From chemistry-request@server.ccl.net Fri Sep 27 09:23:41 2002 Received: from po4.wam.umd.edu ([128.8.10.166]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g8RDNfa02691 for ; Fri, 27 Sep 2002 09:23:41 -0400 Received: from arwen.wam.umd.edu (arwen.umd.edu [129.2.68.73]) by po4.wam.umd.edu (8.9.3/8.9.3) with ESMTP id JAA19500 for ; Fri, 27 Sep 2002 09:23:26 -0400 (EDT) Message-Id: <5.1.1.6.0.20020927090442.00aa4798@imap.wam.umd.edu> X-Sender: oliwalk@imap.wam.umd.edu X-Mailer: QUALCOMM Windows Eudora Version 5.1.1 Date: Fri, 27 Sep 2002 09:25:23 -0700 To: chemistry@ccl.net From: olivier walker Subject: useful software for dual domain protein conformational search? Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed Hi all, I'm currently studying a dual domain protein. I would like to generate all possible conformations including some restraints. Basically, I want to study all possible conformation of the link between the two domains (8 residues) and freeze the two domains (not totally because I would like to follow the shift of the domains with the conformation change of the link). My questions are: * what method should I consider (MD, monte carlo, annealing.....)? * The most important: what is the best suitable software for this kind of study ? * using this software, is it possible to monitor energy, distances between given residues and other features? Thanks in advance for your help olivier. ************************************************** Olivier WALKER Department of Chemistry & Biochemistry University of Maryland College Park, MD 20742 USA ************************************************** Fax : 301-314-0386 Phone : 301-405-8710 E-mail : oliwalk@wam.umd.edu ************************************************** From chemistry-request@server.ccl.net Fri Sep 27 10:06:55 2002 Received: from matisse.bmc.uu.se ([130.238.37.97]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g8RE6sv03645 for ; Fri, 27 Sep 2002 10:06:55 -0400 Received: (from spoel@localhost) by matisse.bmc.uu.se (8.11.6/8.11.6) id g8RE2Gk25536; Fri, 27 Sep 2002 16:02:16 +0200 X-Authentication-Warning: matisse.bmc.uu.se: spoel set sender to spoel@xray.bmc.uu.se using -f Subject: Re: CCL:useful software for dual domain protein conformational search? From: David van der Spoel To: olivier walker Cc: chemistry@ccl.net In-Reply-To: <5.1.1.6.0.20020927090442.00aa4798@imap.wam.umd.edu> References: <5.1.1.6.0.20020927090442.00aa4798@imap.wam.umd.edu> Content-Type: text/plain Content-Transfer-Encoding: 7bit X-Mailer: Ximian Evolution 1.0.3 (1.0.3-6) Date: 27 Sep 2002 16:02:16 +0200 Message-Id: <1033135336.19284.9.camel@matisse> Mime-Version: 1.0 On Fri, 2002-09-27 at 18:25, olivier walker wrote: > Hi all, > > > I'm currently studying a dual domain protein. I would like to generate all > possible conformations including some restraints. > Basically, I want to study all possible conformation of the link between > the two domains (8 residues) and freeze the two domains (not totally > because I would like to follow the shift of the domains with the > conformation change of the link). > > My questions are: > > * what method should I consider (MD, monte carlo, annealing.....)? > * The most important: what is the best suitable software for this kind of > study ? you want to use dyndom first to define the hinge and rotation vectors: http://asgard.sys.uea.ac.uk:8080/dyndom/main.jsp > * using this software, is it possible to monitor energy, distances between > given residues and other features? Then you can use GROMACS (http://www.gromacs.org, program g_dyndom) to analyze the results, make interpolations and extrpolations of the rotatiom motion -- 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 Fri Sep 27 04:11:52 2002 Received: from smtp.csc.fi ([193.166.0.99]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g8R8Bpa30582 for ; Fri, 27 Sep 2002 04:11:51 -0400 Received: from ISOSIRRI (dhcp-116.csc.fi [193.166.2.116]) by smtp.csc.fi (8.9.3/8.9.3/CSC) with ESMTP id LAA30446 for ; Fri, 27 Sep 2002 11:11:50 +0300 From: "Leif Laaksonen" To: Subject: Version 2.20 of gOpenMol available Date: Fri, 27 Sep 2002 11:10:36 +0300 Message-ID: <001b01c265fd$5bd8eeb0$7402a6c1@ISOSIRRI> MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="----=_NextPart_000_001C_01C26616.812626B0" X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook, Build 10.0.4024 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1106 Importance: Normal This is a multi-part message in MIME format. ------=_NextPart_000_001C_01C26616.812626B0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit Compadres, Scarecrow Computing and CSC, the Finnish IT center for Science, proudly present the new version of gOpenMol. The flexible toolbox for the display and analysis of molecular systems. The new gOpenMol web pages are located at: http://www.csc.fi/gopenmol/ We currently support gOpenMol on Windows and Linux but hope to be able to support the program also on other platforms in the future. Yours, -leif laaksonen ------=_NextPart_000_001C_01C26616.812626B0 Content-Type: text/x-vcard; name="Leif Laaksonen.vcf" Content-Transfer-Encoding: 7bit Content-Disposition: attachment; filename="Leif Laaksonen.vcf" BEGIN:VCARD VERSION:2.1 N:Laaksonen;Leif FN:Leif Laaksonen ORG:Center for Scientific Computing;CSC New Technologies TITLE:New Technologies Group Manager NOTE;ENCODING=QUOTED-PRINTABLE:My personal Web page: http://www.csc.fi/~laaksone/=0D=0A=0D=0AMy personal fa= x: +44-870-831-8909=0D=0A=0D=0A=0D=0A TEL;WORK;VOICE:+358 9 457 2378 TEL;CELL;VOICE:+358500425203 TEL;WORK;FAX:+358 9 457 2302 TEL;HOME;FAX:+44 870 831 8909 ADR;WORK;ENCODING=QUOTED-PRINTABLE:;;Tekniikantie 15 a D=0D=0AP.O.Box 405;Espoo;;FIN-02101;Finland LABEL;WORK;ENCODING=QUOTED-PRINTABLE:Tekniikantie 15 a D=0D=0AP.O.Box 405=0D=0AEspoo FIN-02101=0D=0AFinland URL:http://laaksonen.csc.fi/ URL:http://www.csc.fi/ EMAIL;PREF;INTERNET:Leif.Laaksonen@csc.fi EMAIL;INTERNET:Leif.Laaksonen@iki.fi EMAIL;INTERNET:laaksone@csc.fi REV:20010502T202010Z END:VCARD ------=_NextPart_000_001C_01C26616.812626B0-- From chemistry-request@server.ccl.net Fri Sep 27 05:48:10 2002 Received: from mx04.nexgo.de ([151.189.8.80]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g8R9m9a32295 for ; Fri, 27 Sep 2002 05:48:09 -0400 Received: from ice.mpg.de (dialin-212-144-179-131.arcor-ip.net [212.144.179.131]) by mx04.nexgo.de (Postfix) with ESMTP id 2724837BF9; Fri, 27 Sep 2002 11:48:08 +0200 (CEST) Message-ID: <3D942958.5040106@ice.mpg.de> Date: Fri, 27 Sep 2002 11:48:08 +0200 From: Christoph Steinbeck Reply-To: steinbeck@ice.mpg.de User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.1) Gecko/20020826 X-Accept-Language: en-us, en MIME-Version: 1.0 To: Iain Wallace Cc: CCL Subject: Re: CCL:2D pictures/structure generator References: <000c01c2656a$f8620f70$626ce286@wallaceiwork> Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit Iain Wallace wrote: > Hi all, > > I have two quick questions if you don't mind: > 1) Does any one know of a free program that convert molecules in smiles > format ( or some other format) into a picture, using a command line for > windows. I want to create an excel spreadsheet with a picture of each of > my molecules, by using a simple script. > 2) Does any one know of a free program that can generate molecules based > on a given fragment. I have a drug molecule, and a protein, and would > like to generate molecules by modifying some of the substituents of the > drug molecule and attempt to dock them. > > Thanks for any help you can give me > > Iain > Please try our Chemistry Development Kit (CDK), a free Java toolkit for structural chemo- and bioinformatics. It is available from http://cdk.sourceforge.net The CDK provides methods for parsing SMILES and creating coordinates for the molecule by structure diagram layout. Output in a common graphics format can then be done using the BATIK toolkit. I guess, that is as close as you can get to solving your problem with free software. Admittedly, there is no command line wrapper for this, but that would be just 5 to 10 lines of code. The CDK also contains some stochastic structure generators but they might not be easily adapted to your problem, because they are isomer generators, which only produce isomers of a given molecular formula. Cheers, Chris -- Dr. Christoph Steinbeck (http://www.ice.mpg.de/departments/ChemInf) MPI of Chemical Ecology, Winzerlaer Str. 10, Beutenberg Campus, 07745 Jena, Germany Tel: +49(0)3641 571263 - Fax: +49(0)3641 571202 What is man but that lofty spirit - that sense of enterprise. ... Kirk, "I, Mudd," stardate 4513.3.. From chemistry-request@server.ccl.net Fri Sep 27 13:03:05 2002 Received: from research.dfci.harvard.edu ([155.52.50.28]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g8RH34v07103 for ; Fri, 27 Sep 2002 13:03:04 -0400 Received: from [155.52.22.78] (account reche HELO research.dfci.harvard.edu) by research.dfci.harvard.edu (CommuniGate Pro SMTP 3.5.9) with ESMTP-TLS id 833974 for chemistry@ccl.net; Fri, 27 Sep 2002 13:07:55 -0400 Sender: par@ccl.net Message-ID: <3D949075.BCC1447D@research.dfci.harvard.edu> Date: Fri, 27 Sep 2002 13:08:05 -0400 From: Pedro A Reche Reply-To: reche@research.dfci.harvard.edu Organization: Dana-Farber Cancer Institute X-Mailer: Mozilla 4.7C-SGI [en] (X11; I; IRIX64 6.5 IP28) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: PROTEIN CONTACTS Content-Type: multipart/alternative; boundary="------------A4A6D843F00B9B2B2EFB41A8" --------------A4A6D843F00B9B2B2EFB41A8 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi all, I am interesting in listing the protein contacts between molecules, chains, side-chains etc for whole set of structures, and I wonder if someone could suggest me a good UNIX program preferably working on the command line to to the job. If the program could also identify the type of contacts (VW, H-bonds, salt bridges) will be great. Thanks for consideration, Pedro ******************************************************************* PEDRO A. RECHE , pHD TL: 617 632 3824 Dana-Farber Cancer Institute, FX: 617 632 4569 Harvard Medical School, EM: reche@research.dfci.harvard.edu 44 Binney Street, D1510A, EM: reche@mifoundation.org Boston, MA 02115 URL: http://www.reche.org ******************************************************************* --------------A4A6D843F00B9B2B2EFB41A8 Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit Hi all,
I am interesting in listing the protein contacts between  molecules, chains, side-chains etc for whole set of structures, and I wonder if someone could suggest me a good  UNIX program preferably working on the command line to to the job. If the program could also identify the type of contacts (VW, H-bonds, salt bridges) will be great.
Thanks for consideration,
 
 

Pedro 

*******************************************************************
PEDRO A. RECHE , pHD            TL: 617 632 3824
Dana-Farber Cancer Institute,   FX: 617 632 4569
Harvard Medical School,         EM: reche@research.dfci.harvard.edu
44 Binney Street, D1510A,       EM: reche@mifoundation.org              
Boston, MA 02115                URL: http://www.reche.org                                               
*******************************************************************
  --------------A4A6D843F00B9B2B2EFB41A8-- From chemistry-request@server.ccl.net Fri Sep 27 01:17:39 2002 Received: from kdmail2.netcologne.de ([194.8.194.86]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g8R5Hda25662 for ; Fri, 27 Sep 2002 01:17:39 -0400 Received: from cosmologic.de (xdsl-213-168-108-252.netcologne.de [213.168.108.252]) by kdmail2.netcologne.de (Mirapoint Messaging Server MOS 2.9.3.5) with ESMTP id BNQ30613; Fri, 27 Sep 2002 07:17:06 +0200 (CEST) Message-ID: <3D93E9C5.7CC69FA2@cosmologic.de> Date: Fri, 27 Sep 2002 07:16:53 +0200 From: "Dr. Andreas Klamt" Organization: COSMOlogic GmbH&CoKG X-Mailer: Mozilla 4.7 [de] (WinNT; I) X-Accept-Language: en,pdf MIME-Version: 1.0 To: Zhijian Wu CC: chemistry@ccl.net Subject: Re: CCL:solvation energy References: Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit For a charged species the dipole moment is only defined if you specify an almost arbitrary reference point. Anyway, solvation energies for charged species mainly depend on the details of the charge distribution and they strongly depend on the shape of the cavity. Just forget about simple Onsager models. Use PCM or COSMO. Andreas Klamt Zhijian Wu schrieb: > > Hi, cclers, > > Does anyone know that for the charged speices (say, +1 and -1), how accurate of the Onsager Model (based on dipole moment) on > the solvation energy? > > Thank you very much for your help! > > Regards, > > Zhijian Wu > > > ------------------------------------------------------------------------------------------------------------------------------ > Chat with friends online, try MSN Messenger: Click Here > > -= 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 -- -------------------------------------------------------------------------------- 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 Fri Sep 27 11:52:52 2002 Received: from mhub16.lvs.dupont.com ([52.128.30.9]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g8RFqqv05759 for ; Fri, 27 Sep 2002 11:52:52 -0400 Received: from mhub14.lvs.dupont.com by mhub16.lvs.dupont.com with ESMTP for Chemistry@ccl.net; Fri, 27 Sep 2002 11:52:40 -0400 Received: from CDCLN05.LVS.DUPONT.COM by mhub14.lvs.dupont.com with ESMTP for Chemistry@ccl.net; Fri, 27 Sep 2002 11:52:11 -0400 Sensitivity: Subject: coordinates of a carbon nanotube To: Chemistry@ccl.net From: "Ya-Jun Zheng" Date: Fri, 27 Sep 2002 11:52:08 -0400 Message-Id: X-MIMETrack: Serialize by Router on CDCLNMH1/DuPont_MHUB(Release 5.0.9a |January 7, 2002) at 09/27/2002 11:52:09 AM MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi, A friend of mine is interested in examining how a carbon nanotube interacts with other molecules. There have been some theoretical studies regarding the structures of some carbon nanotubes and I am wondering whether anyone would be kind to share the coordinates of a nanotube model. Thanks. Yajun This communication is for use by the intended recipient and contains information that may be privileged, confidential or copyrighted under applicable law. If you are not the intended recipient, you are hereby formally notified that any use, copying or distribution of this e-mail, in whole or in part, is strictly prohibited. Please notify the sender by return e-mail and delete this e-mail from your system. Unless explicitly and conspicuously designated as "E-Contract Intended", this e-mail does not constitute a contract offer, a contract amendment, or an acceptance of a contract offer. This e-mail does not constitute a consent to the use of sender's contact information for direct marketing purposes or for transfers of data to third parties. Francais Deutsch Italiano Espanol Portuges Japanese Chinese Korean http://www.DuPont.com/corp/email_disclaimer.html From chemistry-request@server.ccl.net Fri Sep 27 10:50:10 2002 Received: from postoffice.mail.cornell.edu ([132.236.56.7]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g8REoAv04443 for ; Fri, 27 Sep 2002 10:50:10 -0400 Received: from cornell.edu ([128.84.182.122]) by postoffice.mail.cornell.edu (8.9.3/8.9.3) with ESMTP id KAA07500; Fri, 27 Sep 2002 10:50:05 -0400 (EDT) Sender: richard@cornell.edu Message-ID: <3D94701D.9EB4F292@cornell.edu> Date: Fri, 27 Sep 2002 10:50:05 -0400 From: Richard Gillilan X-Mailer: Mozilla 4.77 [en] (X11; U; Linux 2.4.16 i686) X-Accept-Language: en MIME-Version: 1.0 To: olivier walker CC: chemistry@ccl.net Subject: Re: CCL:useful software for dual domain protein conformational search? References: <5.1.1.6.0.20020927090442.00aa4798@imap.wam.umd.edu> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit This sounds like a good candidate for rigid-body mechanics. You could treat the two domains as rigid but NOT fixed in space. You could also apply additional constraints to the bond lengths if you wanted to increase the efficiency of the dynamics run. I believe the MBO(N)D program available from (Accelrys?) can do this sort of thing. There were a couple papers in J. Comp. Chem. on combining quaternion-based mechanics with SHAKE-type constraints a few years ago: Forester TR, Smith W SHAKE, rattle, and roll: Efficient constraint algorithms for linked rigid bodies J COMPUT CHEM 19 (1): 102-111 JAN 15 1998) Wu XW, Sung SS Constraint dynamics algorithm for simulation of semiflexible macromolecules J COMPUT CHEM 19 (14): 1555-1566 NOV 15 1998 Richard Gillilan MacCHESS, Cornell olivier walker wrote: > > Hi all, > > I'm currently studying a dual domain protein. I would like to generate all > possible conformations including some restraints. > Basically, I want to study all possible conformation of the link between > the two domains (8 residues) and freeze the two domains (not totally > because I would like to follow the shift of the domains with the > conformation change of the link). > > My questions are: > > * what method should I consider (MD, monte carlo, annealing.....)? > * The most important: what is the best suitable software for this kind of > study ? > * using this software, is it possible to monitor energy, distances between > given residues and other features? > > Thanks in advance for your help > > olivier. From chemistry-request@server.ccl.net Fri Sep 27 04:07:38 2002 Received: from dove2.cf.ac.uk ([131.251.1.170]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g8R87ca30453 for ; Fri, 27 Sep 2002 04:07:38 -0400 Received: from thor.cf.ac.uk ([131.251.0.1]) by dove2.cf.ac.uk with esmtp (Exim 3.03 #2) id 17uq9t-0003OV-00; Fri, 27 Sep 2002 09:07:33 +0100 Received: from localhost (sacjap@localhost) by thor.cf.ac.uk (8.8.8/8.6.12) with ESMTP id JAA17099; Fri, 27 Sep 2002 09:07:33 +0100 (BST) Date: Fri, 27 Sep 2002 09:07:33 +0100 (BST) From: Jamie Platts X-Sender: sacjap@thor To: Iain Wallace cc: CCL Subject: Re: CCL:2D pictures/structure generator In-Reply-To: <000c01c2656a$f8620f70$626ce286@wallaceiwork> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi Iain - take a look at Daylight's Depict utility: http://www.daylight.com/daycgi/depict where you should be able to save the generated structure as a GIF. Hope that helps, Jamie > > I have two quick questions if you don't mind: > 1) Does any one know of a free program that convert molecules in smiles > format ( or some other format) into a picture, using a command line for > windows. I want to create an excel spreadsheet with a picture of each of > my molecules, by using a simple script. > > From chemistry-request@server.ccl.net Fri Sep 27 16:26:44 2002 Received: from prserv.net ([32.97.166.34]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g8RKQiv11601 for ; Fri, 27 Sep 2002 16:26:44 -0400 Received: from attglobal.net (slip-32-101-104-110.in.us.prserv.net[32.101.104.110]) by prserv.net (out4) with SMTP id <2002092720264220406ugu6se>; Fri, 27 Sep 2002 20:26:43 +0000 Message-ID: <3D9478B6.83BE66D9@attglobal.net> Date: Fri, 27 Sep 2002 15:26:46 +0000 From: jmmckel@attglobal.net Reply-To: jmmckel@attglobal.net X-Mailer: Mozilla 4.79 [en] (WinNT; U) X-Accept-Language: en MIME-Version: 1.0 To: "Dr. Andreas Klamt" CC: Zhijian Wu , chemistry@ccl.net Subject: Re: CCL:solvation energy References: <3D93E9C5.7CC69FA2@cosmologic.de> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit In addition, a molecule with 0.0 dipole moment might not get solvated in a dipole model... charged or not, ... say 1,4 dioxane, or 1,4 diazine..certainly soluble in a lot of solvents... Also, one can disolve 1gr of benzene per liter of water. John McKelvey "Dr. Andreas Klamt" wrote: > For a charged species the dipole moment is only defined if you specify an almost arbitrary reference point. Anyway, solvation > energies for charged species mainly depend on the details of the charge distribution and they strongly depend on the shape of > the cavity. Just forget about simple Onsager models. Use PCM or COSMO. > > Andreas Klamt > > Zhijian Wu schrieb: > > > > Hi, cclers, > > > > Does anyone know that for the charged speices (say, +1 and -1), how accurate of the Onsager Model (based on dipole moment) on > > the solvation energy? > > > > Thank you very much for your help! > > > > Regards, > > > > Zhijian Wu > > > > > > ------------------------------------------------------------------------------------------------------------------------------ > > Chat with friends online, try MSN Messenger: Click Here > > > > -- > -------------------------------------------------------------------------------- > 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 > -------------------------------------------------------------------------------- > > -= 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