From wtwinter@mailbox.syr.edu Wed Apr 12 00:59:02 1995 Received: from mailbox.syr.edu for wtwinter@mailbox.syr.edu by www.ccl.net (8.6.10/930601.1506) id AAA00773; Wed, 12 Apr 1995 00:50:40 -0400 Received: from mothra.syr.edu by mailbox.syr.edu (8.6.9/SUM-V8-1.0) id AAA07991; Wed, 12 Apr 1995 00:52:01 -0400 Received: by mothra.syr.edu (4.1/Spike-2.0) id AA11797; Wed, 12 Apr 95 00:51:48 EDT Date: Wed, 12 Apr 1995 00:51:48 -0400 (EDT) From: "William T. Winter" X-Sender: wtwinter@mothra.syr.edu To: compchem Subject: Polysaccharide Coordinate Database Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII I have seen several postings for coordinates of diffraction based polysaccharide structures. A few such entries do exist in the pdb ( Protein Data Base). These include chondroitin sulfates, iota carrageenan, some hyaluronates, and a capsular polysaccharide from a strain of E. coli. All of these were submitted by the Arnott group during the late 1970's. I was a member of that group then and continue to be active in such studies as does my colleague and department head Anatole Sarko. If you would like to see a separate polysaccharide date base developed, send me a short note of support by email, FAX or regular mail. If you have preferences as to form - pdb format or extension thereof, Cartesian or fractional unit cell etc - let me know about those preferences I am coming into a period where I will have the time to seek support for and initiate development of such a data base but I am certain that no support will be forthcoming unless I can demonstrate a potential community of users. Finally, if such a data base were extended to include other linear or regularly branched polymers both naturally occurring and synthetic would that heighten the interest? I think that the nucleic acid people may already have such a data base but I do not believe that the synthetic polymer people have gotten to this stage yet. =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= Dr. William T. Winter Phone: (315)470-6876 315 Baker Lab FAX: (315)470-6856 SUNY-ESF Internet: wtwinter@mailbox.syr.edu Syracuse, NY 13210-2786 From chrmiri@techunix.technion.ac.il Wed Apr 12 03:29:03 1995 Received: from techunix.technion.ac.il for chrmiri@techunix.technion.ac.il by www.ccl.net (8.6.10/930601.1506) id DAA01837; Wed, 12 Apr 1995 03:18:19 -0400 Received: (from chrmiri@localhost) by techunix.technion.ac.il (8.6.12/8.6.10) id KAA25055; Wed, 12 Apr 1995 10:18:02 +0300 Date: Wed, 12 Apr 1995 10:18:01 +0300 (EET DST) From: Miri Karni To: ccl Subject: MOGADOC Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII HI, Can someone inform me about MOGADOC, I have tried to write directly to Jorgen Vogt at jorgen.vogt@chemie.uni-ulm.de but received no answer. Thanks Miri From joe@dali.chem.wesleyan.edu Wed Apr 12 06:59:05 1995 Received: from dali.chem.wesleyan.edu for joe@dali.chem.wesleyan.edu by www.ccl.net (8.6.10/930601.1506) id GAA03411; Wed, 12 Apr 1995 06:47:30 -0400 Received: by dali.chem.wesleyan.edu (AIX 3.2/UCB 5.64/4.03) id AA18851; Wed, 12 Apr 1995 06:49:40 -0400 Date: Wed, 12 Apr 1995 06:49:40 -0400 From: joe@dali.chem.wesleyan.edu (Joe Ochterski) Message-Id: <9504121049.AA18851@dali.chem.wesleyan.edu> To: chemistry@ccl.net Subject: CBS references, was G94 Accurate Methods? > What I am not familiar with is the complete basis set methods (CBS) > called CBS-4, CBS-q. CBS-Q and CBS-APNO [in GAUSSIAN 94]. These methods were developed by George Petersson (Wesleyan Univ.) and several collaborators. The CBS-Q model produces better results than either G2 or G2(MP2), and is comparable in speed to G2(MP2). CBS-4 is considerably faster and gives results accurate to ~2 kcal/mol. CBS-APNO is accurate to about 0.5 kcal/mol. Here is a brief description of the CBS models: With the development of accurate correlation methods like CCSD(T), QCISD(T), etc., the largest errors in ab initio thermochemical calculations come from basis set truncation. The CBS models use the known asymptotic convergence of pair natural orbital expansions to extrapolate finite basis calculations to an estimated complete basis set (CBS) limit (see references below). These CBS extrapolation techniques have been used by Ochterski, Petersson, and Montgomery to construct a family of CBS model chemistries (CBS-4, CBS-q, CBS-Q and CBS-APNO). Like G2 theory, we obtain the CBS energy via a series of calculations. Our analysis shows that the order by order contributions to chemical energy differences generally decrease with order of perturbation theory, while the computational expense increases rapidly. The CBS models take advantage of these complimentary trends by using progressively smaller basis sets for the higher orders of perturbation theory. The CBS-Q model starts with a geometry optimization at the MP2 level of theory. It then uses a large basis set MP2 calculation as a base energy, and a CBS extrapolation to correct the energy through second order. Two calculations are used to approximate higher order contributions. We use MP4(SDQ)/6-31+(d,p) with extra polarization functions on sulfur phosphorous and chlorine to approximate the higher order effects of polarization functions, and QCISD(T)/6-31+G* for still higher order effects. This model also has corrections for zero-point energy and spin contamination and a size-consistent higher order correction. The CBS-Q model improves the treatment at every level of theory, and the CBS-APNO improves it still further. The CBS-APNO model improves the treatment at every level of theory. We developed the CBS-4 model in a similar way to treat substantially larger systems, althought somewhat less accurately. All the models have been found to reproduce the 125 experimental energy differences in the G2 test set with relatively small errors (63 differences were used for CBS-APNO): Accuracy of Models (kcal/mole) CBS-4 CBS-q CBS-Q G2(MP2) G2 CBS-APNO Mean Abs Dev 2.0 1.7 1.0 1.6 1.2 0.5 RMS Dev 2.5 2.2 1.3 2.0 1.5 0.7 Maximum 7.0 5.4 3.8 6.3 5.1 1.5 Relative Speed Up Molecule CBS-4 CBS-Q G2(MP2) G2 -------- ----- ----- ------- ---- water 3.8 1.4 1.3 1.0 acetylene 5.9 2.1 2.1 1.0 propane 25.3 6.0 2.3 1.0 F2C=O 25.9 3.1 2.5 1.0 SiF4 59.0 9.6 5.1 1.0 benzene 23.8 1.8 1.0 CBS-Q offers better accuracy and speed than the G2 family of models. Molecules with many hydrogens fare particularly well. CBS-4 can be used to treat much larger systems. CBS-APNO is suitable for systems where accuracy is critical. General Complete Basis Set (CBS) Extrapolation References: M. R. Nyden and G. A. Petersson, JCP 75, 1843 (1981) G. A. Petersson, A. Bennett, T. G. Tensfeldt, M. A. Al-Laham, W. A. Shirley and J. Mantzaris, J. Chem. Phys. 89, 2193 (1988). G. A. Petersson and M. A. Al-Laham, JCP 94, 6081 (1991) G. A. Petersson, T. Tensfeldt, and J. A. Montgomery, JCP 94, 6091 (1991) CBS-APNO: J. A. Montgomery, J. W. Ochterski, and G. A. Petersson, JCP 101, 5900 (1994) CBS-4, CBS-q, CBS-Q J. W. Ochterski, G. A. Petersson and J. A. Montgomery, Jr., submitted to J. Chem. Phys. A PostScript version of the CBS-4 paper is available via anonymous FTP to dali.chem.wesleyan.edu, file name:/pub/cbs-4.paper.ps. It is also available on WWW. The URL is: http://dali.chem.wesleyan.edu/papers/paper.950120.ps If neither of these options is available to you, please ask Gaussian, Inc. for a printed copy. They can be reached at info@gaussian.com or (412)279-6700. Joe Ochterski ochtersk@lorentzian.com From CTARG@Levels.UniSA.Edu.Au Wed Apr 12 08:44:06 1995 Received: from Levels.UniSA.Edu.Au for CTARG@Levels.UniSA.Edu.Au by www.ccl.net (8.6.10/930601.1506) id IAA04480; Wed, 12 Apr 1995 08:38:06 -0400 From: Received: from Levels.UniSA.Edu.Au by Levels.UniSA.Edu.Au (PMDF V4.3-13 #9510) id <01HP8Z71PU5S9YDZW4@Levels.UniSA.Edu.Au>; Wed, 12 Apr 1995 10:59:00 +1030 Date: Wed, 12 Apr 1995 10:59:00 +1030 Subject: area of a 2-dimensional projection of a molecule To: chemistry@ccl.net Message-id: <01HP8Z71RPOI9YDZW4@Levels.UniSA.Edu.Au> X-Envelope-to: chemistry@ccl.net X-VMS-To: IN%"chemistry@ccl.net" MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Content-transfer-encoding: 7BIT Hi, My group is interested in (among other things) the effective surface area of surfactants on surfaces. I am wondering if there is a program around that will allow me to calculate the area of a two dimensional projection of a molecule, including the area required for Van der Waals radii. I can see that such a thing should not be to difficult to write a program for but Iwould prefer not to have to reinvent the wheel. Thanks Andrea. From alex@mmiris.ab.umd.edu Wed Apr 12 09:14:07 1995 Received: from comm1.ab.umd.edu for alex@mmiris.ab.umd.edu by www.ccl.net (8.6.10/930601.1506) id JAA04912; Wed, 12 Apr 1995 09:03:43 -0400 From: Received: by comm1.ab.umd.edu (5.65/DEC-Ultrix/4.3) id AA04455; Wed, 12 Apr 1995 09:03:42 -0400 Received: by mmiris.ab.umd.edu (931110.SGI/911001.SGI) for @comm1.ab.umd.edu:CHEMISTRY@ccl.net id AA27771; Wed, 12 Apr 95 09:17:05 -0400 Date: Wed, 12 Apr 95 09:17:05 -0400 Message-Id: <9504121317.AA27771@mmiris.ab.umd.edu> To: wtwinter@mailbox.syr.edu Cc: CHEMISTRY@ccl.net In-Reply-To: "William T. Winter"'s message of Wed, 12 Apr 1995 00:51:48 -0400 (EDT) Subject: CCL:Polysaccharide Coordinate Database Dr. Winter, I support your efforts to compile a database of polysaccharide structural data. This database should include both linear and branched systems. My interests include the parameterization of biological systems for empirical force field calculations. The availability of structural data on polysaccharides will enhance our ability to accurately parameterize carbohydrates. Sincerely, Alex MacKerell, alex@mmiris.ab.umd.edu School of Pharmacy University of Maryland at Baltimore 20 North Pine Street Baltimore, MD 21201 410-706-7442 From ramon@ce.ifisicam.unam.mx Wed Apr 12 09:59:07 1995 Received: from ce.ifisicam.unam.mx.ifisicam.unam.mx for ramon@ce.ifisicam.unam.mx by www.ccl.net (8.6.10/930601.1506) id JAA05835; Wed, 12 Apr 1995 09:44:42 -0400 Message-Id: <199504121344.JAA05835@www.ccl.net> Received: by ce.ifisicam.unam.mx (1.38.193.3/16.2) id AA11798; Wed, 12 Apr 95 07:46:17 -0500 From: Ramon Garduno Subject: PROCHECK located To: chemistry@ccl.net (POST MSG's) Date: Wed, 12 Apr 95 7:46:17 CDT Mailer: Elm [revision: 70.85] Dear netters: To those of you who responded to my inquire about PROCHECK, I am very grateful for sharing your information. Also, for those on the CCL interested in the same program, it can be found in the anonymous ftp site pdb.pdb.bnl.gov (C.S. Raman provided the location). With a time constrain in mind, I want to send my thanks via this msg to the following people for their valuable comments: J. Labanowski D. Agrafroti J. Nauss S. Hammerum L. Noskov M. Peterson H. Leung D. Heisterberg C.S. Raman E. Arcia C. Nervi C. Thys H. Homeier Emiel H. Hommier Istvan G. Mullier M. Tennant V. Rosas-Garcia This is another example that the CCL works when we need it. Try to keep it alive! Cheers, -- ____________________________________________________________________________ Dr. Ramon Garduno-Juarez Research Professor in Biophysics INSTITUTO DE FISICA | EMAIL: ramon@ce.ifisicam.unam.mx UNIVERSIDAD NAL. AUTONOMA DE MEXICO | rgard@redvax1.dgsca.unam.mx Laboratorio de Cuernavaca | VOICE: (73)175388 Apdo. Postal 139-B | (73)111611 62191 Cuernavaca, Morelos | FAX: (73)111603 MEXICO | (73)173077 ___________________________________ EOF _____________________________________ From nauss@ucmod2.che.uc.EDU Wed Apr 12 10:05:34 1995 Received: from ROCK.SAN.UC.EDU for nauss@ucmod2.che.uc.EDU by www.ccl.net (8.6.10/930601.1506) id JAA05995; Wed, 12 Apr 1995 09:48:25 -0400 Received: from ucmod2.che.uc.edu by UCBEH.SAN.UC.EDU (PMDF V4.3-10 #7238) id <01HP8WPTZNY8HSO43F@UCBEH.SAN.UC.EDU>; Wed, 12 Apr 1995 09:47:38 -0500 (EST) Received: by ucmod2.che.uc.edu (920330.SGI/920502.SGI.AUTO) for @uc.edu:CHEMISTRY@ccl.net id AA22866; Wed, 12 Apr 95 09:51:23 -0400 Date: Wed, 12 Apr 1995 09:51:23 -0400 From: nauss@ucmod2.che.uc.EDU (Jeffrey L. Nauss) Subject: Searching for sequences To: CHEMISTRY@ccl.net Reply-to: nauss@ucmod2.che.uc.EDU Message-id: <9504121351.AA22866@ucmod2.che.uc.edu> Content-transfer-encoding: 7BIT I want to search the PDB for structures that have the tripeptide sequence Asn-X-Glu where X is any amino acid. The purpose of the search is to identify possible structural motifs for the sequence within proteins. Thus far, I have not found how to do this using the Brookhaven search engines on the WWW. Does any one have a way to perform this search? Alternatively, I could search sequence databases such as SWISS-Prot and then cross-reference the hits with the PDB. However, I have yet to find a way to perform the search using wildcards. Any suggestions? Thanks in advance... Jeff Nauss **************************************************************************** * UU UU Jeffrey L. Nauss, PhD * * UU UU Director, Molecular Modeling Services * * UU UU Department of Chemistry * * UU UU CCCCCCC University of Cincinnati * * UU UU CCCCCCCC Cincinnati, OH 45221-0172 * * UUUU CC * * CC Telephone: 513-556-0148 Fax: 513-556-9239 * * CC * * CCCCCCCC e-mail: nauss@ucmod2.che.uc.edu * * CCCCCCC http://www.che.uc.edu/~nauss * **************************************************************************** From czernek@chemi.muni.cz Wed Apr 12 10:29:08 1995 Received: from aragorn.ics.muni.cz for czernek@chemi.muni.cz by www.ccl.net (8.6.10/930601.1506) id KAA06884; Wed, 12 Apr 1995 10:26:22 -0400 Received: from bilbo.chemi.muni.cz by aragorn.ics.muni.cz with SMTP id AA03306 (5.67a8/IDA-1.4.4 for ); Wed, 12 Apr 1995 16:26:08 +0200 Received: by bilbo.chemi.muni.cz id AA00404 (5.67b/IDA-1.4.4 for chemistry@ccl.net); Wed, 12 Apr 1995 17:06:15 +0200 From: Jiri Czernek Message-Id: <199504121506.AA00404@bilbo.chemi.muni.cz> Subject: 1st row - F EXCITED STATES To: chemistry@ccl.net Date: Wed, 12 Apr 1995 17:06:13 +0200 (MET DST) Cc: czernek@chemi.muni.cz (Jiri Czernek) X-Mailer: ELM [version 2.4 PL23] Content-Type: text Content-Length: 688 Dear sirs , A coleague of mine who does spectroscopical research needs energies of EXCITED STATES for (biatomic) molecules, including ionic forms. Perhaps he'd need the results of EXTENSIVE Configuration Interaction (at least mono- and biexcitations) for biatomic fragments ( 1st row element) - Fluorine mainly for C-F, and for S-F. 1. Could you point us ANY references on this subject. 2. Which program are most suitable for such investigations ? Any suggestions/comments/advices would be strongly appreciated. Thank you in advance. Cordially , czernek@chemi.muni.cz From rao@ddix4.monsanto.com Wed Apr 12 10:44:15 1995 Received: from tin for rao@ddix4.monsanto.com by www.ccl.net (8.6.10/930601.1506) id KAA07005; Wed, 12 Apr 1995 10:32:42 -0400 Received: from ddix4.monsanto.com by tin (5.65/Monsanto1.7) id AA25863; Wed, 12 Apr 1995 09:32:11 -0500 Received: by ddix4.monsanto.com id AA23545; 931110.SGI/CRI-%I%; Wed, 12 Apr 95 09:32:07 -0500 From: "Shashi Rao" Message-Id: <9504120932.ZM23542@ddix4.monsanto.com> Date: Wed, 12 Apr 1995 09:32:06 -0500 X-Mailer: Z-Mail (3.1.0 22feb94 MediaMail) To: CHEMISTRY@ccl.net Subject: CCCC seminar 4/13/95 Cc: rao@ddix4.monsanto.com Content-Type: text/plain; charset=us-ascii Mime-Version: 1.0 April 12, 1995 This is a reminder on the CCCC seminar by Dr. Joe Golab to be held at Amoco Research center tomorrow (4/13/95). Please inform either me (rao@ddix4.monsanto.com) or Dr. Joe Golab (jtgolab@amoco.com) if you will be attending so that a reasonably right amount of pizza can be obtained. Upon reaching the Amoco Research Center, please identify yourself as coming to the "CCCC meeting in Building 602" to the security officials. Please contact Dr. Joe Golab ((708) 961-7878) for further details. Shashi Rao ================================================================ The Chicago Computational Chemistry Club Presents Dr. J. T. Golab Amoco Research Center "What is Chemistry Modeling?: An Industrial Perspective" Thursday, the 13th April, 1995 at 7:30 p.m. (Pizza at 6:30 p.m.). Venue : Amoco Research Center, Building 602, Room 1218, Naperville. Abstract: ======== Modeling by computational methods can be a general purpose, less expensive alternative to the traditional experimental methods of problem solving. Advances in software and hardware technologies have made the use of computational chemistry techniques practical for industrial applications. As a result, chemistry modeling is slowly becoming more mainstream in industrial R&D, although it is still considered a relatively unproven information source. In this talk, we will discuss the foundations of chemistry modeling in regards the kinds of industrial problems it can help solve. We will also discuss several current examples; in particular a recent computational survey of methane to methanol catalysis based on compounds containing third row transition metals. Finally, the promise of chemistry modeling as a modern business tool will be addressed. Directions : =========== To get to Amoco Research Center: From West or East bound I-88 take the Naperville Road exit and turn left (North) onto Naperville Road. The first street light is Warrenville Road; turn left (West) onto Warrenville. Proceed approximately 1.5 miles to Herrick Road; turn left (South) into the Amoco Research Center. From tripos!metis!matt@uunet.uu.net Wed Apr 12 10:59:16 1995 Received: from relay3.UU.NET for tripos!metis!matt@uunet.uu.net by www.ccl.net (8.6.10/930601.1506) id KAA07540; Wed, 12 Apr 1995 10:52:58 -0400 Received: from uucp5.UU.NET by relay3.UU.NET with SMTP id QQyldr00936; Wed, 12 Apr 1995 10:52:57 -0400 Received: from tripos.UUCP by uucp5.UU.NET with UUCP/RMAIL ; Wed, 12 Apr 1995 10:52:57 -0400 Received: from metis.UUCP by tripos (4.1/SMI-4.0) id AA19590; Wed, 12 Apr 95 09:18:21 CDT Received: by metis.UUCP (4.0/4.7) id AA20636; Wed, 12 Apr 95 09:18:14 CDT Message-Id: <9504121418.AA20636@metis.UUCP> To: uunet!ccl.net!chemistry@uunet.uu.net, uunet!umdd.und.edu!biotech@uunet.uu.net, unet!iubvm.ucs.indiana.edu!cheminf-l@uunet.uu.net, uunet!quant.chem.rpi.edu!sybyl@uunet.uu.net Subject: Mass Screening Seminars in California Date: Wed, 12 Apr 95 09:18:14 CDT From: Matthew Clark ------------ Seminars on High Throughput Screening ---------- There are two seminars on mass screening libraries and using computer analysis to optmize mass screening libraries in California next week. The seminars run from 9:00a to 1:00p and cover using computational tools to optimize and analyze mass screening libraries, and the BioSTAR mass screening database management system. The seminars feature speakers from ONYX Pharmaceuticals on the BioSTAR system. Lunch will be served. The seminars will be held at: April 18 at the Valerie Timken Ampitheatre at Scripps Institute in La Jolla, CA April 19 at the Zymogenetics Auditorium, Seattle, WA Call Marthellen Cain at 800 323 2960 email at mcain@tripos.com, or fax her at 314 647 9241 for directions and more information. See you there! From mikes@bioch.ox.ac.uk Wed Apr 12 11:14:21 1995 Received: from oxmail.ox.ac.uk for mikes@bioch.ox.ac.uk by www.ccl.net (8.6.10/930601.1506) id LAA07709; Wed, 12 Apr 1995 11:01:13 -0400 From: Received: from opal.bioch.ox.ac.uk by oxmail.ox.ac.uk with SMTP (PP) id <17926-0@oxmail.ox.ac.uk>; Wed, 12 Apr 1995 15:59:37 +0100 Received: from ocms.ox.ac.uk (nmrpcd.ocms) by bioch.ox.ac.uk (5.x/SMI-SVR4) id AA18434; Wed, 12 Apr 1995 16:00:27 +0100 Received: by ocms.ox.ac.uk (940816.SGI.8.6.9/bioch3.0) id QAA07895; Wed, 12 Apr 1995 16:00:26 +0100 Date: Wed, 12 Apr 1995 16:00:26 +0100 Message-Id: <199504121500.QAA07895@nmrpcd.ocms.ocms.ox.ac.uk> To: chemistry@ccl.net Subject: Re: CCL:PROCHECK located X-Mailer: [XMailTool v3.1.0] Or, to be up-to-date, check out the PROCHECK home page: http://bsmcha1.biochem.ucl.ac.uk:80/~roman/procheck/procheck.html# Mike --------------------------------------------------------------------- Michael Smith, | Phone: +44 1865 275981/275720 Department of Biochemistry, | e-mail: mikes@bioch.ox.ac.uk Oxford University. | URL: http://nmra.ocms.ox.ac.uk/~mikes/ From feaster@tessa.iaf.uiowa.edu Wed Apr 12 11:44:10 1995 Received: from ns-mx.uiowa.edu for feaster@tessa.iaf.uiowa.edu by www.ccl.net (8.6.10/930601.1506) id LAA08425; Wed, 12 Apr 1995 11:32:10 -0400 Received: from tessa.iaf.uiowa.edu by ns-mx.uiowa.edu (8.6.10/19950309.1) on Wed, 12 Apr 1995 10:31:36 -0500 id KAA47680 with ESMTP Received: by tessa.iaf.uiowa.edu (950215.405.SGI.8.6.10/891024) on Wed, 12 Apr 1995 10:29:37 -0500 id KAA01280 Date: Wed, 12 Apr 1995 10:22:24 -0500 (CDT) From: shawn feaster Subject: Re: CCL:PDB files, residue solvent exposure To: heelisp@delta.newi.ac.uk cc: CHEMISTRY@ccl.net In-Reply-To: <95041110445687@delta.newi.ac.uk> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi Pual, Would you please forward replies to me. I think that in the new version of Sybyl you may be able to calculate the exposure of a residue, but as far as I know the second part of your question is still up is the "air". I hope that this has been helpful. If you need the e-mail address for Tripos, let me know and I'll dig it out for you. Cheers, Shawn Feaster feaster@tessa.iaf.uiowa.edu On Tue, 11 Apr 1995 heelisp@delta.newi.ac.uk wrote: > Dear CCL chemists, > Does anyone know of a program that can analyse a Brookhaven PDB file and > determine the degree of exposure of a particular residue to the surrounding > solvent and/or measure the effective dielectric constant of its environment. > > I will summarise for the net if I receive useful replies. > > Paul Heelis > Heelisp@newi.ac.uk > > North East Wales Institute > UK From brian@bert.chem.wsu.edu Wed Apr 12 11:59:11 1995 Received: from cheetah.it.wsu.edu for brian@bert.chem.wsu.edu by www.ccl.net (8.6.10/930601.1506) id LAA08834; Wed, 12 Apr 1995 11:54:03 -0400 Received: from bert.chem.wsu.edu (bert.chem.wsu.edu [134.121.43.22]) by cheetah.it.wsu.edu (8.6.10/WSUit-1.1) with SMTP id IAA24093; Wed, 12 Apr 1995 08:54:03 -0700 Received: by bert.chem.wsu.edu (AIX 3.2/UCB 5.64/4.03) id AA15761; Wed, 12 Apr 1995 08:54:10 -0700 From: brian@bert.chem.wsu.edu (Brian W. Beck) Message-Id: <9504121554.AA15761@bert.chem.wsu.edu> Subject: Re: CCL:Searching for sequences To: nauss@ucmod2.che.uc.EDU Date: Wed, 12 Apr 1995 08:54:09 -0800 (PDT) Cc: CHEMISTRY@ccl.net In-Reply-To: <9504121351.AA22866@ucmod2.che.uc.edu> from "Jeffrey L. Nauss" at Apr 12, 95 09:51:23 am X-Mailer: ELM [version 2.4 PL13] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Length: 1666 Jeffrey L. Nauss wrote: : : : I want to search the PDB for structures that have the tripeptide : sequence Asn-X-Glu where X is any amino acid. The purpose of the : search is to identify possible structural motifs for the sequence : within proteins. Thus far, I have not found how to do this using the : Brookhaven search engines on the WWW. Does any one have a way to : perform this search? : : Alternatively, I could search sequence databases such as SWISS-Prot : and then cross-reference the hits with the PDB. However, I have yet : to find a way to perform the search using wildcards. : : Any suggestions? : : Thanks in advance... : Jeff Nauss : There is a sequence database version of the PDB structural database called "NRL_3D". I know that the GCG suite of sequence analysis programs includes it, but I imagine it's probably available from other sources as well. I have no idea whether it's commercial or public. Your best bet would be to find someone who has GCG or Intelligenetics and collaborate. -Brian -- ============================================================================= | .---------.| Brian W. Beck | E-mail Addresses: | |/\ | ||--------------------| brian@bert.chem.wsu.edu | || \\ WSU || Biochem/Biophysics | brian_beck@wsu.edu | |\ - *|| WSU , 261 Fulmer | URL http://elmo.chem.wsu.edu/~brian | | | || Pullman, WA | VOICE (509) 335-4083 | | \___________|| 99164-4660 | FAX (509) 335-9688 | ============================================================================= From feaster@tessa.iaf.uiowa.edu Wed Apr 12 12:44:11 1995 Received: from ns-mx.uiowa.edu for feaster@tessa.iaf.uiowa.edu by www.ccl.net (8.6.10/930601.1506) id MAA09574; Wed, 12 Apr 1995 12:36:46 -0400 Received: from tessa.iaf.uiowa.edu by ns-mx.uiowa.edu (8.6.10/19950309.1) on Wed, 12 Apr 1995 11:36:08 -0500 id LAA68670 with ESMTP Received: by tessa.iaf.uiowa.edu (950215.405.SGI.8.6.10/891024) on Wed, 12 Apr 1995 11:34:09 -0500 id LAA01641 Date: Wed, 12 Apr 1995 10:38:12 -0500 (CDT) From: shawn feaster Subject: Re: CCL:Sftware for Review To: "Stephen R. Heller" cc: jcicshelp , chemistry@ccl.net, chminf-l@iubvm.ucs.indiana.edu, orgchem@extreme.chem.rpi.edu In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi Steve, I would enjoy reviewing the software listed below. I am currently a fifth year graduate student in organic chemistry at the University of Iowa. My specialy is in the realm of biophysical/physical organic chemistry, and my group focuses on transition state analog inhibition of proteins. My work to this point has mainly focused on QSAR studies, molecular modeling protein-lingand interactions using Sybyl, Charmm, and Insight, and protein mechanism elucidation and evaluation. Also, I am the University of Iowa's "in house" molecular modeling consultant. I am familiar with the older version of ChemWindows and would like to evaluate the new version in order to determine if they have removed its limitations as well as to determine if the output is suitable for CAS structure searches. > 1. ChemWindow, Version 3.1 from SoftShell. This is a structure > drawing program which runs under Windows. > I am not familiar with the Lab Glassware collection, but I assume that it deals with drawing glassware setup. If this is true, I would be very interested in evaluating how well it works since I am in the habit of keeping my research notebook electronically. My greatest limitation so far in keeping the notebook electronically has been in the quaility of the diagrams that I have been able to incorperate. I have tried Harvard graphics, Correl draw, and Aldus freehand, but they are very time consuming to draw glassware setup, and I am not the world's greatest freehand artist. > 2. Lab Glassware collection, Version 1.0 from SoftShell. This > requires ChemWindow 3.1 or later. > Finally, as I mensioned earlier, my research group focuses on QSAR and mechanism elucidation and evaluation. Specifically, we have recently been calculating logP values by hand as well as by using the QSAR utility within Sybyl. It would be interesting to determine how all of the methods compare with each other. I currently have Excel 4.0. In my opinion, if the software can run in Excel then it is much more useful to the average user strickly based on cost. > 3. SciLogP from SciVision. One needs either HyperChem 3.0 or 4.0 > and Excel 4.0 or 5.0 to run this program. The program calculates > logP values. The reviewer will have to contact SciVision to get > the unlocking code for the program. If I can be of help, please contact me at the followin address. Shawn Feaster University of Iowa Department of Chemistry Iowa City, Iowa 52242 phone: (319)335-1335 or (319)335-7900 e-mail: feaster@tessa.iaf.uiowa.edu I think that I will be able to use the software quite a bit in the next few months since I plan to begin writing my thesis soon. Thanks, Shawn Feaster From ponder@comet.wustl.edu Wed Apr 12 12:59:17 1995 Received: from comet.wustl.edu for ponder@comet.wustl.edu by www.ccl.net (8.6.10/930601.1506) id MAA09798; Wed, 12 Apr 1995 12:48:17 -0400 From: Received: from localhost by comet.wustl.edu; (5.65/1.1.8.2/29Aug94-0516PM) id AA02025; Wed, 12 Apr 1995 11:50:59 -0500 Message-Id: <9504121650.AA02025@comet.wustl.edu> To: chemistry@ccl.net Subject: Searching the PDB for general Sequences, etc. Date: Wed, 12 Apr 95 11:50:59 -0500 X-Mts: smtp > Jeff Nauss writes: > > I want to search the PDB for structures that have the tripeptide > sequence Asn-X-Glu where X is any amino acid. The purpose of the > search is to identify possible structural motifs for the sequence > within proteins. Thus far, I have not found how to do this using the > Brookhaven search engines on the WWW. Does any one have a way to > perform this search? > > Alternatively, I could search sequence databases such as SWISS-Prot > and then cross-reference the hits with the PDB. However, I have yet > to find a way to perform the search using wildcards. > > Any suggestions? Check out the SLEUTH software written in my group. It was designed to do just that sort of thing. It lets you search a database compiled from the current PDB structures for generalized sequence, phi-psi-chi angle ranges, solvent accessibility, secondary structure type, ranges of interresidue distances, etc. Get the package via anon.ftp or WWW from dasher.wustl.edu (128.252.162.151). Jay Ponder Asst. Prof., Biochemistry Washington Univ. Med. School, St. Louis email: ponder@comet.wustl.edu From Don_Gregory@msi.com Wed Apr 12 13:44:16 1995 Received: from msi.com for Don_Gregory@msi.com by www.ccl.net (8.6.10/930601.1506) id NAA10772; Wed, 12 Apr 1995 13:39:10 -0400 Received: from qmail-gw.msi.com by msi.com (4.1/SMI-4.1) id AA20608; Wed, 12 Apr 95 13:36:19 EDT Message-Id: <9504121736.AA20608@msi.com> Date: 12 Apr 1995 13:35:12 +0000 From: "Don Gregory" Subject: Re: CCL-Searching for sequen To: "Comp. Chem. Listserver" Reply to: RE>CCL:Searching for sequences On 4/12; Jeff Nauss wrote: ================= "I want to search the PDB for structures that have the tripeptide sequence Asn-X-Glu where X is any amino acid. The purpose of the search is to identify possible structural motifs for the sequence within proteins. Thus far, I have not found how to do this using the Brookhaven search engines on the WWW. Does any one have a way to perform this search? Alternatively, I could search sequence databases such as SWISS-Prot and then cross-reference the hits with the PDB. However, I have yet to find a way to perform the search using wildcards. Any suggestions? Thanks in advance... Jeff Nauss" ================== Jeff, This is a capability that Quanta has had for quite some time in it's Protein Design toolset. In addition, one can request that the peptide also have a specified secondary structure type, and/or specific phi,psi angles. I did a quick search on a small subset database of the pdb that we use for demos (only 40 proteins recommended for using as a homology construction reference set), and I got the following results, superimposed around the backbone of the "x" residue: (Note, I only list the central residue, as they are all asn-x-glu) Protein res. no. middle res. 3app 13 asp 1f19 L:77 leu 1f19 L:164 thr 5cha A:18 gly (note that the 5cha has a B chain of the same sequence) This can also be done on the whole of the pdb, which we have as well, but I only searched our demo subset. Hope this helps a bit. Don Gregory Mgr. Life Science Applications MSI From arne@hodgkin.mbi.ucla.edu Wed Apr 12 13:59:11 1995 Received: from hodgkin.mbi.ucla.edu for arne@hodgkin.mbi.ucla.edu by www.ccl.net (8.6.10/930601.1506) id NAA10967; Wed, 12 Apr 1995 13:50:25 -0400 Received: by hodgkin.mbi.ucla.edu; id AA03243; Wed, 12 Apr 1995 10:56:46 -0700 Message-Id: <9504121756.AA03243@hodgkin.mbi.ucla.edu> To: heelisp@delta.newi.ac.uk Cc: chemistry@ccl.net Subject: Re: CCL:PDB files, residue solvent exposure Reply-To: arne@hodgkin.mbi.ucla.edu In-Reply-To: Your message of "Tue, 11 Apr 1995 10:44:57 +0100" References: <95041110445687@delta.newi.ac.uk> X-Mailer: Mew beta version 0.89 on Emacs 19.28.0.1 Mime-Version: 1.0 Content-Type: Text/Plain; charset=us-ascii Date: Wed, 12 Apr 95 10:56:46 -0700 From: "Arne Eofsson (arne@uclaue.mbi.ucal.edu)" X-Mts: smtp I guess you have received somethng usefull by now. All (?) the major Molecular mechanics packages does this. I use the algorithm by Legrand & Merz (JCC 1993) and could probably make you a quick hack if you do not find anything else. (at the moment the routines are incorporated in a way too big program). Unfortunately it is in fortran, so you'd need a fortran compiler. arne From marcus@acsu.buffalo.edu Wed Apr 12 15:15:32 1995 Received: from destrier.acsu.buffalo.edu for marcus@acsu.buffalo.edu by www.ccl.net (8.6.10/930601.1506) id PAA11908; Wed, 12 Apr 1995 15:00:36 -0400 Received: (marcus@localhost) by destrier.acsu.buffalo.edu (8.6.10/8.6.4) id PAA21269; Wed, 12 Apr 1995 15:00:35 -0400 From: Emil Marcus Message-Id: <199504121900.PAA21269@destrier.acsu.buffalo.edu> Subject: CCL:PROCHECK located WWW_page... To: chemistry@ccl.net Date: Wed, 12 Apr 1995 15:00:34 -0400 (EDT) Cc: ramon@ce.ifisicam.unam.mx Inst: Roswell Park Cancer Institute - BPH X-Mailer: ELM [version 2.4 PL22] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Length: 1446 && From chemistry-request@ccl.net Wed Apr 12 13:15 EDT 1995 && From: Ramon Garduno && Subject: CCL:PROCHECK located && To: chemistry@ccl.net (POST MSG's) && Date: Wed, 12 Apr 95 7:46:17 CDT && Sender: Computational Chemistry List && && Dear netters: && && To those of you who responded to my inquire about PROCHECK, I am && very grateful for sharing your information. Also, for those on the && CCL interested in the same program, it can be found in the anonymous && ftp site pdb.pdb.bnl.gov (C.S. Raman provided the location). && ... && Dr. Ramon Garduno-Juarez && Research Professor in Biophysics && ... && INSTITUTO DE FISICA | EMAIL: ramon@ce.ifisicam.unam.mx && UNIVERSIDAD NAL. AUTONOMA DE MEXICO | rgard@redvax1.dgsca.unam.mx && Laboratorio de Cuernavaca | VOICE: (73)175388 && Apdo. Postal 139-B | (73)111611 && 62191 Cuernavaca, Morelos | FAX: (73)111603 && MEXICO | (73)173077 && ________________________________ EOF _____________________________________ WWW Page: Procheck 3.2 Roman Laskovski et al. http://bsmchal.biochem.ucl.ac.uk/~roman/procheck/procheck.html Source code available by anon_ftp from: 128.40.46.11 . ("pdb.pdb.bnl.gov" is 130.199.144.1). Emil -- Emil Marcus RPCI / SUNYAB marcus@acsu.buffalo.edu From rameshg@phar.umich.edu Wed Apr 12 15:29:14 1995 Received: from iris.phar.umich.edu for rameshg@phar.umich.edu by www.ccl.net (8.6.10/930601.1506) id PAA12351; Wed, 12 Apr 1995 15:27:24 -0400 Received: from iris.phar.umich.edu (iris.phar.umich.edu [35.211.128.3]) by iris.phar.umich.edu (8.6.10/8.6.10) with SMTP id PAA19050; Wed, 12 Apr 1995 15:26:31 -0400 Date: Wed, 12 Apr 1995 15:26:30 -0400 (EDT) From: Ramesh Gopalaswamy To: chemistry cc: c2-l@msi.com Subject: mm2-params Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi folks Could anyone give refs for mm2-parameter updates after 1985? I have been using mm2-85 force field as provided with Cerius2. For some of my molecules I get a warning about undefined torsional params. I'm attaching that message at the end of this mail. My guess is the warning has to do with alpha,beta-unsatd carbonyl system in these molecules. So my question is, any ideas about publications in which these parameters are updated? If not, is it OK to ignore these "undefined params" ? How much would these torsional energies contribute to overall energy. The energies (atleast relative) are important to me as I need to save low energy conformers of these molecules. I really do not want to change force fields at this point :( as I have already made some progress with mm2-85 and plus as these are small organic molecules (steroids) mm2 is most appropriate, right? ****************************************************************************** The warning message from Cerius2 is as follows: Reading force field from: ./Cerius2-Resources/FORCE-FIELD/untested/mm2_85_1.01 Finished reading force field parameter file. WARNING: The following force field atom types have undefined torsions parameters. O_3_L C_3 C_2+ C_3 O_3_L C_3 C_2+ O_2+ Torsion terms are missing. Quitting energy expression setup. All terms with missing parameters may be ignored if the `ignore undefined terms` toggle is turned on. See `Open Force Field/Energy Expression/Setup.` Automatic setup for model ste8 failed ****************************************************************************** Please send your suggestions to me directly. Thanks in advance for your help. Ramesh From tripos!rigel!david@uunet.uu.net Wed Apr 12 15:45:32 1995 Received: from relay3.UU.NET for tripos!rigel!david@uunet.uu.net by www.ccl.net (8.6.10/930601.1506) id PAA12567; Wed, 12 Apr 1995 15:38:05 -0400 Received: from uucp5.UU.NET by relay3.UU.NET with SMTP id QQyled19319; Wed, 12 Apr 1995 13:59:33 -0400 Received: from tripos.UUCP by uucp5.UU.NET with UUCP/RMAIL ; Wed, 12 Apr 1995 13:59:33 -0400 Received: from rigel.tripos by tripos (4.1/SMI-4.0) id AA21691; Wed, 12 Apr 95 12:48:23 CDT Received: by rigel.tripos (940816.SGI.8.6.9/5.6) id MAA24669; Wed, 12 Apr 1995 12:49:03 -0500 Date: Wed, 12 Apr 1995 12:49:03 -0500 From: tripos!rigel!david@uunet.uu.net (David Mosenkis) Message-Id: <199504121749.MAA24669@rigel.tripos> To: uunet!ucmod2.che.uc.EDU!nauss@uunet.uu.net Subject: Re: Searching for sequences Cc: uunet!ccl.net!CHEMISTRY@uunet.uu.net Jeff, If you have access to Sybyl from Tripos, the "Search Protein Database" item on the Biopolymer menu supports the kind of query you specified (Asn-X-Glu), and provides convenient access to view and analyze the resulting 3D fragments and perform more complex searches. BTW, I did a quick search of that pattern on a non-redundant subset of 343 structures from the PDB, and got 227 hits. A quick followup search revealed that 38 of these 3-residue fragments are fully contained within alpha helices, and 14 are fully contained within beta strands. Let me know if you'd like more information. David Mosenkis (david@tripos.com) Tripos, Inc.