From chemistry-request@server.ccl.net Thu Jan 31 02:48:11 2002 Received: from dsa.mpi-muelheim.mpg.de ([192.108.70.121]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g0V7mBc09069 for ; Thu, 31 Jan 2002 02:48:11 -0500 Received: from pctri ([172.17.110.13]) by dsa.mpi-muelheim.mpg.de (8.11.3/8.11.3) with SMTP id g0V7m4Y433534 for ; Thu, 31 Jan 2002 08:48:04 +0100 (MET) Reply-To: From: "Rolf Trinoga" To: Subject: AW: g98 LINUX installation? Date: Thu, 31 Jan 2002 08:46:38 +0100 Message-ID: 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 IMO, Build 9.0.2416 (9.0.2911.0) In-Reply-To: <3.0.6.32.20020129134120.009b0e90@access.etsu.edu> X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 Importance: Normal We compiled G98 Rev A9 on a Linux Box (Red Hat 7.1) with the Portland compiler V3.2.4 without any problems. Until now we do not have noticed any errors using G98 on this LINUX systems. --- Rolf Trinoga Max-Planck-Institut fuer Strahlenchemie Stiftstr. 34-36 D-45470 Muelheim a.d. Ruhr Germany Tel.: +49(208)306-3558 trinoga@mpi-muelheim.mpg.de http://www.mpi-muelheim.mpg.de/mpistr-home.html From chemistry-request@server.ccl.net Thu Jan 31 03:34:39 2002 Received: from mailrelay.netcologne.de ([194.8.194.96]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g0V8Ycc09891 for ; Thu, 31 Jan 2002 03:34:38 -0500 Received: from cosmologic.de (dial-194-8-209-5.netcologne.de [194.8.209.5]) by mailrelay.netcologne.de (8.11.6/8.11.6) with ESMTP id g0V8YHu05673; Thu, 31 Jan 2002 09:34:17 +0100 (MET) Message-ID: <3C59020F.7E052EC1@cosmologic.de> Date: Thu, 31 Jan 2002 09:36:31 +0100 From: "Dr. Andreas Klamt" Organization: COSMOlogic GmbH&CoKG X-Mailer: Mozilla 4.7 [de] (Win98; I) X-Accept-Language: en,pdf MIME-Version: 1.0 To: Russ Johnson CC: Ali Rashid , CHEMISTRY@ccl.net Subject: Re: CCL:Calculated Electric Dipoles References: <5.0.0.25.2.20020130124445.00a83928@mailserver.nist.gov> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit I have two problems with the recommended NIST database: - the first is that it only allows to get data for single compounds, one after the other. In this way it is very complicated to get an overview over trends. - more severe is the fact that the data reported for the semi-empirical methods are just wrong: For example they report for nitromethane: semi-empirical AM1 1.641 PM3 1.568 The correct results are Nitromethane exp= 3.460 AM1= 4.170 PM3= 3.984 Most probably the authors just took the dipole moments resulting from the atomic charges and forgot to add the hybridazation dipole contributions. I hope that the dipole moments reported from the ab-initio and DFT methods are complete. Andreas Russ Johnson schrieb: > > Hello Ali, > > The NIST Computational Chemistry Comparison and Benchmark Database > has some data on electric dipoles, both experimental and from a variety of > ab initio methods. You can compare various methods there to get an idea of > how well the calculations agree with experiment. The website is: > > http://srdata.nist.gov/cccbdb > > Look at sections: > III.A.8 Calculated dipoles > IV.E.1 Compare electric dipoles > > >does anyone know of a book or a paper which discusses how well calculated > >dipoles are with respect to the experimental ones. > > > > Dr. Russell D. Johnson III > Research Chemist > National Institute of Standards and Technology > Computational Chemistry Group > 100 Bureau Drive, Stop 8380 > Gaithersburg, MD 20899-8380 > voice 301+975-2513 fax 301+869-4020 > email: russell.johnson@nist.gov > > -= 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 -- -------------------------------------------------------------------------------- Dr. Andreas Klamt COSMOlogic GmbH&CoKG Burscheider Str. 515 51381 Leverkusen, Germany Tel.: 49-2171-73168-1 Fax: ...-9 e-mail: andreas.klamt@cosmologic.de web: www.cosmologic.de -------------------------------------------------------------------------------- COSMOlogic Your Competent Partner for Computational Chemistry and Fluid Thermodynamics -------------------------------------------------------------------------------- From chemistry-request@server.ccl.net Thu Jan 31 07:20:15 2002 Received: from hermes.bmc.uu.se ([130.238.39.245]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g0VCKEc15362 for ; Thu, 31 Jan 2002 07:20:14 -0500 Received: from XRAY.bmc.uu.se ([130.238.37.10]) by hermes.bmc.uu.se (Post.Office MTA v3.5.3 release 223 ID# 0-62649U1500L1000S0V35) with ESMTP id se for ; Thu, 31 Jan 2002 13:19:56 +0100 Received: from werkman.bmc.uu.se (werkman.bmc.uu.se [130.238.37.169]) by XRAY.bmc.uu.se (8.11.6/8.8.7) with ESMTP id g0VCMYb22888 for ; Thu, 31 Jan 2002 13:22:34 +0100 Date: Thu, 31 Jan 2002 15:17:03 +0100 (CET) From: David van der Spoel X-X-Sender: To: Subject: xmol source Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, Is there anybody that knows where to get the latest (1.5) xmol source code? -- Groeten, David. ________________________________________________________________________ Dr. David van der Spoel, Biomedical center, Dept. of Biochemistry Husargatan 3, Box 576, 75123 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 spoel@xray.bmc.uu.se spoel@gromacs.org http://zorn.bmc.uu.se/~spoel ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From chemistry-request@server.ccl.net Wed Jan 30 16:30:42 2002 Received: from uhura.curagen.com ([12.40.255.155]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g0ULUgc19231 for ; Wed, 30 Jan 2002 16:30:42 -0500 Received: by uhura.curagen.com with Internet Mail Service (5.5.2653.19) id ; Wed, 30 Jan 2002 16:32:39 -0500 Message-ID: <715118539AC7D311A0DF009027DE6E190524AAD4@uhura.curagen.com> From: "Gusev, Vladimir" To: "'chemistry@ccl.net'" Subject: Peptides-in-Cell-Membranes Simulations Date: Wed, 30 Jan 2002 16:32:38 -0500 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01C1A9D5.A3E33830" 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_01C1A9D5.A3E33830 Content-Type: text/plain; charset="iso-8859-1" Hello, I would appreciate sending me any pointers to the resources regarding MD or MC simulations of the peptides confined in cell membranes, such as, for example, membrane-penetrating peptides. I will summarize to the list. Thank you. Vladimir LEGAL NOTICE - Unless expressly stated otherwise, this message is confidential and may be privileged. It is intended for the addressee(s) only. Access to this e-mail by anyone else is unauthorized. If you are not an addressee, any disclosure or copying of the contents or any action taken (or not taken) in reliance on it is unauthorized and may be unlawful. If you are not an addressee, please inform the sender immediately. ------_=_NextPart_001_01C1A9D5.A3E33830 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable RE: peptide sequince homology calculations
Hello,
 
    I would appreciate = sending me any=20 pointers to the resources regarding MD or MC simulations of the = peptides=20 confined in cell membranes, such as, for example, membrane-penetrating = peptides.=20 I will summarize to the list. Thank you.
 
Vladimir

= LEGAL NOTICE - Unless = expressly stated otherwise, this message is confidential and may be = privileged. It is intended for the addressee(s) only. Access to this = e-mail by anyone else is unauthorized. If you are not an addressee, any = disclosure or copying of the contents or any action taken (or not = taken) in reliance on it is unauthorized and may be unlawful. If you = are not an addressee, please inform the sender immediately.

------_=_NextPart_001_01C1A9D5.A3E33830-- From chemistry-request@server.ccl.net Thu Jan 31 07:56:01 2002 Received: from mailrelay.netcologne.de ([194.8.194.96]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g0VCu1c16463 for ; Thu, 31 Jan 2002 07:56:01 -0500 Received: from cosmologic.de (dial-213-168-64-238.netcologne.de [213.168.64.238]) by mailrelay.netcologne.de (8.11.6/8.11.6) with ESMTP id g0VCtqs18679 for ; Thu, 31 Jan 2002 13:55:52 +0100 (MET) Message-ID: <3C593F5F.2667A5B1@cosmologic.de> Date: Thu, 31 Jan 2002 13:58:07 +0100 From: "Dr. Andreas Klamt" Organization: COSMOlogic GmbH&CoKG X-Mailer: Mozilla 4.7 [de] (Win98; I) X-Accept-Language: en,pdf MIME-Version: 1.0 To: chemistry@ccl.net Subject: Re: CCL:Calculated Electric Dipoles References: <5.0.0.25.2.20020130124445.00a83928@mailserver.nist.gov> <3C59020F.7E052EC1@cosmologic.de> <000701c1aa3f$74829120$b25ad29b@qottfp3> Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit I was just pointed by two CCLers to the fact, that apparently the values reported on the NIST homepage for the semi-empirical methods are in a.u. while all others are in Debye. But the page says that all values are in Debye and they even built differences of the experimental value (in Debye) and the semi-empirical values, which are in a.u. Thus the resume keeps the same: Although I do not believe that the standard semi-empirical models ae extremely good for dipole moments, they are much better than they look on that page. Andreas Jesus Orduna schrieb: > > As I see from the values you report, those obtained from the database are in > atomic units (Bohr electron) while the values you give as exact are in > Debye. The former should be multiplied by a factor of c.a. 2.54 > > Regards > > ============================================ > Jesus Orduna > Instituto de Ciencia de Materiales de Aragon > Unidad de Nuevos Materiales Orgánicos > Facultad de Ciencias > CSIC-Universidad de Zaragoza > E-50009 Zaragoza (Spain) > Phone/FAX: +34 976 761194 > e-mail: jorduna@posta.unizar.es > ============================================= -- -------------------------------------------------------------------------------- Dr. Andreas Klamt COSMOlogic GmbH&CoKG Burscheider Str. 515 51381 Leverkusen, Germany Tel.: 49-2171-73168-1 Fax: ...-9 e-mail: andreas.klamt@cosmologic.de web: www.cosmologic.de -------------------------------------------------------------------------------- COSMOlogic Your Competent Partner for Computational Chemistry and Fluid Thermodynamics -------------------------------------------------------------------------------- From chemistry-request@server.ccl.net Thu Jan 31 09:05:36 2002 Received: from mercury.chem.nwu.edu (hutchisn@[129.105.116.2]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g0VE5ac18443 for ; Thu, 31 Jan 2002 09:05:36 -0500 Received: from localhost (hutchisn@localhost) by mercury.chem.nwu.edu (8.11.3/8.11.3) with ESMTP id g0VE5TH20086 for ; Thu, 31 Jan 2002 08:05:29 -0600 (CST) Date: Thu, 31 Jan 2002 08:05:29 -0600 (CST) From: Geoff Hutchison X-X-Sender: To: Subject: Announcement: Open Babel 1.99 (beta) Release Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Open Babel 1.99 ---------------- The Open Babel team is pleased to announce the release of Open Babel 1.99, a first beta release for the 2.0 version of the free, open-source replacement for the Babel chemistry file translation program. Open Babel is a project designed to pick up where Babel left off, as a cross-platform program and library designed to interconvert between many file formats used in molecular modeling and computational chemistry. At the moment, the beta release is not yet a drop-in replacement for babel as some file formats are not implemented and bond orders are not calculated for QM file formats. Open Babel includes two components, a command-line utility and a C++ library. The command-line utility is intended to be used as a replacement for the original babel program, to translate between various chemical file formats. The C++ library includes all of the file-translation code as well as a wide variety of utilities to foster development of other open source chemistry software. For more information, check the Open Babel website and FAQ: Website: FAQ: Release: From chemistry-request@server.ccl.net Thu Jan 31 09:26:54 2002 Received: from lipid.biocomp.unibo.it (postfix@[137.204.193.11]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g0VEQrc19299 for ; Thu, 31 Jan 2002 09:26:53 -0500 Received: by lipid.biocomp.unibo.it (Postfix, from userid 514) id E5A1627A7E; Thu, 31 Jan 2002 15:27:11 +0100 (CET) Received: from localhost (localhost [127.0.0.1]) by lipid.biocomp.unibo.it (Postfix) with ESMTP id D81CF2EAEB; Thu, 31 Jan 2002 15:27:11 +0100 (CET) Date: Thu, 31 Jan 2002 15:27:11 +0100 (CET) From: Ivan Rossi To: David van der Spoel Cc: chemistry@ccl.net Subject: Re: CCL:xmol source In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Thu, 31 Jan 2002, David van der Spoel wrote: > Hi, > > Is there anybody that knows where to get the latest (1.5) xmol source > code? xmol used to be closed source. i never remember its source code to be available. However there is an open source lookalike (clone)of xmol, calle xmakemol, which does a good job of replacing it. if you are using debian woody/sid just do an apt-get otherwise you can find it at http://vegemite.chem.nott.ac.uk/~xmakemol/index.html Hope it helps. Ivan -- Dr. Ivan Rossi - PNACoS Consulting & CIRB Biocomputing Unit PNACoS, Via della Grada 4/F, I-40122 Bologna, ITALY e-mail: ivan@biocomp.unibo.it Web: http://www.biocomp.unibo.it/ivan From chemistry-request@server.ccl.net Thu Jan 31 11:47:36 2002 Received: from mole.chem.iupui.edu ([134.68.136.192]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g0VGlac23044 for ; Thu, 31 Jan 2002 11:47:36 -0500 Received: from mole.chem.iupui.edu (mole.chem.iupui.edu [134.68.136.192]) by mole.chem.iupui.edu (8.9.1/8.9.1) with ESMTP id LAA87989 for ; Thu, 31 Jan 2002 11:47:26 -0500 (EST) Date: Thu, 31 Jan 2002 11:47:26 -0500 From: Daquan Gao To: CHEMISTRY@ccl.net Subject: autodock question Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi autodock users: Did anyone try to use autodock for a protein and a oligonucleotide? Because both are big, either can be the ligand. Here is the problem, I can't get autotors to work. It either takes forever and stop or does not work at all, because the size of the ligand. Did anyone try to bypass the many recurcive calls inside autotors and just to get the very basic looking result, the .pdbq file for the ligand? This problem seems to be too specific, I just hope some one has more experience with the code could help. TIA, daquan From chemistry-request@server.ccl.net Thu Jan 31 08:28:21 2002 Received: from hotmail.com ([207.68.163.124]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g0VDSKc17207 for ; Thu, 31 Jan 2002 08:28:21 -0500 Received: from mail pickup service by hotmail.com with Microsoft SMTPSVC; Thu, 31 Jan 2002 05:28:09 -0800 Received: from 193.146.42.30 by sea1fd.sea1.hotmail.msn.com with HTTP; Thu, 31 Jan 2002 13:28:09 GMT X-Originating-IP: [193.146.42.30] From: "Mus Musculus" To: chemistry@ccl.net Subject: Help with transition states Date: Thu, 31 Jan 2002 14:28:09 +0100 Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1; format=flowed Message-ID: X-OriginalArrivalTime: 31 Jan 2002 13:28:09.0787 (UTC) FILETIME=[1FF350B0:01C1AA5B] Hello! Excuse me if my question seems too basic for this forum, but I'm a newcomer in this field and I'm feeling quite lost. I'm trying to locate the transition state of a electrocyclic opening of a cyclopropane ring to yield an allyl cation. Is there a kind of established methodology to follow in this cases (a way of making an "educated guess" for the geometry of the TS)? Do you think the outcoming of the reaction being two ions requires a special treatment? I would gladly receive any piece of information about the location of transition states either in general or in electrocyclic reactions. Thank you in advance. Viv. _________________________________________________________________ Con MSN Hotmail súmese al servicio de correo electrónico más grande del mundo. http://www.hotmail.com/ES From chemistry-request@server.ccl.net Thu Jan 31 09:08:10 2002 Received: from mail2.zrz.tu-berlin.de ([130.149.4.14]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g0VE89c18551 for ; Thu, 31 Jan 2002 09:08:09 -0500 Received: from mailszrz.zrz.tu-berlin.de ([130.149.4.11]) by mail2.zrz.tu-berlin.de with esmtp (exim-3.34) id 16WHsb-0001ke-00; Thu, 31 Jan 2002 15:07:57 +0100 Received: from natrium.chem.tu-berlin.de ([130.149.169.143]) by mailszrz.zrz.tu-berlin.de with esmtp (exim-3.34) id 16WHsb-0006Ar-00; Thu, 31 Jan 2002 15:07:57 +0100 Mime-Version: 1.0 X-Sender: chwu0531@mailszrz.zrz.tu-berlin.de Message-Id: In-Reply-To: <200201302313.MAA06872@celeborn.otago.ac.nz> References: <200201302313.MAA06872@celeborn.otago.ac.nz> Date: Thu, 31 Jan 2002 15:07:55 +0100 To: timr@alkali.otago.ac.nz From: Christoph van =?iso-8859-1?Q?W=FCllen?= Subject: Re: CCL:Gaussian scratch disk limit Cc: chemistry@ccl.net Content-Type: text/plain; charset="iso-8859-1" ; format="flowed" Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id g0VE8Ac18553 >Hi Folks, >I was wondering whether there is (still?) an upper limit on total rwf >file size. AFAIK there was a max limit of 16GB for linux >architecture (8 files at 2GB each). In principle, everything can be in a single file (LINUX now supports it). The problem is rather that a FORTRAN double precision array has a limited size (16 GByte if the index runs from 1 to 2**31), so the only way around is to use 64-bit integers. This is the default for g98 on 64-bit workstations. If you are really so "keen" on larger files, try compiling g98 with 64-bit integers and the INTEL compiler -- be sure some hacking is required to do so. +---------------------------------+----------------------------------+ | Prof. Christoph van Wüllen | Tele-Phone (+49) (0)30 314 27870 | | Technische Universität Sekr. C3 | Tele-Fax (+49) (0)30 314 23727 | | Straße des 17. Juni 135 | eMail | | D-10623 Berlin, Germany | Christoph.vanWullen@TU-Berlin.De | +---------------------------------+----------------------------------+ -- From chemistry-request@server.ccl.net Thu Jan 31 09:22:37 2002 Received: from tigris.klte.hu ([193.6.138.33]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g0VEMac19150 for ; Thu, 31 Jan 2002 09:22:36 -0500 Received: from anti07 (193.6.133.59) by tigris.klte.hu (MX V5.1-A Vn6f) with SMTP for ; Thu, 31 Jan 2002 15:21:35 +0100 Message-ID: <000401c1aa63$3e2ceb60$3b8506c1@chem.klte.hu> From: "Tamas Gunda" To: References: Subject: Re: CCL:how to convert .rdf to .sdf file? Date: Thu, 31 Jan 2002 09:42:24 +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 Formally it can be done with ChemFinder: On inputting the rdf file a new database will be created, which can be exported as an sdf file. This sdf file will contain all molecules and textual data fields, but without the reactant/product separation. So it can be used in molecular databases, but not in reaction ones. Dr. Tamas E. Gunda Research Group for Antibiotics Hungarian Academy of Sciences University of Debrecen, POBox 36 H-4010 Debrecen, Hungary ----- Original Message ----- > >Could you kindly tell me how to convert .rdf to .sdf file. > >Is there any program to do such work? > > You can no more convert an .rdf file to an .sdf file than you can > convert a cube to a square. RD files contain data types that SD > files cannot. For more information, don't post to a mailing list -- > go directly to the source (gee, have I said that before?) -- which in > this case is http://www.mdli.com/downloads/ctfile/ctfile_subs.html > > If you've *got* to do that conversion and you don't care how much > data you lose, there are many programs that will do the conversion as > best as the file formats will permit. MDL's own ISIS/Base and our CS > ChemFinder come to mind. There are likely others, but it hardly > matters given the circumstances. > > > Jonathan Brecher > CambridgeSoft Corporation > jsb@cambridgesoft.com > -- > > > -= 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 Jan 31 10:30:08 2002 Received: from marcos.networkcs.com ([137.66.16.1]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g0VFU8c21366 for ; Thu, 31 Jan 2002 10:30:08 -0500 Received: from us.msp.networkcs.com (us.networkcs.com [137.66.12.15]) by marcos.networkcs.com (8.9.3/8.9.3) with ESMTP id JAA67871; Thu, 31 Jan 2002 09:28:41 -0600 (CST) (envelope-from rbw@networkcs.com) Received: (from rbw@localhost) by us.msp.networkcs.com (8.9.2/8.9.2) id JAA97098; Thu, 31 Jan 2002 09:28:41 -0600 (CST) (envelope-from rbw) Date: Thu, 31 Jan 2002 09:28:41 -0600 (CST) From: Richard Walsh Message-Id: <200201311528.JAA97098@us.msp.networkcs.com> To: ivan@biocomp.unibo.it, spoel@xray.bmc.uu.se Subject: Re: CCL:xmol source Cc: chemistry@ccl.net In-Reply-To: Ivan Rossi wrote: > On Thu, 31 Jan 2002, David van der Spoel wrote: > > > Hi, > > > > Is there anybody that knows where to get the latest (1.5) xmol source > > code? > > xmol used to be closed source. i never remember its source code to be available. > However there is an open source lookalike (clone)of xmol, calle xmakemol, which > does a good job of replacing it. if you are using debian woody/sid just do an > apt-get otherwise you can find it at > > http://vegemite.chem.nott.ac.uk/~xmakemol/index.html > > Hope it helps. > Ivan Xmol as an evolving tool is dead ... viewed/treated as a distractive software development event at a high-performance computing services company. The source spins endlessly on disks at its the thrice bought parent in Minneapolis. Current company name is netASPx. Praying for a second coming is not a good use of one's time ... However, I am aware of an effort nearing completion by one of the original developers to provide a similar easy to use, but very much extended tool. rbw #--------------------------------------------------- # # Richard Walsh # Project Manager, Cluster Computing, Computational # Chemistry and Finance # netASPx, Inc. # 1200 Washington Ave. So. # Minneapolis, MN 55415 # VOX: 612-337-3467 # FAX: 612-337-3400 # EMAIL: rbw@networkcs.com, richard.walsh@netaspx.com # #--------------------------------------------------- # "What you can do, or dream you can, begin it; # Boldness has genius, power, and magic in it." # -Goethe #--------------------------------------------------- # "Without mystery, there can be no authority." # -Charles DeGaulle #--------------------------------------------------- # "Why waste time learning when ignornace is # instantaneous?" -Thomas Hobbes #--------------------------------------------------- # "In the chaos of a river thrashing, all that water # still has to stand in line." -Dave Dobbyn #--------------------------------------------------- ~ From chemistry-request@server.ccl.net Thu Jan 31 11:17:15 2002 Received: from hotmail.com ([207.68.163.72]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g0VGHFc22477 for ; Thu, 31 Jan 2002 11:17:15 -0500 Received: from mail pickup service by hotmail.com with Microsoft SMTPSVC; Thu, 31 Jan 2002 08:17:03 -0800 Received: from 193.146.42.30 by sea1fd.sea1.hotmail.msn.com with HTTP; Thu, 31 Jan 2002 16:17:03 GMT X-Originating-IP: [193.146.42.30] From: "Mus Musculus" To: chemistry@ccl.net Subject: Re: peptide sequence homology calculations Date: Thu, 31 Jan 2002 17:17:03 +0100 Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1; format=flowed Message-ID: X-OriginalArrivalTime: 31 Jan 2002 16:17:03.0720 (UTC) FILETIME=[B83EC680:01C1AA72] Hello, Maybe this addresses can help you; http://www.up.univ-mrs.fr/~wabim/english/ftp.html http://www.pdg.cnb.uam.es/ but I think the "embl" and "expasy" servers should be enough (although I'm not an expert in the field): http://www.embl-heidelberg.de http://www.expasy.ch/ Viv >-----Original Message----- From: a3arzi >[mailto:Arturas.Ziemys@vaidila.vdu.lt] Sent: Wednesday, January 30, 2002 >7:42 AM To: John Wintersteen Cc: chemistry@ccl.net Subject: CCL:peptide >sequince homology calculations > > >Hi all, > >Could anyone shortly point me to www service or downloadable free software >for protein (peptide) sequence homology calculations and modeling ? > >Appreciate any help or advises Arturas S. > >P.S. sorry for the question a bit out of the main CCL topic ... _________________________________________________________________ MSN Photos es la manera más sencilla de compartir, editar e imprimir sus fotos favoritas. http://photos.latam.msn.com/Support/WorldWide.aspx From chemistry-request@server.ccl.net Thu Jan 31 15:24:52 2002 Received: from mxout1.cac.washington.edu ([140.142.32.5]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g0VKOqc28383 for ; Thu, 31 Jan 2002 15:24:52 -0500 Received: from mailhost2.u.washington.edu (mailhost2.u.washington.edu [140.142.33.2]) by mxout1.cac.washington.edu (8.12.1+UW01.12/8.12.1+UW02.01) with ESMTP id g0VKOjUC028660 for ; Thu, 31 Jan 2002 12:24:46 -0800 Received: from donald ([128.95.128.116]) by mailhost2.u.washington.edu (8.12.1+UW01.12/8.12.1+UW02.01) with SMTP id g0VKOjLl013387 for ; Thu, 31 Jan 2002 12:24:45 -0800 From: "Carsten Detering" To: Subject: PASS Date: Thu, 31 Jan 2002 21:13:06 +0100 Message-ID: MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook IMO, Build 9.0.2416 (9.0.2910.0) Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2615.200 Hi CCLers, does anyone of you know a possibility to predict binding sites on RNA or DNA structures? I tried to use PASS, but since this is written for proteins, it obviously does only work for proteins. Thanks for answers, Carsten ------------------------ Carsten Detering, Ph.D. University of Washington Seattle, WA 98195 email: detering@u.washington.edu From chemistry-request@server.ccl.net Thu Jan 31 12:33:35 2002 Received: from emvasteria.chiron.com ([165.140.4.50]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g0VHXZc24355 for ; Thu, 31 Jan 2002 12:33:35 -0500 Received: from 165.140.4.59 by emvasteria.chiron.com (InterScan E-Mail VirusWall NT); Thu, 31 Jan 2002 09:33:17 -0800 Received: by emvkali.chiron.com with Internet Mail Service (5.5.2653.19) id ; Thu, 31 Jan 2002 09:37:10 -0800 Message-ID: <938CCE0495C5D411AD9B0001027598DE03427837@emvshiva.chiron.com> From: "Hoeffel, Thomas" To: "'chemistry@ccl.net'" Subject: Companies Selling Compute Cycles??? Date: Thu, 31 Jan 2002 09:33:16 -0800 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-Type: multipart/mixed; boundary="----=_NextPartTM-000-87fbff5e-1665-11d6-87c2-0001032a571c" This is a multi-part message in MIME format. ------=_NextPartTM-000-87fbff5e-1665-11d6-87c2-0001032a571c Content-Type: text/plain; charset="iso-8859-1" Any one know of companies selling compute cycles via subscriptions or contracts. I thought SGI had a division but can't locate any information. I thought there were a few others out there with large clusters eargerly willing to do the same. thanks for the info Thomas J. Hoeffel Computational Chemistry Chiron Corporation thomas_hoeffel@chiron.com ------=_NextPartTM-000-87fbff5e-1665-11d6-87c2-0001032a571c Content-Type: text/plain; name="InterScan_Disclaimer.txt" Content-Transfer-Encoding: 7bit Content-Disposition: attachment; filename="InterScan_Disclaimer.txt" **** ATTENTION! This message contains information (including any appended information, such as copied or forwarded messages and attachments, and any message to which this is appended) which may be confidential and/or privileged. Unless you are the addressee (or authorized to receive for the addressee), you may not use, copy or disclose to anyone the message or any information contained in the message. If you have received the message in error, please advise the sender by reply e-mail, and delete the message. Thank you for your assistance. **** ------=_NextPartTM-000-87fbff5e-1665-11d6-87c2-0001032a571c-- From chemistry-request@server.ccl.net Thu Jan 31 16:37:20 2002 Received: from adenine.cgl.ucsf.edu ([128.218.27.3]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g0VLbKc30981 for ; Thu, 31 Jan 2002 16:37:20 -0500 Received: from adenine.cgl.ucsf.edu (socrates.cgl.ucsf.edu [128.218.27.3]) by adenine.cgl.ucsf.edu (8.12.2/8.12.2/GSC1.13) with ESMTP id g0VLbE43534079; Thu, 31 Jan 2002 13:37:14 -0800 (PST) Message-Id: <200201312137.g0VLbE43534079@adenine.cgl.ucsf.edu> To: Geoff Hutchison cc: chemistry@ccl.net Subject: Re: CCL:Announcement: Open Babel 1.99 (beta) Release In-Reply-To: Your message of "Thu, 31 Jan 2002 08:05:29 CST." Date: Thu, 31 Jan 2002 13:37:14 -0800 From: "David Konerding, Ph.D." Geoff Hutchison writes: > >Open Babel 1.99 >---------------- > >The Open Babel team is pleased to announce the release of Open Babel >1.99, a first beta release for the 2.0 version of the free, >open-source replacement for the Babel chemistry file translation >program. Are you aware that OElib (www.eyesopen.com) is the "future" of babel? Dave From chemistry-request@server.ccl.net Thu Jan 31 18:09:27 2002 Received: from mercury.chem.nwu.edu (hutchisn@[129.105.116.2]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g0VN9Rc01670 for ; Thu, 31 Jan 2002 18:09:27 -0500 Received: from localhost (hutchisn@localhost) by mercury.chem.nwu.edu (8.11.3/8.11.3) with ESMTP id g0VN8pQ07692; Thu, 31 Jan 2002 17:08:52 -0600 (CST) Date: Thu, 31 Jan 2002 17:08:49 -0600 (CST) From: Geoff Hutchison X-X-Sender: To: "David Konerding, Ph.D." cc: Subject: Re: CCL:Announcement: Open Babel 1.99 (beta) Release In-Reply-To: <200201312137.g0VLbE43534079@adenine.cgl.ucsf.edu> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII > Are you aware that OElib (www.eyesopen.com) is the "future" of babel? OELib was originally released as a GPL'ed library. It has been rewritten and is now closed-source. Matt Stahl says that they may at some future point release binaries to replace babel, but the source will still be closed. As I was one of the contributors to the GPL'ed version of OELib, I took the last open version of the OELib code and spun it into Open Babel with the best wishes of Matt and Open Eyes, Inc. They'd like to see the free version prosper. In short, Open Babel *is* OELib. I even wrote a migration guide for code written to OELib and interested in migrating to Open Babel. (The changes are naturally small at the moment.) -- -Geoff Hutchison Marks/Ratner Groups (847) 491-3295 Northwestern Chemistry From chemistry-request@server.ccl.net Thu Jan 31 19:17:16 2002 Received: from mtiwmhc24.worldnet.att.net ([204.127.131.49]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g110HGc04521 for ; Thu, 31 Jan 2002 19:17:16 -0500 Received: from daveg.cachesoftware.com ([12.81.204.60]) by mtiwmhc24.worldnet.att.net (InterMail vM.4.01.03.27 201-229-121-127-20010626) with ESMTP id <20020201001645.UFZU13117.mtiwmhc24.worldnet.att.net@daveg.cachesoftware.com>; Fri, 1 Feb 2002 00:16:45 +0000 Message-Id: <5.1.0.14.0.20020131160249.03489190@pop3.norton.antivirus> X-Sender: X-Mailer: QUALCOMM Windows Eudora Version 5.1 Date: Thu, 31 Jan 2002 16:20:19 -0800 To: "Mus Musculus" From: David Gallagher Subject: Re: CCL:Help with transition states Cc: chemistry@ccl.net In-Reply-To: Mime-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1"; format=flowed Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id g110HGc04522 Minimizing the gradient of a starting guess is one approach but there are other methods that may or may not work better. You can download a "Guide to Transition State Modeling" at http://www.cachesoftware.com/solutions/index.shtml or http://www.cachesoftware.com/pdfs/CACheGuideTransitionStateModel.pdf The default MOPAC method (singlet) will force the electrons to remain paired, but you can switch to UHF to allow for radicals. David Gallagher, Fujitsu At 02:28 PM 1/31/2002 +0100, Mus Musculus wrote: >Hello! >Excuse me if my question seems too basic for this forum, but I'm a >newcomer in this field and I'm feeling quite lost. > >I'm trying to locate the transition state of a electrocyclic opening of a >cyclopropane ring to yield an allyl cation. Is there a kind of established >methodology to follow in this cases (a way of making an "educated guess" >for the geometry of the TS)? >Do you think the outcoming of the reaction being two ions requires a >special treatment? >I would gladly receive any piece of information about the location of >transition states either in general or in electrocyclic reactions. > >Thank you in advance. > >Viv. > > > > >_________________________________________________________________ >Con MSN Hotmail súmese al servicio de correo electrónico más grande del >mundo. http://www.hotmail.com/ES > > > >-= 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 Jan 31 20:47:00 2002 Received: from gandalf.cber.nih.gov ([128.231.52.5]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g111l0c07863 for ; Thu, 31 Jan 2002 20:47:00 -0500 Received: from localhost (rvenable@localhost) by gandalf.cber.nih.gov (980427.SGI.8.8.8/980728.SGI.AUTOCF) via ESMTP id UAA59007; Thu, 31 Jan 2002 20:39:27 -0500 (EST) Date: Thu, 31 Jan 2002 20:39:26 -0500 From: Rick Venable To: "J. Zheng" cc: chemistry@ccl.net Subject: Re: CCL:still need help: pdb --> charmm In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Wed, 30 Jan 2002, J. Zheng wrote: > My research is molecular modeling of protein adsorption. What I want is > to get initial configuration from PDB, then convert to Charmm Format. > It is only way that I can use CHARMM force field. So, from charmm program, > I want to get > > 1) COOR file which includes atomtype of charmm. Depends on what you mean by "atomtype"-- the COOR file really contains just atom names; the atom parameter type info is stored in the PSF as an integer type code, which corresponds to to those declared with MASS statements at the beginning of the RTF. > 2) PSF file which includes connectivity table. It also enumerates the energy terms, which includes bonding, i.e. connectivity, as well as all angles and torsions which will be explicitly evaluated. > Based on these two files, I will code by myself for a speicfic protein > adsorption. In order to do this project, our group purchase CHARMM. But > nobody know how to use it. That is why I ask you guys for helping. > > After 2 days, I have got prelimitary results. But I don't know whether > it is right. If correct, I will summary what I do and what you guys > suggested later. otherwise, I have to still struggle on this conversion. > > ------------------------------------------------------------------------- > > 1. Charmm program > > suggested by Torsten Becker > Xiang(Simon) WANG > Marcin Krol > Dr. Richard L. Wood > Szilveszter Juhos > > following I will list COMMAND I inputed. (based on Becker's script) > > ok 1) * Emacs generated Charmm Inputfile > * It's generally better to use a more descriptive title. > ok 2) bomlev 0 (i don't know what means of this command though) A negative bomlev will tolerate errors-- bomlev -1 will forgive typing errors, so that CHARMM won't stop if you misspell a command, keyword or filename. Very useful for interactive sessions. See miscom.doc > ok 3) open read unit 1 card name > /charmm/c27b4/toppar/top_all22_prot.inp > read rtf card unit 1 > close unit 1 > > ok 4) open read unit 1 card name > /charmm/c27b4/toppar/par_all22_prot.inp > read param card unit 1 > close unit 1 > > ----------------------------------------------------------- > when I read param card unit 1, screen prints lots of > information as following format > PARRDR> Multiple terms for dihedral type: INDEX 99 CODE 1369603 CT2 > -SM -SM -CT2 > PARRDR> Multiple terms for dihedral type: INDEX 98 CODE 1369603 CT2 -SM > -SM -CT2 > PARRDR> Multiple terms for dihedral type: INDEX 96 CODE 1367651 CT2 -C > -NH1 -CT2 > ------------------------------------------------------------------ > > I was supposed that it is right. They are informational messages-- don't worry about for now, unless you've actually modified the parameter file. > ok?? 5) open read unit 1 card name "7lyz.pdb" > read sequ pdb unit 1 > close unit 1 > > ------charmm gives this information------ > > ***** Message from SEQRDR ***** THE SYSTEM CONTAINS 18 TITRATABLE GROUPS > THE USER MUST PREDETERMINE THE PROTONATION STATE THROUGH THE SEQUENCE AND > RTF > HIS - 0 ASP - 7 GLU - 2 LYS - 6 TYR - 3 > > what does it means? Default protonation states haev been used for the above residues, which is typically okay for ASP, GLU, LYS, and TYR unless they are buried deep inside the protein. The HIS residue is more complicated, because it has neutral tautomers and a protonated state, and allowing the default could be a serious mistake. Each form has a different residue name. > -------------------------------------------- > > ok?? 6) generate 7lyz Possibly not okay; you should probably included the SETUP option to create an internal coordinate (IC) table; more about this later. > > ------------------------------------- > CHARMM> generate 7lyz > THE PATCH 'NTER ' WILL BE USED FOR THE FIRST RESIDUE > THE PATCH 'CTER ' WILL BE USED FOR THE LAST RESIDUE > GENPSF> Segment 1 has been generated. Its identifier is 7LYZ. > PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. > PSFSUM> Summary of the structure file counters : > Number of segments = 1 Number of residues = 129 > Number of atoms = 1968 Number of groups = 586 > Number of bonds = 1988 Number of angles = 3547 > Number of dihedrals = 5183 Number of impropers = 351 > Number of HB acceptors = 186 Number of HB donors = 271 > Number of NB exclusions = 0 Total charge = 8.00000 > ----------------------------------------------- > > not ok 7) open read unit 1 card name "7lyz.pdb" > read coor pdb unit 1 > close unit 1 > > -------------------------------------------------- > ** WARNING ** For atom in coordinate file, the corresponding residue in > the PSF lacks that atom: > INDEX= 996 IRES= 129 RESID=129 RES=LEU ATOM=O > ** WARNING ** After reading, there are no coordinates for selected atom: > 2 1 LYS HT1 > ** WARNING ** After reading, there are no coordinates for selected atom: > 3 1 LYS HT2 > ** WARNING ** After reading, there are no coordinates for selected atom: > 4 1 LYS HT3 > ** WARNING ** After reading, there are no coordinates for selected atom: > 6 1 LYS HA > ** WARNING ** After reading, there are no coordinates for selected atom: > 8 1 LYS HB1 > ** WARNING ** After reading, there are no coordinates for selected atom: > 9 1 LYS HB2 > ** WARNING ** After reading, there are no coordinates for selected atom: > 11 1 LYS HG1 > ** WARNING ** After reading, there are no coordinates for selected atom: > 12 1 LYS HG2 > ** WARNING ** After reading, there are no coordinates for selected atom: > 14 1 LYS HD1 > ** WARNING ** After reading, there are no coordinates for selected atom: > 15 1 LYS HD2 > ** A total of 970 selected atoms have no coordinates > *** LEVEL 2 WARNING *** BOMLEV IS 0 > --------------------------------------------------------------------- Many PDB files do not have hydrogens, and even if they do, the names probably aren't the same as those that CHARMM uses. THe typical solution is build the H atom positions via either the IC BUILD (intcor.doc) or HBUILD (hbuild.doc) commands (see below). > > ok?? 8) open write unit 2 card name "a.crd" > write coor unit 2 card > * 7lyz coor > * > close unit 2 Sort of-- none of the H atoms will have coords. Also, the file is automatically closed when writing, hence the next message. > ------------------------------------------------------- > CLOLGU> ***** > WARNING ***** Attempt to close unit that was not open. > --------------------------------------------------------------- > > ok?? 9) open write unit 3 card name "a.psf" > write psf unit 3 card > * 7lyz psf > * > close unit 3 Likewise for CLOSE command-- not needed after a WRITE; the file should be okay, unless the protein has disulfide bonds. > ================================================================= > > RESULTS: > > I have check a.crd and a.psf file. I found that there are 1968 atoms. > Compared with original 1000 atom of 7lyz.pdf, there are more 968 atom in > a.crd and a.psf files. and some atoms don't have coordinate since the > coordinates were labelled 9999.0000.. > > That is what I done. I felt these initial configurature may not be > right. I have to resort to you guys. The CHARMM forcefield represents all atoms, including non-polar H atoms, explicitly; many crystal structures of proteins have only heavy atom coordinates. Most of atoms w/o coordinates are probably H atoms. Add the SETUP keyword to the GENERATE command (struct.doc), and after reading the heavy atom coords from the PDB file you can (N.B. the ! char starts a comment in CHARMM syntax): ic purge ! CLEANUP IC TABLE ic param ! GET MISSING BONDS AND ANGLES FROM PARAMETER FILE ic build ! PLACE ANY MISSING COORDS, E.G. TERMINAL O ON CO2- ! CHECK FOR MISSING HEAVY ATOM COORDS define test sele ( .not. type H* ) .and. ( .not. init ) show end ! USE HBUILD TO REBUILD H ATOMS; SPINS METHYLS, ETC. TO LOCAL MINIMUM coor init sele type H* end hbuild sele type H* end ! CHECK FOR ANY MISSING COORDS define test sele .not. init show end =+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+= Rick Venable 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 =+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=