From chemistry-request@server.ccl.net Mon Nov 26 04:36:02 2001 Received: from tigris.klte.hu ([193.6.138.33]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fAQ9a2B01248 for ; Mon, 26 Nov 2001 04:36:02 -0500 Received: from anti07 (193.6.133.59) by tigris.klte.hu (MX V5.1-A Vn6f) with SMTP for ; Mon, 26 Nov 2001 10:35:59 +0100 Message-ID: <000b01c1765e$114ac240$3b8506c1@chem.klte.hu> From: "Tamas Gunda" To: Subject: Mol2Mol 4.0 announcement Date: Mon, 26 Nov 2001 10:38:12 +0100 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 5.50.4522.1200 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4522.1200 Dear CCL Members, The new 4.0 version of the molecule file conversion, manipulation and utility program Mol2Mol is now available > from CompuChem Ltd. The current version of Mol2Mol recognizes, and interconverts about 40 different file formats (including subtypes). Contrary to the previous versions, there is no limit in the number of inputted atoms (apart from memory limitations). It can slice multiple structural files to single ones (such as PDB models or MDL SD files to single ones) and vice versa in several variations. Support for PDB Chime subformat (with 1-2-3 bonds). It contains a simple graphical display module to inspect the currently loaded molecule. It possesses chemical intelligence for recognizing detailed atom types, hybridization and chemical environments, which is necessary for converting simpler formats (like X-ray crystallographic files) to more advanced ones, or when hydrogen atoms are automatically to be added. Calculation of pyramidalities, ring puckerings, checking for failors in protein backbones. Mol2Mol is a very handy tool for everybody dealing with molecular modelling. It is impossible to write here all of the features of Mol2Mol, but have a look to the following links: A very brief summary for those who don't like reading too much: http://dragon.klte.hu/~gundat/m2m/mol2mol-sum.htm For more info see: http://www.compuchem.com/mol2mol.htm and/or http://dragon.klte.hu/~gundat/mol2mola.htm POV-Ray users may also have a look at: http://dragon.klte.hu/~gundat/povraya.htm Demo and normal versions are available from CompuChem. http://www.compuchem.com From chemistry-request@server.ccl.net Mon Nov 26 05:59:47 2001 Received: from gobble.peptor.co.il ([212.150.27.195]) by server.ccl.net (8.11.6/8.11.0) with SMTP id fAQAxeB02259 for ; Mon, 26 Nov 2001 05:59:42 -0500 Received: (qmail 24986 invoked from network); 26 Nov 2001 10:59:26 -0000 Received: from utzli.peptor.co.il (HELO peptor.co.il) (192.168.10.26) by gobble.peptor.co.il with SMTP; 26 Nov 2001 10:59:26 -0000 Sender: hanoch@ccl.net Message-ID: <3C02208E.1FF4CF34@peptor.co.il> Date: Mon, 26 Nov 2001 12:59:26 +0200 From: Hanoch Senderowitz Reply-To: hanoch@peptor.co.il Organization: Peptor X-Mailer: Mozilla 4.76C-SGI [en] (X11; I; IRIX64 6.5 IP30) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: Molecular Modeling Course Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear members of the Computational Chemistry List I was recently asked to give an introductory workshop on molecular modeling with a particular emphasis on small molecules QSAR. The workshop is intended to combine theory with hands-on tutorials, using primarily Accelrys software (i.e., Cerius2). I would be grateful for any help in building this workshop in the form of course outlines, lecture notes, slides etc. Once completed, I'll be happy to send to this list the workshop outline and slides. Regards, Hanoch -- ======================================================== Hanoch Senderowitz Peptor Ltd., Kiriyat Weizmann, Rehovot 76326, Israel e-mail: hanoch@peptor.co.il phone : 972-8-938-7764 fax : 972-8-940-7737 ======================================================== From chemistry-request@server.ccl.net Mon Nov 26 05:59:36 2001 Received: from orionl0.ccf.auth.gr ([155.207.199.31]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fAQAxZB02254 for ; Mon, 26 Nov 2001 05:59:35 -0500 Received: from vanpc3 (vanpc3.chem.auth.gr [155.207.64.163]) by orionl0.ccf.auth.gr (8.11.6/8.11.4/8.11.4) with SMTP id fAQAxTs27643 for ; Mon, 26 Nov 2001 12:59:29 +0200 (EET) Organization: Message-ID: <001c01c17669$d75107a0$a340cf9b@chem.auth.gr> From: "Aleka L." To: Subject: SCIPCM/PCM questions Date: Mon, 26 Nov 2001 13:02:28 +0200 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0019_01C1767A.9A0A0480" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.50.4522.1200 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4522.1200 This is a multi-part message in MIME format. ------=_NextPart_000_0019_01C1767A.9A0A0480 Content-Type: text/plain; charset="iso-8859-7" Content-Transfer-Encoding: quoted-printable Dear CCL'ers,=20 I'm runing solvent effect calculations on a series of molecules = containing 20-28 atoms (C, H, O) using the SCIPCM model; the dielectric = constant values I use range from 1.92 to 80. My questions are as = follows: = = 1) what is the appropriate number of integration points I should use? = I've already read = the answer cited on = = = recommending a) the non-default = single-center integration procedure and b) for molecules possessing more = than 20 atoms the use of at least NAtoms*100 total points. However, I've = run the SCIPCM example of Gaussian 98W, which used 734 points for = formaldehyde (4 atoms) and not the suggested value of 434 points. = = 2) Is = there any way to compute the second derivatives of the energy = analytically and not numerically with the SCIPCM model or other = continuum models (PCM, CPCM, IEFPCM) with the new Gaussian 98W = RevisionA.11version? = = 3) I often get one negative frequency value. Does anyone know of = any method to determine that in advance, in order to interrupt my = running, since each one of my runs lasts for a rather long time? Thanking you in advance. =20 Alexandra Lithoxoidou =20 PhD candidate = Aristotle = University of Thessaloniki = School of Chemistry = = Lab of Applied Quantum = Chemistry = P.O. Box 135 = = 54-006 Thessaloniki, Greece =20 e-mail: alithoxo@chem.auth.gr = =20 ------=_NextPart_000_0019_01C1767A.9A0A0480 Content-Type: text/html; charset="iso-8859-7" Content-Transfer-Encoding: quoted-printable

Dear CCL’ers,

I’m runing solvent effect calculations on a series of molecules = containing=20 20-28 atoms (C, H, O) using the SCIPCM model; the dielectric constant = values I=20 use range from 1.92 to 80. My questions are as=20 follows:           = ;            =             &= nbsp;           &n= bsp;           &nb= sp;           &nbs= p;            = ;            =             &= nbsp;           &n= bsp;           &nb= sp;       =20 1) what is the appropriate number of integration points I should=20 use?           &nb= sp;           &nbs= p;            = ;            =      =20 I’ve already read the answer cited=20 on            = ;            =             &= nbsp;           &n= bsp;           &nb= sp;  =20   =20 <http://server.ccl.net/cgi-bin/ccl/message.cgi?1996+07+18+001+raw><= /FONT>          &nb= sp;           &nbs= p;            = ;      =20 recommending a) the non-default single-center integration procedure and = b) for=20 molecules possessing more than 20 atoms the use of at least NAtoms*100 = total=20 points. However, I’ve run the SCIPCM example of Gaussian 98W, = which used 734=20 points for formaldehyde (4 atoms) and not the suggested value of 434=20 points.           =             &= nbsp;           &n= bsp;           &nb= sp;           &nbs= p;            = ;            =             &= nbsp;           &n= bsp;           &nb= sp;           &nbs= p;          =20 2) Is there any way to compute the second derivatives of the energy = analytically=20 and not numerically with the SCIPCM model or other continuum models = (PCM, CPCM,=20 IEFPCM) with the new Gaussian 98W=20 RevisionA.11version?         = ;            =             &= nbsp;           &n= bsp;           &nb= sp;           &nbs= p;            = ;            =             &= nbsp;           &n= bsp;           &nb= sp;=20 3) I often get one negative frequency value. Does anyone know of any = method to=20 determine that in advance, in order to interrupt my running, since each = one of=20 my runs lasts for a rather long time?

Thanking you in advance.   

Alexandra=20 Lithoxoidou          &n= bsp;           &nb= sp;           &nbs= p;           

PhD=20 candidate          &nbs= p;            = ;            =             &= nbsp;           &n= bsp;           &nb= sp;           &nbs= p;            = ;            =             &= nbsp; =20 Aristotle University of=20 Thessaloniki          &= nbsp;           &n= bsp;           &nb= sp;           &nbs= p;            = ;            =             &= nbsp;           =20 School of=20 Chemistry          &nbs= p;            = ;            =             &= nbsp;           &n= bsp;           &nb= sp;           &nbs= p;            = ;            =            =20 Lab of Applied Quantum=20 Chemistry          &nbs= p;            = ;            =             &= nbsp;           &n= bsp;           &nb= sp;           &nbs= p;            = ;=20 P.O. Box=20 135           &nbs= p;            = ;            =             &= nbsp;           &n= bsp;           &nb= sp;           &nbs= p;            = ;            =             &= nbsp;       =20 54-006 Thessaloniki, Greece  

e-mail: alithoxo@chem.auth.gr &nbs= p;            = ;            =             &= nbsp;           &n= bsp;           &nb= sp;           &nbs= p;            = ;       

------=_NextPart_000_0019_01C1767A.9A0A0480-- From chemistry-request@server.ccl.net Mon Nov 26 06:39:14 2001 Received: from hotmail.com ([207.68.162.205]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fAQBdDB02939 for ; Mon, 26 Nov 2001 06:39:14 -0500 Received: from mail pickup service by hotmail.com with Microsoft SMTPSVC; Mon, 26 Nov 2001 03:39:05 -0800 X-Originating-IP: [212.244.147.4] From: "Victor Anisimov" To: Subject: Large biomolecules Date: Mon, 26 Nov 2001 12:40:48 +0100 MIME-Version: 1.0 Content-Type: text/plain; charset="windows-1251" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.50.4133.2400 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4133.2400 Message-ID: X-OriginalArrivalTime: 26 Nov 2001 11:39:05.0133 (UTC) FILETIME=[F3C4DDD0:01C1766E] Dear CCLers: I'm looking for biggest available bio-molecule, preferably protein, for running NDDO type quantum-chemical calculation on it on my Windows PC. Could someone please share with me Cartesian coordinates of such sample. Before asking your help I investigated PDB database and could find only Chaperonin with PDB id 1AON containing about 120 000 atoms after adding hydrogen atoms. This molecule is not that big as I need. It may happen that there is no bigger experimentally available protein structure than the mentioned above. In this case I would be quite happy to get Cartesian coordinates of 3D structure of a really large protein created by some modeling program. I also wonder is there any application that could read sequence of DNA base letters and construct corresponding 3D model of the DNA? May I ask users of such program to generate a realistic 3D model of a Human DNA fragment for me corresponding to single Gene (your favorite, for example), that should produce several million atoms' structure, I believe. Thank you for your time. With kind regards, Victor. Victor Anisimov, PhD. E-Mail: Victor_Anisimov@hotmail.com Mobile: +48 606 945 326 From chemistry-request@server.ccl.net Mon Nov 26 05:41:55 2001 Received: from relay-4v.club-internet.fr ([194.158.96.115]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fAQAfsB02068 for ; Mon, 26 Nov 2001 05:41:54 -0500 Received: from sungam (nas1-69.kll.n.club-internet.fr [213.44.91.69]) by relay-4v.club-internet.fr (Postfix) with SMTP id 1B35616FD for ; Mon, 26 Nov 2001 11:41:49 +0100 (CET) Message-ID: <004301c17667$7d795fe0$455b2cd5@sungam> From: "Magnus" To: Subject: Heat of Formation in AM1 Date: Mon, 26 Nov 2001 11:45:32 +0100 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0040_01C1766F.DA7606A0" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 4.72.3110.5 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 This is a multi-part message in MIME format. ------=_NextPart_000_0040_01C1766F.DA7606A0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hello there, I am wondering how do AM1 calculate the heat of formation of the = chemical compouds you provide as input. I would like to compare these = figures with the result you can obtain using methods such as Benson or = Pedley.=20 Do you know if we can find on the Internet databases holding = thermodynamical properties of compounds ? It would be quite useful to me = if i could compare the calculated heat of formations to those who were = observed. Michel Julien ------=_NextPart_000_0040_01C1766F.DA7606A0 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
 
    Hello there,
 
    I am wondering how do AM1 = calculate the=20  heat of formation of the chemical compouds you provide as input. I = would=20 like to compare these figures with the result you can obtain using = methods such=20 as Benson or Pedley.
    Do you know if we can find on the = Internet=20 databases holding thermodynamical properties of compounds ? It would be = quite=20 useful to me if i could compare the calculated heat of formations to = those who=20 were observed.
 
    Michel Julien
 
------=_NextPart_000_0040_01C1766F.DA7606A0-- From chemistry-request@server.ccl.net Mon Nov 26 11:45:14 2001 Received: from relay1.scripps.edu ([137.131.200.29]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fAQGjDB09267 for ; Mon, 26 Nov 2001 11:45:14 -0500 Received: from gamow.scripps.edu (gamow.scripps.edu [137.131.252.67]) by relay1.scripps.edu (8.11.6/TSRI-4.0.1r) with ESMTP id fAQGj4v28303; Mon, 26 Nov 2001 08:45:04 -0800 (PST) Received: (from case@localhost) by gamow.scripps.edu (8.9.2/TSRI-3.0.1) id IAA85027; Mon, 26 Nov 2001 08:44:57 -0800 (PST) Date: Mon, 26 Nov 2001 08:44:57 -0800 From: David Case To: temper Cc: chemistry@server.ccl.net Subject: Re: CCL:Broken symmetry calculations Message-ID: <20011126084457.A85054@gamow.scripps.edu> References: <004001c13f5b$78ec2400$5e40cf9b@chem.auth.gr> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline User-Agent: Mutt/1.2.5i In-Reply-To: <004001c13f5b$78ec2400$5e40cf9b@chem.auth.gr>; from temper@chem.auth.gr on Mon, Sep 17, 2001 at 12:30:58PM +0300 On Mon, Sep 17, 2001, temper wrote: > > In the course of the theoretical ab initio treatment of magnetic exchange > in dinuclear transition metal systems some authors use the method of broken > symmetry. Is there anybody to help me in how to do broken symmetry calculations? > Is there any recipe for it? On of the more detailed early discussions of this is in the following review: %A L. Noodleman %A D.A. Case %T Density-functional theory of spin polarization and spin coupling in iron-sulfur clusters %J Adv. Inorg. Chem. %V 38 %P 423-470 As for "how-to": this is discussed in many papers. Generally, we recommend converging first a high-spin (fully symmetric) SCF calculation, then exchanging the alpha and beta spins on one side of the molecule to create a starting configuration for the broken symmetry calculation. Exactly how to "flip spins" depends on the program you are using. ADF and Jaguar (maybe others) offer built-in support for this; with other programs one generally has to manually edit a molecular orbital coefficient file or something similar to that. Be prepared for convergence difficulties (that is, be prepared to be patient). ...hope this helps...dac -- ================================================================== David A. Case | e-mail: case@scripps.edu Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896 The Scripps Research Institute | phone: +1-858-784-9768 10550 N. Torrey Pines Rd. | home page: La Jolla CA 92037 USA | http://www.scripps.edu/case ================================================================== From chemistry-request@server.ccl.net Mon Nov 26 13:42:07 2001 Received: from linman.isisph.com ([204.255.125.131]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fAQIg7B11521 for ; Mon, 26 Nov 2001 13:42:07 -0500 Received: from domino2.isisph.com (mail.isisph.com [10.1.1.5]) by linman.isisph.com (8.9.1/8.9.1) with ESMTP id KAA12259 for ; Mon, 26 Nov 2001 10:42:03 -0800 Subject: Biopolymer modeling and Docking on windows NT To: chemistry@ccl.net X-Mailer: Lotus Notes Release 5.0.8 June 18, 2001 Message-ID: From: PDande@isisph.com Date: Mon, 26 Nov 2001 10:37:00 -0800 X-MIMETrack: Serialize by Router on Domino2/ISIS(Release 5.0.8 |June 18, 2001) at 11/26/2001 10:39:44 AM MIME-Version: 1.0 Content-type: text/plain; charset=us-ascii Hi All! I am looking for some information on available molecular modeling software for modeling of biopolymers (proteins and nucleic acids) on the windows NT platform. I need something that is capable of performing basic calculations on proteins and nucleic acids, including protein-nucleic acid docking operations. Thanks, Prasad ************************************************************************************************************************************************************** Prasad Dande, Ph. D. Senior Scientist Research Chemistry ISIS Pharmaceuticals 2292 Faraday Avenue Carlsbad, CA 92008 Tel: 760 603 4671 Fax: 760 603 4654 Prasad_Dande@isisph.com From chemistry-request@server.ccl.net Mon Nov 26 13:37:41 2001 Received: from email.nist.gov ([129.6.2.7]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fAQIbeB11465 for ; Mon, 26 Nov 2001 13:37:40 -0500 Received: from silyl.nist.gov (silyl.nist.gov [129.6.194.163]) by email.nist.gov (8.9.3/8.9.3) with ESMTP id NAA26342 for ; Mon, 26 Nov 2001 13:37:36 -0500 (EST) Message-Id: <5.0.0.25.2.20011116153736.023b8970@mailserver.nist.gov> X-Sender: rdj3@mailserver.nist.gov X-Mailer: QUALCOMM Windows Eudora Version 5.0 Date: Fri, 16 Nov 2001 15:48:24 -0500 To: CHEMISTRY@ccl.net From: Russ Johnson Subject: Fluid Simulation Challenge Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed ANNOUNCEMENT FIRST INDUSTRIAL FLUID PROPERTIES SIMULATION CHALLENGE The Computational Molecular Science and Engineering Forum http://www.comsef.aiche.org/ of the American Institute of Chemical Engineers (AIChE) has established an open competition for scientists and engineers to use molecular simulation methods to calculate results for specific sets of posed problems. The primary goal of the Industrial Fluid Properties Simulation Challenge is to obtain an in-depth and objective assessment of our current abilities and inabilities to predict thermophysical properties of industrially challenging fluids using computer simulation. Another goal of this competition is to help drive development of molecular simulation methodology toward a closer alignment with the needs of the chemical industry. We anticipate that this challenge will be an annual event. The competition begins in November 2001 when the problems are announced. Entries are due no later than September 3, 2002. Full details are available at http://www.cstl.nist.gov/FluidSimulationChallenge Participants must register at this web site to ensure that their proposed methodology is eligible. Two half-day sessions at the 2002 Annual Meeting of the AIChE in Indianapolis (Nov.3-8, 2002) will be held to discuss the results and announce the winners. The winners will be presented with an award and prize at the AIChE meeting. It is anticipated that significant monetary prizes will be provided by industrial donors. Industry is seeking successful methods, based on molecular simulation techniques, for prediction of properties of fluids and mixtures. This challenge is in part geared towards ensuring the relevance of academic simulation activities to industrial requirements. Successful participants will have the opportunity to transfer their methods to industry. This competition is a result of The Workshop on Simulation Methods to Predict the Thermophysical Properties of Fluids http://www.ctcms.nist.gov/~fstarr/ptpfms/home.html. All inquiries should be directed to Raymond Mountain Competition Committee Chair National Institute of Standards and Technology raymond.mountain@nist.gov 301-975-2484. From chemistry-request@server.ccl.net Mon Nov 26 10:10:43 2001 Received: from netmaster.kds.com.ua ([194.44.106.42]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fAQFALB06884 for ; Mon, 26 Nov 2001 10:10:23 -0500 Received: (from akhavr@localhost) by netmaster.kds.com.ua (8.11.6/8.11.6) id fAQF9uU06328; Mon, 26 Nov 2001 17:09:56 +0200 Sender: akhavr@netmaster.kds.com.ua To: "Victor Anisimov" Cc: Subject: Re: Large biomolecules References: From: Andrey Khavryuchenko Organization: KDS Software Group X-Attribution: AVK Content-Type: text/plain; charset=US-ASCII Date: 26 Nov 2001 17:09:54 +0200 In-Reply-To: Message-ID: Lines: 22 User-Agent: Gnus/5.0808 (Gnus v5.8.8) XEmacs/21.1 (Cuyahoga Valley) MIME-Version: 1.0 Victor, "VA" == Victor Anisimov wrote: VA> I'm looking for biggest available bio-molecule, preferably protein, VA> for running NDDO type quantum-chemical calculation on it on my Windows VA> PC. Could someone please share with me Cartesian coordinates of such VA> sample. VA> Before asking your help I investigated PDB database and could find VA> only Chaperonin with PDB id 1AON containing about 120 000 atoms after VA> adding hydrogen atoms. This molecule is not that big as I need. I am curious why you would want such large protein to be calculated using NDDO? And, of course, what hardware and software you're going to utilize? -- Andrey V Khavryuchenko http://www.kds.com.ua/ Offshore Software Development From chemistry-request@server.ccl.net Mon Nov 26 14:12:15 2001 Received: from srv.cip.physik.tu-muenchen.de ([129.187.137.223]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fAQJCEB12051 for ; Mon, 26 Nov 2001 14:12:14 -0500 Received: from xi.cip.physik.tu-muenchen.de (xi.cip.physik.tu-muenchen.de [129.187.184.65]) by srv.cip.physik.tu-muenchen.de (8.10.2/8.10.2) with ESMTP id fAQJCA426317; Mon, 26 Nov 2001 20:12:11 +0100 (MET) Received: from localhost (thuber@localhost) by xi.cip.physik.tu-muenchen.de (8.8.5/8.8.6) with SMTP id UAA19215; Mon, 26 Nov 2001 20:12:10 +0100 (MET) X-Authentication-Warning: xi.cip.physik.tu-muenchen.de: thuber owned process doing -bs Date: Mon, 26 Nov 2001 20:12:10 +0100 (MET) From: Thomas Huber To: a3arzi cc: CCL Subject: Re: CCL:BSA 3D structure - does anybody knows aby hook ? In-Reply-To: <216794208.20011026144555@vaidila.vdu.lt> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Arturas, if you search the PDB for albumin (www.rcsb.org), you'll find many structures, even of complexes with hydrophobic substances, but for human serum albumin. If there is a specific reason for you to look for the bovine/cow form, then I would probably try a homology modeling server (www.expasy.ch) Swiss-Prot/Model. Hope this helps! Thomas ----------------------------------------------------------------------------- Dr.Thomas Huber University of Arizona Tel.: (520) 621-2537 Department of Chemistry FAX: (520) 621-8407 1306 E. University Blvd. email thuber@physik.tu-muenchen.de Tucson, Arizona 85721-0041 On Fri, 26 Oct 2001, a3arzi wrote: > Hi, > > I am searching for BSA - Bovine Serum Albumin - tertiary structure. > I surfed www, icuding PDB www database, and it was without any results. > ( Here is the last tray .... ) > > Coul anybody point to any reference about the experimental tertiary > structure of BSA ? > > Bets regards to all > Arturas Z. > > > > -= 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 Mon Nov 26 11:23:25 2001 Received: from ucidoor.unitedcatalysts.com ([208.23.162.2]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fAQGNOB08800 for ; Mon, 26 Nov 2001 11:23:25 -0500 Received: by ucidoor.unitedcatalysts.com; (8.8.8/1.3/10May95) id LAA08349; Mon, 26 Nov 2001 11:23:21 -0500 (EST) Received: from 10.1.0.50 by ucismtp02.unitedcatalysts.com (InterScan E-Mail VirusWall NT); Mon, 26 Nov 2001 11:23:07 -0500 (Eastern Standard Time) Received: from lvlxch01.unitedcatalysts.com ([10.16.100.88]) by lvlmail.unitedcatalysts.com (PMDF V6.0-24 #41777) with ESMTP id <0GNF00GB11A96P@lvlmail.unitedcatalysts.com> for chemistry@ccl.net; Mon, 26 Nov 2001 11:18:09 -0500 (EST) Received: by lvlxch01.unitedcatalysts.com with Internet Mail Service (5.5.2650.21) id ; Mon, 26 Nov 2001 11:23:07 -0500 Content-return: allowed Date: Mon, 26 Nov 2001 11:23:01 -0500 From: "Shobe, Dave" Subject: Gamess non-analytic frequencies To: "'CCL'" Message-id: <157A51F55AAAD3119CD70008C7B1629D01C15725@lvlxch01.unitedcatalysts.com> MIME-version: 1.0 X-Mailer: Internet Mail Service (5.5.2650.21) 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 fAQGNPB08801 The following is about Gamess US (Windows version): When analytical gradients are not available for a given method, in Gamess one uses Trudge for geometry optimization. (It's not too too bad with only one geometric parameter). But once the minimum is found, how does one calculate the frequency and zero-point energy? In other words, what is the Gamess equivalent of (Gaussian's) freq=numer? --David Shobe Süd-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.