From chemistry-request@server.ccl.net Tue Oct 8 13:25:34 2002 Received: from cse.nd.edu (root@[129.74.25.101]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g98HPYJ20718 for ; Tue, 8 Oct 2002 13:25:34 -0400 Received: from dylan.cse.nd.edu (ako@dylan.cse.nd.edu [129.74.32.170]) by cse.nd.edu (8.11.2/8.11.2) with ESMTP id g98HPU907719 for ; Tue, 8 Oct 2002 12:25:31 -0500 (EST) Received: from localhost (ako@localhost) by dylan.cse.nd.edu (8.11.2/8.10.1) with ESMTP id g98HPSg08043 for ; Tue, 8 Oct 2002 12:25:28 -0500 (EST) Date: Tue, 8 Oct 2002 12:25:27 -0500 (EST) From: Alice NgarKit Ko To: chemistry@ccl.net Subject: calculate rmsd from two pdb files in CHARMM Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, I have two pdb files. I want to find the rmsd of 3 of the atoms. Can someone tell me how to do that? Thanks Alice From chemistry-request@server.ccl.net Mon Oct 7 20:43:28 2002 Received: from viper.abbott.com ([130.36.44.77]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g980hSa27786 for ; Mon, 7 Oct 2002 20:43:28 -0400 Received: from abtmr1.abbott.com (abtmr1.abbott.com [10.254.245.1]) by viper.abbott.com (Switch-2.1.4/Switch-2.1.0) with ESMTP id g980iJn23583 for ; Mon, 7 Oct 2002 19:44:20 -0500 (CDT) Received: from abtapn55.cmis.abbott.com (localhost [127.0.0.1]) by abtmr1.abbott.com (Switch-2.0.6/Switch-2.0.6) with ESMTP id g980hRr04715 for ; Mon, 7 Oct 2002 19:43:27 -0500 (CDT) Subject: CCL:small molecule conformational analysis using charmm To: chemistry@ccl.net Cc: james.metz@abbott.com X-Mailer: Lotus Notes Release 5.0.5 September 22, 2000 Message-ID: From: james.metz@abbott.com Date: Mon, 7 Oct 2002 19:42:44 -0500 X-MIMETrack: Serialize by Router on ABTAPN55/ESVR/ABBOTT(Release 5.0.5 |September 22, 2000) at 10/07/2002 07:39:30 PM MIME-Version: 1.0 Content-type: text/plain; charset=us-ascii CHARMM Users on the CCL, Does anyone have any charmm scripts for gas phase conformational analysis of small molecules that they would like to share ? Specifically, I am looking for: 1) Automatic detection of dihedral angles. I need a script which can be easily automated for processing hundreds of small molecules in background without using a GUI (e.g, QUANTA). 2) Elimination of duplicate structures (clustering) within a user-specified RMS dev. 3) Minimization, storage of energies, and calculation of relative energies 4) User specified number of structures allowed, and maximum energy window allowed. Thank you, Jim Metz James T. Metz, Ph.D. Research Investigator Chemist GPRD R46Y AP10-2 Abbott Laboratories 100 Abbott Park Road Abbott Park, IL 60064-6100 U.S.A. Office (847) 936 - 0441 FAX (847) 935 - 0548 james.metz@abbott.com From chemistry-request@server.ccl.net Mon Oct 7 17:58:55 2002 Received: from mail-01.med.umich.edu ([141.214.93.149]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g97Lwsa17174 for ; Mon, 7 Oct 2002 17:58:54 -0400 Received: from gwia-01-MTA by mail-01.med.umich.edu with Novell_GroupWise; Mon, 07 Oct 2002 17:58:53 -0400 Message-Id: X-Mailer: Novell GroupWise Internet Agent 6.0.2 Date: Mon, 07 Oct 2002 17:58:38 -0400 From: "Renxiao Wang" To: Subject: Release of X-CScore v1.0: New scoring function available Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Disposition: inline Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id g97Lwta17175 Dear All, We would like to announce the release of X-CScore v1.0, a program for estimating protein-ligand binding affinites. Basically, X-CScore is a consensus scoring scheme that consists of three individual empirical scoring functions. It makes fast prediction based purely on protein-ligand complex structures and thus will see its major application to molecular docking approaches. The X-CScore algorithm is described in details on J. Comp.-Aided Mol. Des. 2002, 16:11-26. This program is currently accessible at http://sw16.im.med.umich.edu/software/xtool/. After filling out a user license agreement, you will be able to download the whole X-CScore packet there, including the source codes, user manual, and other supplementary material. This program is written in ANSI C++ and has been tested on UNIX and LINUX platforms. There is NO CHARGE for obtaining this program, applied to all the users from both industry and academia. If you experience any problem in downloading or using this program, you may contact us directly. Happy scoring, Renxiao Wang, Ph.D. Research Investigator Department of Internal Medicine University of Michigan Medical School From chemistry-request@server.ccl.net Tue Oct 8 07:36:50 2002 Received: from evia.ccf.auth.gr ([155.207.1.3]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g98Bana12635 for ; Tue, 8 Oct 2002 07:36:49 -0400 Received: from katrin (chem011.chem.auth.gr [155.207.64.94]) by evia.ccf.auth.gr (8.12.4/8.12.4/8.12.4) with SMTP id g98Balgg003317 for ; Tue, 8 Oct 2002 14:36:48 +0300 (EET DST) Organization: Message-ID: <004901c26ebe$fe312370$5e40cf9b@katrin> From: "teber" To: Subject: GAPT charges Date: Tue, 8 Oct 2002 14:36:50 +0300 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0046_01C26ED8.235FD6F0" 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 X-Virus-Scanned: by mail.auth.gr, virus data file v4227 created Oct 02 2002 This is a multi-part message in MIME format. ------=_NextPart_000_0046_01C26ED8.235FD6F0 Content-Type: text/plain; charset="iso-8859-7" Content-Transfer-Encoding: quoted-printable I would like to calculate GAPT charges using G98W. Does anyone know how to print these values? =20 Thanks, Bill. ------=_NextPart_000_0046_01C26ED8.235FD6F0 Content-Type: text/html; charset="iso-8859-7" Content-Transfer-Encoding: quoted-printable
I would like to calculate GAPT charges = using=20 G98W.
Does anyone know how to print these=20 values?
 
Thanks,=20 Bill.

------=_NextPart_000_0046_01C26ED8.235FD6F0-- From chemistry-request@server.ccl.net Mon Oct 7 16:37:16 2002 Received: from quimera.imim.es (IDENT:root@[193.146.190.149]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g97KbFa15611 for ; Mon, 7 Oct 2002 16:37:15 -0400 Received: (from jvilla@localhost) by quimera.imim.es (8.9.3/8.9.3) id WAA06880; Mon, 7 Oct 2002 22:34:27 +0200 Date: Mon, 7 Oct 2002 22:34:27 +0200 From: Jordi Villa Message-Id: <200210072034.WAA06880@quimera.imim.es> To: chemistry@ccl.net, mbarbany@imim.es Subject: MIPSIM release ********************************************************************** * * * MIPSIM 2.1beta Release * * * ********************************************************************** October 2002 The Research Group in Biomedical Informatics (GRIB) is proud to announce the release of a new version of MIPSIM. MIPSIM is a computational system developed by the GRIB at the Institut Municipal d'Investigació Mèdica (IMIM) of Barcelona for the automatic exploration of biomolecular similarities on the basis of molecular interaction potentials. MIPSIM can be used as a standalone program for the automatic exploration of biomolecular similarities but it is specially powerful when interfacing to other well-known external programs: * The quantum package GAMESS. Current version of MIPSIM has been tested with June 2001 version of GAMESS. Other versions may be compatible with the scripts distributed with MIPSIM with very few changes. * A molecular interaction potential evaluator (GRID). Current supported version of MIPSIM interfaces with GRID19 (Linux version), or Grid 20 (IRIX VERSIONS). * statistical tools for the partial least squares (PLS) calculations needed for the derivation of 3D-QSAR models (GOLPE), and * visualization packages (GOPENMOL,INSIGTHII) The current is a beta version and may be not bug free. We encourage the users to help in the development of more robust and powerful versions by reporting bugs and suggesting improvements. The program can be accessed at the web address: http://www1.imim.es/modeling/mipsim/index.html For further information, please, refer to the above mentioned page or e-mail us at mipsim@imim.es. Reference: MIPSIM: Similarity analysis of Molecular Interaction Potentials Miquel de Cáceres, Jordi Villà, Juan J. Lozano and Ferran Sanz, Bioinformatics 2000, 16, 568-569 Jordi ------------------------------------------------------ Jordi Villà i Freixa Computational Structural Biology Laboratory Research Group on Biomedical Informatics (GRIB) - IMIM/UPF Passeig Marítim de la Barceloneta 37-49. Tel: +34 93 224 0886 E-08003 Barcelona (Spain) Fax: +34 93 224 0875 e-mail: jvilla@imim.es http://www1.imim.es/~jvilla From chemistry-request@server.ccl.net Mon Oct 7 16:21:21 2002 Received: from web13407.mail.yahoo.com ([216.136.175.65]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g97KLLa15426 for ; Mon, 7 Oct 2002 16:21:21 -0400 Message-ID: <20021007202120.15414.qmail@web13407.mail.yahoo.com> Received: from [67.17.165.2] by web13407.mail.yahoo.com via HTTP; Mon, 07 Oct 2002 13:21:20 PDT Date: Mon, 7 Oct 2002 13:21:20 -0700 (PDT) From: quch quch Subject: Re: CCL:dna molecular building To: Michael Banck , chemistry@ccl.net In-Reply-To: <20021007112318.GA11157@stud.ch.tum.de> MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii you may try NAB from case's group. very easy to use. good luck. Jianxin --- Michael Banck wrote: > Hi, > > > I would like to know if there is any dna molecular > building free > > program that, providing the nucleotide sequence, > it outputs > > a first approximation to dna molecular moldel, in > PDB format, > > if possible. > > have a look at > http://rutchem.rutgers.edu/~xiangjun/software.html > or > http://rutchem.rutgers.edu/~xiangjun/3DNA/index.html > > hope that helps, > > Michael > > -= This is automatically added to each message by > mailing script =- > CHEMISTRY@ccl.net -- To Everybody | > CHEMISTRY-REQUEST@ccl.net -- To Admins > Ftp: ftp.ccl.net | WWW: > http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > __________________________________________________ Do you Yahoo!? Faith Hill - Exclusive Performances, Videos & More http://faith.yahoo.com From chemistry-request@server.ccl.net Mon Oct 7 12:38:56 2002 Received: from pacific-carrier-annex.mit.edu ([18.7.21.83]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g97Gcuu10329 for ; Mon, 7 Oct 2002 12:38:56 -0400 Received: from central-city-carrier-station.mit.edu (CENTRAL-CITY-CARRIER-STATION.MIT.EDU [18.7.7.72]) by pacific-carrier-annex.mit.edu (8.9.2/8.9.2) with ESMTP id MAA09528 for ; Mon, 7 Oct 2002 12:38:55 -0400 (EDT) Received: from melbourne-city-street.mit.edu (MELBOURNE-CITY-STREET.MIT.EDU [18.7.21.86]) by central-city-carrier-station.mit.edu (8.9.2/8.9.2) with ESMTP id MAA13521 for ; Mon, 7 Oct 2002 12:38:55 -0400 (EDT) Received: from jwolfskill.mit.edu (ERRATA.MIT.EDU [18.36.0.129]) by melbourne-city-street.mit.edu (8.9.2/8.9.2) with ESMTP id MAA06435 for ; Mon, 7 Oct 2002 12:38:54 -0400 (EDT) Message-Id: <5.0.2.1.2.20021007123659.00aa9f48@po14.mit.edu> X-Sender: dgw@po14.mit.edu (Unverified) X-Mailer: QUALCOMM Windows Eudora Version 5.0.2 Date: Mon, 07 Oct 2002 12:42:45 -0400 To: chemistry@server.ccl.net From: David Weininger Subject: New book on Microarrays available Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed This is a new book on the use of DNA Microarrays in the field of genomics by leaders in the field that I thought might interest some readers of this list. I've included a link where more information can be found. Thanks! Microarrays for an Integrative Genomics Isaac S. Kohane, Alvin Kho, and Atul J. Butte ISBN 0-262-11271-X Publisher: MIT Press 2002 http://mitpress.mit.edu/026211271X This book provides a systematic introduction to the use of DNA microarrays as an investigative tool for functional genomics. The presentation is appropriate for readers from biology or bioinformatics. After presenting a framework for the design of microarray-driven functional genomics experiments, the book discusses the foundations for analyzing microarray data sets, genomic data-mining, the creation of standardized nomenclature and data models, clinical applications of functional genomics research, and the future of functional genomics. Isaac S. Kohane is Director of the Children's Hospital Informatics Program, Associate Professor of Pediatrics at Harvard Medical School, and an Attending Physician in Endocrinology. Alvin Kho is Research Fellow in Medicine. Atul J. Butte is a Staff Informatician in the Children's Hospital Informatics Program, an Instructor in Pediatrics at Harvard Medical School, and an Attending Physician in Endocrinology. All are at Children's Hospital, Boston. David Weininger Associate Publicist MIT Press 5 Cambridge Center, 4th Floor Cambridge, MA 02142 617.253.2079 617.253.1709 fax dgw@mit.edu From chemistry-request@server.ccl.net Tue Oct 8 14:03:33 2002 Received: from gandalf.cber.nih.gov ([128.231.52.5]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g98I3WJ22384 for ; Tue, 8 Oct 2002 14:03:32 -0400 Received: from localhost (rvenable@localhost) by gandalf.cber.nih.gov (980427.SGI.8.8.8/980728.SGI.AUTOCF) via ESMTP id NAA30808; Tue, 8 Oct 2002 13:50:51 -0400 (EDT) Date: Tue, 8 Oct 2002 13:50:50 -0400 From: Rick Venable To: Alice NgarKit Ko cc: chemistry@ccl.net Subject: Re: CCL:calculate rmsd from two pdb files in CHARMM In-Reply-To: Message-ID: ReplyTo: Rick_Venable@nih.gov MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Tue, 8 Oct 2002, Alice NgarKit Ko wrote: > I have two pdb files. I want to find the rmsd of 3 of the atoms. > Can someone tell me how to do that? Thanks The short answer is to put the 2nd set of coords in the COMP coord set, and then use the COOR ORIENT RMS command with the appropriate atom selection for the 3 atoms. If the PDB files are for the same protein and can be read independently via the same PSF, the above is about all that's needed; just use the COMP keyword when reading the 2nd file. For non-identical proteins, the procedure is a bit more complicated. You must create a PSF which encompasses both proteins, and read both sets of coords into the MAIN (default) coord set. Then use COOR COPY COMP to put all coords in the comparison coord set as well. Finally, use COOR DUPL to copy selected atomic coords from one protein to another within the COMP set. Then you can again use COOR ORIENT RMS to compute RMSD for the selected atoms. =+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+= Rick Venable 29/500 FDA/CBER/OVRR Biophysics Lab 1401 Rockville Pike HFM-419 Rockville, MD 20852-1448 U.S.A. (301) 496-1905 Rick_Venable@nih.gov ALT email: rvenable@speakeasy.org =+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+= From chemistry-request@server.ccl.net Tue Oct 8 15:21:34 2002 Received: from ns0.scripps.edu ([192.42.82.58]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g98JLYJ24850 for ; Tue, 8 Oct 2002 15:21:34 -0400 Received: from antigen.scripps.edu (antigen.scripps.edu [137.131.200.100]) by ns0.scripps.edu (8.11.6/TSRI-4.2rx) with SMTP id g98JLYP14412 for ; Tue, 8 Oct 2002 12:21:34 -0700 (PDT) Received: from relay1.scripps.edu(137.131.200.29) by antigen.scripps.edu via csmap id 18489; Tue, 08 Oct 2002 12:20:37 -0700 (PDT) Received: from renoir.scripps.edu (renoir.scripps.edu [137.131.252.25]) by relay1.scripps.edu (8.11.6/TSRI-4.2.1rAV) with ESMTP id g98JLIm08044; Tue, 8 Oct 2002 12:21:18 -0700 (PDT) Received: from localhost (crowley@localhost) by renoir.scripps.edu (8.9.2/TSRI-3.0.1) with ESMTP id MAA46897; Tue, 8 Oct 2002 12:21:18 -0700 (PDT) Date: Tue, 8 Oct 2002 12:21:18 -0700 From: Michael Crowley To: Rick Venable cc: Alice NgarKit Ko , chemistry@ccl.net Subject: Re: CCL:calculate rmsd from two pdb files in CHARMM In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Apologies to Alice, I missed the title that you were using charmm. I had suggested that the easiest way for 3 atoms was to do it by hand. However if you have charmm already set up for this system, then Rick's suggestion is definitely the easiest. Mike ----------------------------------------------------------------- Physical mail: Dr. Michael F. Crowley Department of Molecular Biology, TPC6 The Scripps Research Institute 10550 North Torrey Pines Road La Jolla, California 92037 Electronic mail: crowley@scripps.edu Telephone: 858/784-9290 Fax: 858/784-8688 ----------------------------------------------------------------- From chemistry-request@server.ccl.net Tue Oct 8 17:14:03 2002 Received: from srvr5.engin.umich.edu (root@[141.213.75.23]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g98LE2J27367 for ; Tue, 8 Oct 2002 17:14:03 -0400 Received: from TERMINATOR (dhcp-dow33.public.engin.umich.edu [141.212.143.183]) by srvr5.engin.umich.edu (8.12.5/8.12.5/caen srvr5) with ESMTP id g98LE1uc003639 for ; Tue, 8 Oct 2002 17:14:02 -0400 (EDT) From: "Duc Nguyen" To: Subject: Transition state-imaginary frequency Date: Tue, 8 Oct 2002 17:13:45 -0400 Message-ID: <000d01c26f0f$970f9a90$b78fd48d@engin.umich.edu> MIME-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook, Build 10.0.4024 Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1106 Dear CCLers, I accidentally ran by your comments in CCL.net about the transition state should have one and only one imaginary frequency. Please suggest me some references to read more about the matter as why it is true and how to eliminate the other imaginary frequencies. I would greatly appreciate your help. Regards, Duc From chemistry-request@server.ccl.net Tue Oct 8 19:15:14 2002 Received: from pink.rahul.net (IDENT:5KWKT0AZUi+4MNq8DBK4M91rjVL8+cGV@[66.237.72.7]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g98NFEJ32642 for ; Tue, 8 Oct 2002 19:15:14 -0400 Received: from yellow.rahul.net (yellow.rahul.net [192.160.13.18]) by pink.rahul.net (Postfix) with ESMTP id 656D72FE75 for ; Tue, 8 Oct 2002 16:15:14 -0700 (PDT) Received: by yellow.rahul.net (Postfix, from userid 1448) id 0AF7F7C26; Tue, 8 Oct 2002 16:15:08 -0700 (PDT) From: "Peter C. McCluskey" To: chemistry ccl Subject: Re: CCL:dna molecular building In-Reply-To: <3DA16090.7010307@iqm.unicamp.br> References: <3DA16090.7010307@iqm.unicamp.br> X-Mailer: VM 7.05 under Emacs 19.34.1 Message-Id: <20021008231508.0AF7F7C26@yellow.rahul.net> Date: Tue, 8 Oct 2002 16:15:08 -0700 (PDT) If you're building a short sequence, B (http://www.scripps.edu/case/Biomer/index.html) is easy to learn. If you're building a long sequence, Namot (http://namot.lanl.gov/) is more powerfull. -- ------------------------------------------------------------------------------ Peter McCluskey | Free Jon Johansen! http://www.rahul.net/pcm |