY@LISTSERV.ARIZONA.EDU Subject: Chemoinformatics conf: Sheffield, 2001 (fwd) Date: Wed, 19 Jul 2000 11:13:13 +0100 Call For Papers The Chemical Structure Association and the Molecular Graphics and Modelling Society announce their Second Joint Sheffield Conference on Chemoinformatics: Computational Tools for Lead Discovery. The conference will be held in Stephenson Hall, University of Sheffield, UK from 9th to 11th April 2001. Offers of papers are welcomed in all aspects of lead discovery. Possible topics include (but are not limited to): * 3D databases, including docking and pharmacophore analysis; * assay QC and its influence on data mining; * chemical data mining; * descriptor validation; * design of leadlike combinatorial libraries; * design of screening collections; * e-business to facilitate lead discovery; * novel software and hardware systems for lead discovery; * selective compound acquisition from in house and commercial suppliers; * similarity and clustering methods; * structure-activity methods for lead identification and early optimisation; * structure-based design for lead identification and early optimisation; * virtual screening; * case histories incorporating any of the above. Authors interested in submitting a paper for consideration should send a title and brief abstract to Val Gillet (v.gillet@sheffield.ac.uk) by 15th September 2000. Further details of the conference and registration information will follow later in the year and will be posted at www.shef.ac.uk/cisrg/shef2001. From chemistry-request@server.ccl.net Thu Jul 20 10:24:24 2000 Received: from nmr-v.ioc.ac.ru (root@nmr-v.ioc.ac.ru [193.233.3.213]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id KAA07429 for ; Thu, 20 Jul 2000 10:24:22 -0400 From: val@nmr-v.ioc.ac.ru Received: (from val@localhost) by nmr-v.ioc.ac.ru (8.9.3/8.9.3) id SAA17696; Sat, 22 Jul 2000 18:27:04 +0400 Date: Sat, 22 Jul 2000 18:27:04 +0400 MIME-Version: 1.0 To: CHEMISTRY@ccl.net Subject: G98: ONIOM and Amber on TM systems Message-ID: <1000_17693_964276024_1@nmr-v> Content-ID: <1000_17693_964276024_2@nmr-v> Content-type: text/richtext Content-Transfer-Encoding: quoted-printable Hi! I am trying to optimize platinum organometallic complex at the ONIOM(HF/lanl2dz:Amber) level. Where platinum atom and the neighbors are defined as the high layer (HF) = and the rest system as low layer (MM). Unfortunately, the program stops with the error message: > Missing atomic parameters for atom 1 IAtTyp=3D 0 where atom 1 is platinum, which is defined as high layer and should not be treated with MM. Is it a known thing in G98? What the solution possible? Can anybody send me an example of input file of oniom/amber application on transition metal containing system? thanks! will be summarized. best regards, Valentine. =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D , , , , Valentine P. Ananikov |\\\\ ////| /////| NMR Group | \\\|/// | ///// | ND Zelinsky Institute of Organic Chemistry | |~~~| | |~~~| | Leninsky Prospect 47 | |=3D=3D=3D| | |=3D=3D=3D= | | Moscow 117913 | | | | | | | Russia | | A | | | Z | | \ | | / | | / e-mail: val@cacr.ioc.ac.ru \|=3D=3D=3D|/ |=3D=3D=3D= |/ http://nmr.ioc.ac.ru/Staff/AnanikovVP/ '---' '---' Fax +7 (095)1355328 Phone +7 (095)9383536 =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D From chemistry-request@server.ccl.net Thu Jul 20 14:01:46 2000 Received: from medicor.wustl.edu (medicor.wustl.edu [128.252.223.195]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id OAA08536 for ; Thu, 20 Jul 2000 14:01:46 -0400 From: ReichertD@mir.wustl.edu Subject: visualizing data To: chemistry@ccl.net X-Mailer: Lotus Notes Release 5.0.1b September 30, 1999 Message-ID: Date: Thu, 20 Jul 2000 13:01:57 -0500 X-MIMETrack: Serialize by Router on Medicor/Washington University(Release 5.0.2c |February 2, 2000) at 07/20/2000 01:01:59 PM MIME-Version: 1.0 Content-type: text/plain; charset=us-ascii Hi, I'm hoping that the list can provide some recommendations. I'm trying to visualize some output from ab initio calculations (Jaguar in particular) specifically a surface map of charge density from electrostatic fitting(data formatted as x,y,z coords and charge), and plots of electron density and potential. Can anyone recommend software that can do this, preferably for Linux or Irix? I'll summarize if there is any interest. thanks in advance, -david David Reichert, Ph.D. Washington University School of Medicine 510 S. Kingshighway, Campus Box 8225 St Louis, MO 63110 e-mail: reichertd@mir.wustl.edu voice: (314) 362-8461 fax: (314) 362-9940 From chemistry-request@server.ccl.net Thu Jul 20 14:11:51 2000 Received: from mserve1.acs.ucalgary.ca (root@mserve1.acs.ucalgary.ca [136.159.34.51]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id OAA08596 for ; Thu, 20 Jul 2000 14:11:51 -0400 Received: from acs1.acs.ucalgary.ca(136.159.34.221) by mserve1.acs.ucalgary.ca via smap (V2.0) id ZZ087226; Thu, 20 Jul 2000 12:11:39 -0600 Received: from localhost (patchkov@localhost) by ucalgary.ca (AIX4.3/UCB 8.8.8/8.8.8) with ESMTP id MAA83438; Thu, 20 Jul 2000 12:11:38 -0600 Date: Thu, 20 Jul 2000 12:11:38 -0600 (MDT) From: Serguei Patchkovskii X-Sender: patchkov@acs1.acs.ucalgary.ca To: Jens Spanget-Larsen cc: CHEMISTRY@ccl.net Subject: Re: CCL:Seeing molecular orbitals? In-Reply-To: <92CE6BB1672@virgil.ruc.dk> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Thu, 20 Jul 2000, Jens Spanget-Larsen wrote: > In a recent, most interesting publication ('Seeing molecular orbitals', > Chem.Phys.Letters 321, 78-82 [2000]) scanning tunneling microscopy is used to > observe the shapes of single molecular orbitals of the fullerene C60: > > "..the scanning tunneling microscope (STM) is probing a single molecular > orbital (MO)." See the essay by S.-G. Wang and W.H.E. Schwarz "On Closed-Shell Interactions, Polar Covalences, d Shell Holes, and Direct Images of Orbitals: The Case of Cuprite", published in Angew. Chem. Intl. Ed. 2000, 39(10), pages 1757-1762. They do analyse, in quite some detail, that is *actually* seen in this kind of experiments - and it is not a direct image of a single molecular orbital. /Serge.P --- Home page: http://www.cobalt.chem.ucalgary.ca/ps/ From chemistry-request@server.ccl.net Thu Jul 20 14:23:02 2000 Received: from qtp.ufl.edu (zwart.qtp.ufl.edu [128.227.89.3]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id OAA08671 for ; Thu, 20 Jul 2000 14:23:01 -0400 Received: from pc1 (pc1 [128.227.192.187]) by qtp.ufl.edu (8.9.1a/8.9.1) with SMTP id OAA15412; Thu, 20 Jul 2000 14:19:23 -0400 (EDT) Message-ID: <02cd01bff277$585fb300$bbc0e380@qtp.ufl.edu> From: "Stefan Fau" To: Cc: "CCL - all" References: <1000_17693_964276024_1@nmr-v> Subject: Re: CCL:G98: ONIOM and Amber on TM systems Date: Thu, 20 Jul 2000 14:21:37 -0400 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.00.2314.1300 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2314.1300 Hi Valentine, The ONIOM method requires 3 calculations for a molecule: a low level calc of the whole molecule (ll/all), a low level calc of the high level part (ll/part) and a high level calc of the high level part (hl/part). The ONIOM energy is defined as E(ONIOM) = E(ll/all) - E(ll/part) + E(hl/part) Although the low level energy contributions of the high level part seem to cancel out, that is not completely true. In order to have well behaved high level parts, broken bonds are saturated with hydrogen. This causes a difference in the MM energy terms between ll/all and ll/part that reaches at least three atoms inside the high level part (dihedral angle with the saturation H). For that reason (and programming reasons, I assume), you need MM parameters for all atoms in the molecule. In the last few days there was a thread concerning ONIOM energies. One of the mails pointed to an article that explains the ONIOM method in more detail. Stefan ______________________________________________________________________ Dr. Stefan Fau | fau@qtp.ufl.edu Quantum Theory Project | (352) 392-6714 University of Florida Gainesville, FL 32611-8435 From chemistry-request@server.ccl.net Thu Jul 20 17:09:57 2000 Received: from ivory.trentu.ca (trentu.ca [192.75.12.103]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id RAA09262 for ; Thu, 20 Jul 2000 17:09:57 -0400 Received: from trentu.ca ([204.225.13.50]) by trentu.ca (PMDF V5.2-32 #29543) with ESMTP id <01JRZXFDXGRW007UEE@trentu.ca> for chemistry@ccl.net; Thu, 20 Jul 2000 17:09:54 EDT Date: Thu, 20 Jul 2000 17:14:22 -0400 From: elewars Subject: PROGRAM FOR SCATTERPLOTS (STEREOSCOPIC?) To: chemistry@ccl.net Message-id: <39776BAE.99ED3100@trentu.ca> MIME-version: 1.0 X-Mailer: Mozilla 4.7 [en] (WinNT; I) Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7bit X-Accept-Language: en Thursday 2000 July 20 Hello, Suppose one has for, say, 50 molecules, 3 properties for each molecule (e.g. dipole moment, frontier orbital gap, ionization energy--I just made up these three merely as an example) and wishes to *see* if the properties are correlated. You could create an x,y,z-type scatterplot with a property for each axis and see how molecules with certain values of the properties group themseves in certain parts of "property space". Maybe there would be two or three well-defined clumps. If for each molecule you have 4 properties you could add a fourth dimension to the 3D plot by using color. QUESTIONS: 1) Is there a good program for creating attractive scatterplots? For adding color and or a number (molecule #1, #2, etc.) to each point in the plot? 2) Is there a program that will create *stereoscopic* 3D scatterplots (for example, by showing two pictures that one can view with standard 3D glasses), so that one can immediately see where in 3D space points lie? I suspect that programs like Maple and Mathematica can't do all this. Thanks E. Lewars ========= From chemistry-request@server.ccl.net Thu Jul 20 20:02:11 2000 Received: from ALPHA6.CC.MONASH.EDU.AU (alpha6.cc.monash.edu.au [130.194.1.25]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id UAA10001 for ; Thu, 20 Jul 2000 20:02:09 -0400 From: Jerome.Wielens@vcp.monash.edu.au Received: from its-pharm1.vcp.monash.edu.au ([130.194.216.13]) by vaxc.cc.monash.edu.au (PMDF V6.0-24 #43886) with ESMTP id <01JS0WRJUJDC9FNWPG@vaxc.cc.monash.edu.au> for chemistry@server.ccl.net; Fri, 21 Jul 2000 10:01:30 +1000 Received: from ITS-PHARM1/SpoolDir by its-pharm1.vcp.monash.edu.au (Mercury 1.48); Fri, 21 Jul 2000 10:01:49 +1000 Received: from SpoolDir by ITS-PHARM1 (Mercury 1.48); Fri, 21 Jul 2000 09:56:56 +1000 Date: Fri, 21 Jul 2000 09:56:49 +1000 Subject: Visualising Autogrid maps To: chemistry@server.ccl.net Message-id: <01JS0WRK2DXI9FNWPG@vaxc.cc.monash.edu.au> Organization: Victorian College of Pharmacy MIME-version: 1.0 X-Mailer: Pegasus Mail for Win32 (v3.12b) Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7BIT Priority: normal Dear all, I have two quick questions. Does anyone have a script to convert Delphi grids into a format that is useable by Autodock? Does anyone have a method to visulalise Autogrid grid maps in either Sybyl or Insight (as we don't have access to AVS)? Thanking you in advance Jerome Wielens From chemistry-request@server.ccl.net Thu Jul 20 20:08:00 2000 Received: from hotmail.com (f62.law9.hotmail.com [64.4.9.62]) by server.ccl.net (8.8.7/8.8.7) with SMTP id UAA10052 for ; Thu, 20 Jul 2000 20:08:00 -0400 Received: (qmail 33834 invoked by uid 0); 21 Jul 2000 00:05:57 -0000 Message-ID: <20000721000557.33833.qmail@hotmail.com> Received: from 138.80.128.19 by www.hotmail.com with HTTP; Thu, 20 Jul 2000 17:05:57 PDT X-Originating-IP: [138.80.128.19] From: "Henry Pang" To: CHEMISTRY@ccl.net Cc: vinutha.ramakrishna@ntu.edu.au, Ted.Lloyd@vcp.monash.edu.au, marg@freon.chem.swin.edu.au, Brian.Yates@chem.utas.edu.au, b_duke@lacebark.ntu.edu.au Subject: Re: CCL:Seeing molecular orbitals? Date: Fri, 21 Jul 2000 00:05:57 GMT Mime-Version: 1.0 Content-Type: text/plain; format=flowed Hi Jens (Denmark) You said observable quantities; MOs have no physical existence> I am new to computational chemistry. My background is medicine and human ecology in Australia. Your post is the first indicator I have seen over a wide range of CCL and books which signals caution. I am overwhelmed by the volume and intensity of work on the methodology and mensuration of molecules, as if that were the end in itself. No where do I see any concern for a Philosophy of Computational Chemistry, which addresses just what is computational chemistry and what its purpose might be in our Universe. I cannot believe the objective is merely to measure everything and simply document these data? Even at my early stage, I am seriously pondering writing material jointly with my academic supervisor who is a computational chemist, which sets out the link (as I see it) between cosmology, quantum theory, relativity and higher dimensions theory on the one hand and computational chemistry on the other. I think molecules are the beautiful building blocks of our Universe and created for a purpose. I decline the view molecules are just chance particles. I suspect from my reading of CCL, my intention may be seen as revolutionary if not outrageous and could well cause an uproar? Best wishes from Australia Dr Henry Pang Postgraduate Student, Computational Chemistry Faculty of Science, Information Technology and Education Northern Territory University PO Box U273 NT University 0815 Australia Mobile 61 419 682121 Fax 61 8 8946 6847 hpangaus@hotmail.com ---------------------------------------------------------------------- >From: "Jens Spanget-Larsen" >To: CHEMISTRY@ccl.net >Subject: CCL:Seeing molecular orbitals? >Date: Thu, 20 Jul 2000 10:43:01 +0100 > >Dear CCL: > >In a recent, most interesting publication ('Seeing molecular orbitals', >Chem.Phys.Letters 321, 78-82 [2000]) scanning tunneling microscopy is used >to >observe the shapes of single molecular orbitals of the fullerene C60: > > "..the scanning tunneling microscope (STM) is probing a single molecular > orbital (MO)." > >However, this reminds me of previous statements in the literature some time >ago, associated with the advent of molecular photoelectron spectroscopy, >f.i. > > "Chemists can see the orbital structure of even fairly large molecules >and no > longer have to rely on the predictions of theoreticians" > > "Photoelectron spectroscopy has demonstrated experimentally to chemists, > physicists and other sceptics that molecular orbitals really do exist" > >I wonder whether this is acceptable terminology, considering the fact >that molecular orbitals are model constructs; they are not physical >observables. By using approximations, such as Koopmans' approximation, many >experimental observations can be conveniently interpreted in terms of >theoretical MO data. But strictly speaking, this does not turn MOs into >observable quantities; MOs have no physical existence. > >Any comments? > >Yours, Jens >--< > >=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= >JENS SPANGET-LARSEN Phone: +45 4674 2000 (RUC) >Department of Chemistry +45 4674 2710 (direct) >Roskilde University (RUC) Fax: +45 4674 3011 >P.O.Box 260 E-Mail: JSL@virgil.ruc.dk >DK-4000 Roskilde, Denmark http://www.rub.ruc.dk/dis/chem/psos/ >=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= > > >-= This is automatically added to each message by mailing script =- >CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To >Admins >MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH >CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net >70 >Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: >jkl@ccl.net > > > > > ________________________________________________________________________ Get Your Private, Free E-mail from MSN Hotmail at http://www.hotmail.com From chemistry-request@server.ccl.net Thu Jul 20 13:35:39 2000 Received: from nic.upatras.gr (nic.upatras.gr [150.140.129.30]) by server.ccl.net (8.8.7/8.8.7) with SMTP id NAA08430 for ; Thu, 20 Jul 2000 13:35:38 -0400 Received: (qmail 9981 invoked from network); 20 Jul 2000 17:33:28 -0000 Received: from pythagoras.physics.upatras.gr (150.140.159.71) by nic.upatras.gr with SMTP; 20 Jul 2000 17:33:28 -0000 Received: (qmail 25891 invoked by uid 1098); 20 Jul 2000 17:37:00 -0000 Received: from localhost (sendmail-bs@127.0.0.1) by localhost with SMTP; 20 Jul 2000 17:37:00 -0000 Date: Thu, 20 Jul 2000 20:37:00 +0300 (EEST) From: Xrhstos Garoufalhs To: CHEMISTRY@ccl.net Subject: GAMESS and symmetry Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII DEAR CCLers I wonder if there is any utility which can read the coordinates of a molecular system and prepare the symmetry input for GAMESS. Thanks in Advance From chemistry-request@server.ccl.net Thu Jul 20 17:55:33 2000 Received: from chala.q1.fcen.uba.ar (chala.q1.fcen.uba.ar [157.92.31.25]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id RAA09495 for ; Thu, 20 Jul 2000 17:55:30 -0400 Received: from localhost (damian@localhost) by chala.q1.fcen.uba.ar (8.9.3/8.9.3) with ESMTP id VAA28280 for ; Thu, 20 Jul 2000 21:15:50 +0200 Date: Thu, 20 Jul 2000 21:15:50 +0200 (MEST) From: =?X-UNKNOWN?Q?Dami=E1n_Scherlis?= To: chemistry@ccl.net Subject: question: how to make movies from rgb files? Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello, I would appreciate if someone tells me where can I find free software to construct an avi or animated gif movie using the output images given by atomtv program (*.rgb, *.iv, *.wrl, *.ray or *.pov files). Thank you very much! Damian