From chemistry-request@ccl.net Mon Feb 2 10:02:20 2004 Received: from mbu.iisc.ernet.in (mail.mbu.iisc.ernet.in [144.16.74.32]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i12F2CU6008398 for ; Mon, 2 Feb 2004 10:02:17 -0500 Received: from mbu.iisc.ernet.in (localhost.localdomain [127.0.0.1]) by mbu.iisc.ernet.in (8.12.8/8.12.8) with ESMTP id i12F3woF032482 for ; Mon, 2 Feb 2004 20:33:58 +0530 Received: from localhost (gyan@localhost) by mbu.iisc.ernet.in (8.12.8/8.12.8/Submit) with ESMTP id i12F3vwx032478 for ; Mon, 2 Feb 2004 20:33:58 +0530 Date: Mon, 2 Feb 2004 20:33:56 +0530 (IST) From: Gyanendra Kumar To: chemistry_at_ccl.net Subject: CCL: dock5? Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Spam-Status: No, hits=0.0 required=7.0 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Dear CCLers, I have just installed Dock5 on my linux machine. And I have ligand and receptor files in mol2 format with charges assigned. How do we calculate molecular surface for the receptor. The one program mentioned in the manual - MS is not a freeware. Are there any free programs for generating molecular surface of proteins which can be used with Dock5. Sincerely, Gyan. From chemistry-request@ccl.net Mon Feb 2 06:47:56 2004 Received: from postag.jerini.de ([62.206.112.102]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i12BltU6001390 for ; Mon, 2 Feb 2004 06:47:56 -0500 Received: from jerini.de ([192.168.0.161]) by postag.jerini.de (Lotus Domino Release 5.0.11) with ESMTP id 2004020212500811:14248 ; Mon, 2 Feb 2004 12:50:08 +0100 Message-ID: <401E391D.2090701^at^jerini.de> Date: Mon, 02 Feb 2004 12:48:45 +0100 From: Uwe Richter User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:0.9.4) Gecko/20011126 Netscape6/6.2.1 X-Accept-Language: en-us MIME-Version: 1.0 To: chemistry^at^ccl.net Subject: peptide conformer generation software X-MIMETrack: Itemize by SMTP Server on Server1Jerini/BioTools/DE(Release 5.0.11 |July 24, 2002) at 02.02.2004 12:50:08, Serialize by Router on Server1Jerini/BioTools/DE(Release 5.0.11 |July 24, 2002) at 02.02.2004 12:50:10, Serialize complete at 02.02.2004 12:50:10 Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii; format=flowed X-Spam-Status: No, hits=0.0 required=7.0 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Dear CCLers, is there software out there which can systematically generate conformations for peptides of up to 8-10 residues, excluding conformations which are sterically forbidden? Thanks, Uwe From chemistry-request@ccl.net Mon Feb 2 10:41:53 2004 Received: from shiva.jussieu.fr (shiva.jussieu.fr [134.157.0.129]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i12FfqU6010016 for ; Mon, 2 Feb 2004 10:41:52 -0500 Received: from ds10.itodys.jussieu.fr (ds10.itodys.jussieu.fr [134.157.24.13]) by shiva.jussieu.fr (8.12.10/jtpda-5.4) with ESMTP id i12Fi5DC083106 for ; Mon, 2 Feb 2004 16:44:06 +0100 (CET) X-Ids: 164 Received: by ds10.itodys.jussieu.fr (8.12.1/1.1.2.11/09Jul02-1200PM) id i12Fi5vS243397; Mon, 2 Feb 2004 16:44:05 +0100 (MET) Date: Mon, 2 Feb 2004 16:44:05 +0100 (MET) From: Michel Petitjean Message-Id: <200402021544.i12Fi5vS243397!at!ds10.itodys.jussieu.fr> To: chemistry!at!ccl.net Subject: Re: CCL:dock5? X-Miltered: at shiva.jussieu.fr with ID 401E7045.003 by Joe's j-chkmail (http://j-chkmail.ensmp.fr)! X-Antivirus: scanned by sophie at shiva.jussieu.fr X-Spam-Status: No, hits=0.0 required=7.0 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net To: chemistry!at!ccl.net Subject: CCL:dock5? Surface computation: submit the mol2 file to the freeware ASV. Programme and documentation with reference: http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html#ASV Michel Petitjean, Email: petitjean!at!itodys.jussieu.fr ITODYS (CNRS, UMR 7086) ptitjean!at!ccr.jussieu.fr http://petitjeanmichel.free.fr/itoweb.petitjean.html ...................................................................... Gyanendra Kumar wrote: Dear CCLers, I have just installed Dock5 on my linux machine. And I have ligand and receptor files in mol2 format with charges assigned. How do we calculate molecular surface for the receptor. The one program mentioned in the manual - MS is not a freeware. Are there any free programs for generating molecular surface of proteins which can be used with Dock5. Sincerely, Gyan. From chemistry-request@ccl.net Mon Feb 2 02:29:45 2004 Received: from mailgw1.technion.ac.il (mailgw1.technion.ac.il [132.68.238.34]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i127ThU6023651 for ; Mon, 2 Feb 2004 02:29:44 -0500 Received: from localhost (localhost.localdomain [127.0.0.1]) by mailgw1.technion.ac.il (Postfix) with ESMTP id 27A52FFE7C for ; Mon, 2 Feb 2004 09:31:55 +0200 (IST) Received: from mailgw1.technion.ac.il ([127.0.0.1]) by localhost (mailgw1.technion.ac.il [127.0.0.1]) (amavisd-new, port 10024) with LMTP id 04891-01-63 for ; Mon, 2 Feb 2004 09:31:54 +0200 (IST) Received: from techunix.technion.ac.il (techunix.technion.ac.il [132.68.1.28]) by mailgw1.technion.ac.il (Postfix) with ESMTP id 5EAC3FFE90 for ; Mon, 2 Feb 2004 09:31:54 +0200 (IST) Received: from localhost (localhost [127.0.0.1]) by techunix.technion.ac.il (Postfix) with ESMTP id 0857A360C for ; Mon, 2 Feb 2004 09:31:50 +0200 (IST) Received: from techunix.technion.ac.il ([127.0.0.1]) by localhost (techunix.technion.ac.il [127.0.0.1]) (amavisd-new, port 10024) with LMTP id 22573-01-34 for ; Mon, 2 Feb 2004 09:31:49 +0200 (IST) Received: from ch507b.tx.technion.ac.il (unknown [132.68.96.220]) by techunix.technion.ac.il (Postfix) with ESMTP id 69BD63607 for ; Mon, 2 Feb 2004 09:31:49 +0200 (IST) Message-Id: <5.2.1.1.0.20040201212523.00b39e08..at..tx.technion.ac.il> X-Mailer: QUALCOMM Windows Eudora Version 5.2.1 Date: Sun, 01 Feb 2004 21:31:53 -0800 To: chemistry..at..ccl.net From: Monica Subject: ONIOM 2 levels Mime-Version: 1.0 Content-Type: multipart/alternative; boundary="=====================_502462963==.ALT" X-Virus-Scanned: by amavisd-new at technion.ac.il X-Virus-Scanned: by amavisd-new at technion.ac.il X-Spam-Status: No, hits=0.5 required=7.0 tests=HTML_20_30,HTML_MESSAGE autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net --=====================_502462963==.ALT Content-Type: text/plain; charset="us-ascii"; format=flowed Hello, I have ONIOM 2 layers calculation failed with the following error message: SCF Done: E(RHF) = -2029.29155165 A.U. after 17 cycles Convg = 0.6294D-08 -V/T = 2.0005 S**2 = 0.0000 Range of M.O.s used for correlation: 36 193 NBasis= 193 NAE= 55 NBE= 55 NFC= 35 NFV= 0 NROrb= 158 NOA= 20 NOB= 20 NVA= 138 NVB= 138 DE2Alg-SaveT2 allocation failure: iend,mxcore= 8572108 6845985 Error termination via Lnk1e in /usr/local/g98/l906.exe. Job cpu time: 0 days 10 hours 40 minutes 17.3 seconds. File lengths (MBytes): RWF= 957 Int= 0 D2E= 0 Chk= 2 Scr= 1 Does anyone have an idea what this error message mean and how to handle it? Thank you in advance, Monica --=====================_502462963==.ALT Content-Type: text/html; charset="us-ascii" Hello,

I have ONIOM 2 layers calculation failed with the following error message:

SCF Done:  E(RHF) =  -2029.29155165     A.U. after   17 cycles
             Convg  =    0.6294D-08             -V/T =  2.0005
             S**2   =   0.0000
 Range of M.O.s used for correlation:    36   193
 NBasis=   193 NAE=    55 NBE=    55 NFC=    35 NFV=     0
 NROrb=    158 NOA=    20 NOB=    20 NVA=   138 NVB=   138
 DE2Alg-SaveT2 allocation failure:  iend,mxcore=   8572108   6845985
 Error termination via Lnk1e in /usr/local/g98/l906.exe.
 Job cpu time:  0 days 10 hours 40 minutes 17.3 seconds.
 File lengths (MBytes):  RWF=  957 Int=    0 D2E=    0 Chk=    2 Scr=    1


Does anyone have an idea what this error message mean and how to handle it?

Thank you in advance,

Monica --=====================_502462963==.ALT-- From chemistry-request@ccl.net Mon Feb 2 12:15:05 2004 Received: from sandmail01.sd.accelrys.com (fw1.sd.accelrys.com [209.120.169.30]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i12HF4U6012177 for >server.ccl.net>; Mon, 2 Feb 2004 12:15:04 -0500 To: chemistry<>server.ccl.net Subject: Call for Posters - 2004 AccelrysWorld - 2nd Notice MIME-Version: 1.0 X-Mailer: Lotus Notes Release 6.0.2CF1 June 9, 2003 Message-ID: >accelrys.com> From: Omoshile Clement >accelrys.com> Date: Mon, 2 Feb 2004 09:17:12 -0800 X-MIMETrack: Serialize by Router on sandmail01/Server/Accelrys(Release 6.0.2CF1|June 9, 2003) at 02/02/2004 09:17:18, Serialize complete at 02/02/2004 09:17:18 Content-Type: multipart/alternative; boundary="=_alternative 005EC29E88256E2E_=" X-Spam-Status: No, hits=0.0 required=7.0 tests=HTML_MESSAGE autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net This is a multipart message in MIME format. --=_alternative 005EC29E88256E2E_= Content-Type: text/plain; charset="US-ASCII" Dear CCLers: The 2nd AccelrysWorld conference on scientific software and IT, will be held at the Hotel del Coronado, San Diego, California, March 8-10, 2004 ( http://www.accelrys.com/accelrysworld/). AccelrysWorld is an international event for anyone with an interest in software solutions to enable R&D. It brings together top names in computational science (chemistry, biology, material science and engineering, etc), key industry analysts and IT practitioners in panel discussions, talks, demonstrations and poster sessions. Detailed agenda can be found at the following URL: http://www.accelrys.com/accelrysworld/agenda.html . The conference is now open for poster submissions. Please use http://www.accelrys.com/accelrysworld/poster_submission.php to submit posters (with 150 word abstracts): The deadline for submitting posters is Thursday February 12, 2004. --=_alternative 005EC29E88256E2E_= Content-Type: text/html; charset="US-ASCII"
Dear CCLers:

The 2nd AccelrysWorld conference on scientific software and IT, will be held at the Hotel del Coronado, San Diego, California, March 8-10, 2004 (http://www.accelrys.com/accelrysworld/). AccelrysWorld is an international event for anyone with an interest in software solutions to enable R&D. It brings together top names in computational science (chemistry, biology, material science and engineering, etc), key industry analysts and IT practitioners in panel discussions, talks, demonstrations and poster sessions.  Detailed agenda can be found at the following URL: http://www.accelrys.com/accelrysworld/agenda.html .  The conference is now open for poster submissions.  

Please use http://www.accelrys.com/accelrysworld/poster_submission.php  to submit posters (with 150 word abstracts):

The deadline for submitting posters is Thursday February 12, 2004.

--=_alternative 005EC29E88256E2E_=-- From chemistry-request@ccl.net Mon Feb 2 07:51:17 2004 Received: from smtp02.syd.iprimus.net.au (smtp02.syd.iprimus.net.au [210.50.76.52]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i12CpFU6003363 for >ccl.net>; Mon, 2 Feb 2004 07:51:16 -0500 Received: from megatron.roach (210.50.178.9) by smtp02.syd.iprimus.net.au (7.0.024) id 40114644002E139E for chemistry<>ccl.net; Mon, 2 Feb 2004 23:54:52 +1100 Date: Mon, 2 Feb 2004 23:53:10 +1100 From: Alex Sutcliffe >iprimus.com.au> To: chemistry<>ccl.net Subject: using DOCK without sybil Message-Id: <20040202235310.20e965e2.a_sutcliffe<>iprimus.com.au> X-Mailer: Sylpheed version 0.9.7 (GTK+ 1.2.10; i386-pc-linux-gnu) Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=0.0 required=7.0 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Hi CCLers, I would like to use DOCK but don't have access to sybil. In order to convert my molecules to mol2 format I had hoped to use openbabel to do a simple conversion, however GRID gave me this: Improper ATOM record substructure id for ***** in ./mymolecule.mol2 I do have an example of a molecule in mol2 format that is acceptable which I intend to compare with mymolecule with but I just thought that someone else had probably been down this road already. Any much appreciated! Alex Sutcliffe From chemistry-request@ccl.net Mon Feb 2 17:44:47 2004 Received: from Post-Office.UH.EDU (Post-Office.UH.EDU [129.7.1.20]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i12MikU6020054 for ; Mon, 2 Feb 2004 17:44:46 -0500 Received: from 129-7-239-124.dhcp.UH.EDU (129-7-239-124.dhcp.UH.EDU [129.7.239.124]) by Post-Office.UH.EDU (PMDF V6.0-025 #30599) with ESMTP id <0HSH01CSZB9JO3(at)Post-Office.UH.EDU> for chemistry(at)ccl.net; Mon, 02 Feb 2004 16:46:31 -0600 (CST) Date: Mon, 02 Feb 2004 16:46:14 -0600 From: Jerry Ebalunode Subject: Re: CCL:using DOCK without sybil In-reply-to: <20040202235310.20e965e2.a_sutcliffe(at)iprimus.com.au> To: Alex Sutcliffe , chemistry(at)ccl.net Reply-to: jebalunode(at)UH.EDU Message-id: <200402021646.15058.jebalunode(at)uh.edu> Organization: University of Houston MIME-version: 1.0 Content-type: text/plain; charset=iso-8859-1 Content-transfer-encoding: 7bit Content-disposition: inline User-Agent: KMail/1.5.4 References: <20040202235310.20e965e2.a_sutcliffe(at)iprimus.com.au> X-Spam-Status: No, hits=0.0 required=7.0 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net if you are using DOCK version 4, you definitely need to set the substructure record for each ligand molecule entry in your mol2 file. To get this done automatically, I modified a version of the OELIB program from openeye scientific. You need to modify the mol2.cpp file in oelib source codes to automate this changes. If you are running your babel conversion calculations on a pentium4 linux station, I could send you a copy of the oelib binary, since this under GPL. Note openbabel is a succesor of oelib. On Monday 02 February 2004 06:53 am, Alex Sutcliffe wrote: > Hi CCLers, > > I would like to use DOCK but don't have access to sybil. In order to > convert my molecules to mol2 format I had hoped to use openbabel to do a > simple conversion, however GRID gave me this: > > Improper ATOM record substructure id for ***** in ./mymolecule.mol2 > > I do have an example of a molecule in mol2 format that is acceptable which > I intend to compare with mymolecule with but I just thought that someone > else had probably been down this road already. > > Any much appreciated! > > Alex Sutcliffe > > > > -= This is automatically added to each message by the mailing script =- > To send e-mail to subscribers of CCL put the string CCL: on your Subject: > line and send your message to: CHEMISTRY(at)ccl.net > > Send your subscription/unsubscription requests to: > CHEMISTRY-REQUEST(at)ccl.net HOME Page: http://www.ccl.net | Jobs Page: > http://www.ccl.net/jobs > > If your mail is bouncing from CCL.NET domain send it to the maintainer: > Jan Labanowski, jlabanow(at)nd.edu (read about it on CCL Home Page) > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ -- Cheers, Jerry Ebalunode Graduate Research Assistant RM 402F Houston Science Center Phone: 713-743-8367 Dept. of Biology and Biochemistry University of Houston 4800 Calhoun Road Houston, TX 77204 From chemistry-request@ccl.net Mon Feb 2 17:54:54 2004 Received: from Post-Office.UH.EDU (NS3.UH.EDU [129.7.1.20]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i12MsrU6020190 for ; Mon, 2 Feb 2004 17:54:53 -0500 Received: from 129-7-239-124.dhcp.UH.EDU (129-7-239-124.dhcp.UH.EDU [129.7.239.124]) by Post-Office.UH.EDU (PMDF V6.0-025 #30599) with ESMTP id <0HSH01C6DBQDKU(at)Post-Office.UH.EDU> for chemistry(at)ccl.net; Mon, 02 Feb 2004 16:56:37 -0600 (CST) Date: Mon, 02 Feb 2004 16:56:21 -0600 From: Jerry Ebalunode Subject: Re: CCL:dock5? In-reply-to: <200402021544.i12Fi5vS243397(at)ds10.itodys.jussieu.fr> To: Michel Petitjean , chemistry(at)ccl.net Reply-to: jebalunode(at)UH.EDU Message-id: <200402021656.21019.jebalunode(at)uh.edu> Organization: University of Houston MIME-version: 1.0 Content-type: text/plain; charset=iso-8859-1 Content-transfer-encoding: 7bit Content-disposition: inline User-Agent: KMail/1.5.4 References: <200402021544.i12Fi5vS243397(at)ds10.itodys.jussieu.fr> X-Spam-Status: No, hits=0.0 required=7.0 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net You could use the DMS program from UCSF. It is an open source program for computing molecular surfaces. However, you need to compile this against some molecule type libraries which are also available as open source from UCSF. Below is the link. http://www.cgl.ucsf.edu/Overview/software.html#dms On Monday 02 February 2004 09:44 am, Michel Petitjean wrote: > To: chemistry(at)ccl.net > Subject: CCL:dock5? > > Surface computation: submit the mol2 file to the freeware ASV. > Programme and documentation with reference: > http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html#ASV > > Michel Petitjean, Email: petitjean(at)itodys.jussieu.fr > ITODYS (CNRS, UMR 7086) ptitjean(at)ccr.jussieu.fr > http://petitjeanmichel.free.fr/itoweb.petitjean.html > > >...................................................................... > > Gyanendra Kumar wrote: > Dear CCLers, > I have just installed Dock5 on my linux machine. And I have ligand and > receptor files in mol2 format with charges assigned. > How do we calculate molecular surface for the receptor. The one program > mentioned in the manual - MS is not a freeware. Are there any free > programs for generating molecular surface of proteins which can be used > with Dock5. > > Sincerely, > Gyan. > > > -= This is automatically added to each message by the mailing script =- > To send e-mail to subscribers of CCL put the string CCL: on your Subject: > line and send your message to: CHEMISTRY(at)ccl.net > > Send your subscription/unsubscription requests to: > CHEMISTRY-REQUEST(at)ccl.net HOME Page: http://www.ccl.net | Jobs Page: > http://www.ccl.net/jobs > > If your mail is bouncing from CCL.NET domain send it to the maintainer: > Jan Labanowski, jlabanow(at)nd.edu (read about it on CCL Home Page) > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ -- Cheers, Jerry Ebalunode Graduate Research Assistant RM 402F Houston Science Center Phone: 713-743-8367 Dept. of Biology and Biochemistry University of Houston 4800 Calhoun Road Houston, TX 77204 From chemistry-request@ccl.net Mon Feb 2 18:13:17 2004 Received: from smtp.cnc.com (smtp.chemnavigator.com [12.22.207.36]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i12NDGU6020796 for ; Mon, 2 Feb 2004 18:13:16 -0500 Received: by smtp.chemnavigator.com with Internet Mail Service (5.5.2653.19) id ; Mon, 2 Feb 2004 14:58:06 -0800 Message-ID: <2B0CF44FC7E8D3118B4900508BA599EF015569B6(at)smtp.chemnavigator.com> From: Duncan Beniston To: "'CHEMISTRY(at)ccl.net'" Subject: CCL:Rapid Database Docking System - 3-DPL Map - Now Available Date: Mon, 2 Feb 2004 14:58:05 -0800 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-Type: text/plain; charset="iso-8859-1" X-Spam-Status: No, hits=0.0 required=7.0 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Dear CCLers: ChemNavigator is pleased to announce the availability of its patented 3-Dimensional Protein - Ligand Docking System (3-DPL Map) for rapid, flexible docking of millions of drug-like molecules to a 3D protein target. 3-DPL Map combines the concepts of "directed tweak" conformational flexing with a patented strategy of pre-calculating derivative field grids. These derivative fields enable the rapid calculation of energy scores. This approach allows 3-DPL to analyze up to 15 flexible structures per second per CPU while also addressing multiple binding sites on the protein. 3-DPL has three major advantages over current technologies: 1. Knowledge of Active Site Not Required: 3-DPL includes an automated site detection method called the Convex Hull Method. This method automatically determines all potential binding regions on the protein surface as well as initial starting position parameters for each ligand. 3-DPL Map analyzes each small molecule at all potential binding sites on the 3-D protein surface and avoids the need for active site pre-definition. 2. Automatic Conformational Analysis: Each small molecule ligand is flexed and re-oriented thousands of times "on the fly" in the search for potential matches between the ligand and the protein surface. 3-DPL Map employs a unique and patented derivative field grid to direct small molecules to favorable binding conformations. 3. Speed Enables in silico Screening of Millions of Small Molecules: Running on a single 1.4GHz Windows server, 3-DPL is able to evaluate over 8 million flexible chemical structures for binding across all potential sites on the protein surface in less than 4 days. For more information on 3-DPL Map and to request an evaluation, please contact Duncan Beniston at ChemNavigator. Duncan Beniston Director of Business Development ChemNavigator dbeniston(at)chemnavigator.com +858-450-9740 From chemistry-request@ccl.net Mon Feb 2 19:42:43 2004 Received: from pickering.cc.nd.edu (pickering.cc.nd.edu [129.74.250.225]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i130ggU6022960 for ; Mon, 2 Feb 2004 19:42:42 -0500 Received: from localhost (localhost [127.0.0.1]) by pickering.cc.nd.edu (Switch-3.1.3/Switch-3.1.0) with ESMTP id i130iuo6011260 for ; Mon, 2 Feb 2004 19:44:56 -0500 (EST) Received: from 129.74.52.62 ([129.74.52.62]) by webmail.nd.edu (IMP) with HTTP for ; Mon, 2 Feb 2004 19:44:56 -0500 Message-ID: <1075769096.401eef0883e09:at:webmail.nd.edu> Date: Mon, 2 Feb 2004 19:44:56 -0500 From: "Jan K. Labanowski" To: chemistry:at:ccl.net Subject: MGMS 2004 International Meeting (Sept 7-10, 2004; Manchester, UK) MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit User-Agent: Internet Messaging Program (IMP) 3.2.2 X-Originating-IP: 129.74.52.62 X-ND-MTA-Date: Mon, 02 Feb 2004 19:44:57 -0500 (EST) X-ND-Virus-Scan: engine v4.2.40; dat v4321 X-Spam-Status: No, hits=0.0 required=7.0 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net ----- Forwarded message from Richard A Bryce ----- Date: Mon, 2 Feb 2004 16:06:11 -0000 CONFERENCE ANNOUNCEMENT (first circular) Towards Accurate Calculation of Biomolecular Recognition and Reactivity MGMS 2004 International Meeting University of Manchester, UK 7th-10th September 2004 This conference will be held in honour of Professor Ian Hillier. For more details, please see the conference website at http://pharmacy.man.ac.uk/rab/mgms CONFIRMED SPEAKERS FE Blaney (GlaxoSmithKline) Q Cui (Wisconsin) PM Dean (De Novo Pharmaceuticals) MJ Field (CNRS, Grenoble) J Gao (Minnesota) RC Glen (Cambridge) J Goodfellow (Birkbeck) DVS Green (GlaxoSmithKline) N Gresh (CNRS, Paris) M Guest (Daresbury) WF Van Gunsteren (ETH Zurich) MB Hall (Texas A&M) IH Hillier (Manchester) WL Jorgensen (Yale) R Lavery (Paris) J Naismith (St. Andrews) PLA Popelier (UMIST) C Reynolds (Essex) WG Richards (Oxford) M Stahl (Roche) RC Wade (Heidelberg) B Waskowycz (Tularik) ______________________________________________________ Richard A. Bryce School of Pharmacy and Pharmaceutical Sciences, University of Manchester, Manchester, M13 9PL, U.K. Tel:(+44) (0)161 275 8345 Fax: (+44) (0)161 275 2481 http://pharmacy.man.ac.uk/rab R.A.Bryce:at:man.ac.uk ______________________________________________________ From chemistry-request@ccl.net Mon Feb 2 19:43:57 2004 Received: from Post-Office.UH.EDU (NS3.UH.EDU [129.7.1.20]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i130hvU6023015 for ; Mon, 2 Feb 2004 19:43:57 -0500 Received: from nyssa.bchs.uh.edu (Nyssa.BCHS.UH.EDU [129.7.238.204]) by Post-Office.UH.EDU (PMDF V6.0-025 #30599) with ESMTP id <0HSH02B7RGSFIU:at:Post-Office.UH.EDU> for chemistry:at:ccl.net; Mon, 02 Feb 2004 18:45:51 -0600 (CST) Date: Mon, 02 Feb 2004 18:56:49 -0600 From: Jerry Ebalunode Subject: Re: CCL:using DOCK without sybil In-reply-to: <414DD173-55DC-11D8-8CB9-000A9579AE94:at:csiro.au> To: Kim Branson Cc: chemistry:at:ccl.net Reply-to: jebalunode:at:UH.EDU Message-id: <200402021856.49304.jebalunode:at:uh.edu> Organization: University of Houston MIME-version: 1.0 Content-type: text/plain; charset=iso-8859-1 Content-disposition: inline User-Agent: KMail/1.5.4 References: <200402021646.15058.jebalunode:at:uh.edu> <414DD173-55DC-11D8-8CB9-000A9579AE94:at:csiro.au> X-Spam-Status: No, hits=0.0 required=7.0 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id i130hwU6023019 First of all this works with Oelib source code, which is a C++ source code. I haven't attempted this on the Babel since it is coded in C. You could get Oelib for free at openeye scientific site at ftp://ftp.eyesopen.com/pub/oelib/oelib.tgz the C++ source file to modify is mol2.cpp You need to modify lines 204 to reflect recording of the number of substructures for each ligand in the mol2 database in this case I use 1 following the example decribed somewhere in the dock manual. Then on line 276 the additional lines provides the actual substructure entry required by DOCK4. However note that for DOCK5 you could still do your docking without any of these entries to your database mol2 file. here is the "diff" between the old and modified mol2.cpp, it should be sufficient. The changes apply to the write section of mol2.cpp. 204c204 < sprintf(buffer, " %d %d 0 0 0", mol.NumAtoms(), mol.NumBonds()); --- > sprintf(buffer, " %d %d 1 0 0", mol.NumAtoms(), mol.NumBonds()); 276c276,277 < --- > ofs << "@SUBSTRUCTURE" << oeendl; > ofs << " 1 **** 1 TEMP 0 **** **** 0 ROOT " << oeendl; On Monday 02 February 2004 06:02 pm, Kim Branson wrote: > hi jerry, > > i'd be keen to add this to babel. can you post your changes or make a > patch file? > cheers > > Kim > > On 03/02/2004, at 9:46 AM, Jerry Ebalunode wrote: > > if you are using DOCK version 4, you definitely need to set the > > substructure > > record for each ligand molecule entry in your mol2 file. To get this > > done > > automatically, I modified a version of the OELIB program from openeye > > scientific. You need to modify the mol2.cpp file in oelib source codes > > to > > automate this changes. If you are running your babel conversion > > calculations > > on a pentium4 linux station, I could send you a copy of the oelib > > binary, > > since this under GPL. Note openbabel is a succesor of oelib. > > > > On Monday 02 February 2004 06:53 am, Alex Sutcliffe wrote: > > > Hi CCLers, > > > > > > I would like to use DOCK but don't have access to sybil. In order to > > > convert my molecules to mol2 format I had hoped to use openbabel to > > > > do a > > > > > simple conversion, however GRID gave me this: > > > > > > Improper ATOM record substructure id for ***** in ./mymolecule.mol2 > > > > > > I do have an example of a molecule in mol2 format that is acceptable > > > > which > > > > > I intend to compare with mymolecule with but I just thought that > > > > someone > > > > > else had probably been down this road already. > > > > > > Any much appreciated! > > > > > > Alex Sutcliffe > > > > > > > > > > > > To send e-mail to subscribers of CCL put the string CCL: on your > > > > Subject: > > > Send your subscription/unsubscription requests to: > > > CHEMISTRY-REQUEST:at:ccl.net HOME Page:http://www.ccl.net | Jobs Page: > > >http://www.ccl.net/jobs > > > > -- > > Cheers, > > > > Jerry Ebalunode > > Graduate Research Assistant > > RM 402F Houston Science Center > > Phone: 713-743-8367 > > Dept. of Biology and Biochemistry > > University of Houston > > 4800 Calhoun Road > > Houston, TX 77204 > > > > > > > > > > -= This is automatically added to each message by the mailing script =- > > To send e-mail to subscribers of CCL put the string CCL: on your > > Subject: line > > and send your message to: CHEMISTRY/at/ccl.net > > > > Send your subscription/unsubscription requests to: > > CHEMISTRY-REQUEST/at/ccl.net > > HOME Page:http://www.ccl.net | Jobs Page:http://www.ccl.net/jobs > > > > If your mail is bouncing from CCL.NET domain send it to the maintainer: > > Jan Labanowski, jlabanow/at/nd.edu (read about it on CCL Home Page) > > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+- > > +-+ -- Cheers, Jerry Ebalunode Graduate Research Assistant RM 402F Houston Science Center Phone: 713-743-8367 Dept. of Biology and Biochemistry University of Houston. 4800 Calhoun Road Houston, TX 77204