From chemistry-request@ccl.net Tue Jun 22 17:57:27 2004 Received: from smtp2.es.uci.edu (smtp2.es.uci.edu [128.200.80.5]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i5MMvQMk027261 for ; Tue, 22 Jun 2004 17:57:26 -0500 Received: from frenkel.ps.uci.edu (frenkel.ps.uci.edu [128.200.11.119]) by smtp2.es.uci.edu (8.12.8/8.12.8) with ESMTP id i5MN24Pu018980 for ; Tue, 22 Jun 2004 16:02:06 -0700 Content-Type: text/plain; charset="us-ascii" From: wei Reply-To: weiz:at:mail.rochester.edu Organization: university of california at Irvine To: chemistry:at:ccl.net Subject: charmm parameters for the non-neutral residues. Date: Tue, 22 Jun 2004 16:00:31 -0400 User-Agent: KMail/1.4.1 MIME-Version: 1.0 Message-Id: <200406221600.31561.wzhuang:at:uci.edu> X-NACS_ES-MailScanner: No viruses found X-Spam-Status: No, hits=0.7 required=7.5 tests=DATE_IN_PAST_03_06 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 i5MMvRMk027270 Dear Charmm: I am simulating the dynamics of a small protein, it has some non-neutral residues like ARG ,ASP ...etc. for some reason I want them to be neutral. I noticed that for HIS,you can choose its neutral form. can I find the similar thing for other non-neutral residues? Wei From chemistry-request@ccl.net Tue Jun 22 20:22:43 2004 Received: from gothmog.gpcc.itd.umich.edu (gothmog.gpcc.itd.umich.edu [141.211.2.180]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i5N1MgMk010835 for ; Tue, 22 Jun 2004 20:22:42 -0500 Received: from tetris.gpcc.itd.umich.edu (tetris.gpcc.itd.umich.edu [141.211.2.208]) by gothmog.gpcc.itd.umich.edu (8.9.3p2/4.3-mailhub) with ESMTP id VAA07193 for ; Tue, 22 Jun 2004 21:27:31 -0400 (EDT) Received: from localhost (weishi@localhost) by tetris.gpcc.itd.umich.edu (8.9.3p2/5.1-client) with ESMTP id VAA02828 for ; Tue, 22 Jun 2004 21:27:30 -0400 (EDT) Precedence: first-class Date: Tue, 22 Jun 2004 21:27:30 -0400 (EDT) From: Wei Shi X-X-Sender: weishi$at$tetris.gpcc.itd.umich.edu To: chemistry$at$ccl.net Subject: protein cross the boundary of the box in PBC Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Spam-Status: No, hits=0.0 required=7.5 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 CHARMmers, I am planning to do MD simulations for a pretty large system. The system is composed of several protein molecules. I want to apply periodic boundary condition in the Z direction for the system. However, one of the protein will cross the boundary of the PBC box I am going to use. How does the CHARMm (academic cersion) deal with this kind of probelm? Can I just simply truncate the part out of the primary box and put it back into the image position in the primary box? Based on my experience for small molecule simulations, this needs carefulness to deal with the inter and intra interactions. I am not sure how CHARMm deal with it. Thanks for all your experts help, Wei Shi From chemistry-request@ccl.net Wed Jun 23 06:59:15 2004 Received: from srv2.cyf-kr.edu.pl (srv2.cyf-kr.edu.pl [149.156.2.15]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i5NBxElW031798 for ; Wed, 23 Jun 2004 06:59:14 -0500 Received: from kinga.cyf-kr.edu.pl (kinga.cyf-kr.edu.pl [149.156.2.32]) by srv2.cyf-kr.edu.pl (8.12.8/8.12.8) with ESMTP id i5NC4384008922; Wed, 23 Jun 2004 14:04:03 +0200 Received: (from mykrol@localhost) by kinga.cyf-kr.edu.pl (8.12.11/8.12.11/Submit) id i5NC3dbd023842; Wed, 23 Jun 2004 14:03:39 +0200 (METDST) Date: Wed, 23 Jun 2004 14:03:39 +0200 (METDST) From: Marcin Krol To: wei cc: chemistry~at~ccl.net Subject: Re: CCL:charmm parameters for the non-neutral residues. In-Reply-To: <200406221600.31561.wzhuang~at~uci.edu> Message-ID: References: <200406221600.31561.wzhuang~at~uci.edu> MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Spam-Status: No, hits=0.0 required=7.5 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 I think, EEF1 parameter set uses neutralized residues to account for screening of charges. You can look into test/data/toph19_eef1.inp there are parameters for neutralized AA, but this is polar hydrogen FF only and I don't know if you can use it in non-EEF1 simulations, you must check if other paranters (for other AA) are not different. Best marcin > Dear Charmm: I am simulating the dynamics of a small protein, it has > some non-neutral residues like ARG ,ASP ...etc. for some reason I want > them to be neutral. I noticed that for HIS,you can choose its neutral > form. can I find the similar thing for other non-neutral residues? > > > Wei > > > > -= 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) > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > > From chemistry-request@ccl.net Wed Jun 23 06:24:31 2004 Received: from up.univ-mrs.fr (mailup.univ-mrs.fr [147.94.113.16]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i5NBOSlW030653 for ; Wed, 23 Jun 2004 06:24:28 -0500 Received: from localhost (localhost [127.0.0.1]) by up.univ-mrs.fr (Postfix) with ESMTP id AFDB41F7187; Wed, 23 Jun 2004 13:26:18 +0200 (CEST) Received: from up.univ-mrs.fr ([127.0.0.1]) by localhost (mailup.univ-mrs.fr [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id 210979-01; Wed, 23 Jun 2004 13:26:17 +0200 (CEST) Received: from up.univ-mrs.fr (unknown [147.94.185.160]) by up.univ-mrs.fr (Postfix) with ESMTP id 3A8DD1F0C46; Wed, 23 Jun 2004 13:26:17 +0200 (CEST) Message-ID: <40D96936.1090707~at~up.univ-mrs.fr> Date: Wed, 23 Jun 2004 13:27:50 +0200 From: =?ISO-8859-1?Q?Nicolas_Ferr=E9?= Organization: LCTMM User-Agent: Mozilla/5.0 (X11; U; Linux i686; fr-FR; rv:1.6) Gecko/20040113 X-Accept-Language: fr-fr, en-us, en MIME-Version: 1.0 To: Kadir Diri Cc: caroline taylor , CCL list Subject: Re: CCL:ifc8.0 error References: <40D7DB16.3090001~at~visual1.chem.pitt.edu> In-Reply-To: <40D7DB16.3090001~at~visual1.chem.pitt.edu> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 8bit X-Virus-Scanned: by amavisd-new at up.univ-mrs.fr X-Spam-Status: No, hits=4.0 required=7.5 tests=NO_RDNS,NO_RDNS2,RM_ft_Iso8859 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, actually a script exists to source the ifc8.0 environment: /opt/intel_fc_8.0/bin/ifortvars.sh or iccvars.sh. By the way, the fortran compiler is named ifort now. Hope this helps. Nicolas Kadir Diri a icrit : > Hi! This looks like a simple path problem, but in that case the Intel > people would probably catch it immediately. Is /opt/intel_fc_80/lib/ in > your path? Make sure it is, when you run your executable. Is > $LD_LIBRARY_PATH defined in your login shell profile file, or do you at > least define this variable before running your executable? > kadir > > > caroline taylor wrote: > >>Hello, all. >> >>I'm trying to get version 8 of the intel fortran compiler working (ifc7 >>is fine), and everything runs fine if I do a static build of some >>program. The compiler appears to build/install correctly, and will build a >>(dynamic) executable, but I get the following error when I try to run that >>executable: >> >> >> >>>./a.out: error while loading shared libraries: libcxa.so.5: cannot open >>> >>> >>shared object file: No such file or directory >> >> >>The file _is_ in the directory that the compiler looks in: >> >> >>>ls -l /opt/intel_fc_80/lib/ >>> >>> >>-rw-r--r-- 1 root root 229564 Oct 29 2003 libcxa.a >>-rw-r--r-- 1 root root 1052 Oct 29 2003 libcxaguard.a >>-rwxr-xr-x 1 root root 27 Oct 29 2003 libcxaguard.so >>-rwxr-xr-x 1 root root 2496 Oct 29 2003 libcxaguard.so.5 >>-rwxr-xr-x 1 root root 22 Oct 29 2003 libcxa.so >>-rwxr-xr-x 1 root root 172615 Oct 29 2003 libcxa.so.5 >> >>and the $LD_LIBRARY_PATH variable is set correctly in the run scripts >>(this is the only suggestion provided by Intel, and hasn't helped anyone >>else, either). >> >>Does anyone out there have a solution to this? >> >>Thanks in advance!!! >> Caroline >> >>--------------------------------------------- >>Dr. Caroline M. Taylor >>Department of Chemistry >>University of Chicago, James Franck Institute >>5640 S. Ellis Avenue >>Chicago, Illinois 60637 >>(773) 702-7223 >>http://kff1.uchicago.edu/~cmtaylor >>--------------------------------------------- >> >> >> >>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 >> >>Jan Labanowski, jlabanow~at~nd.edu (read about it on CCL Home Page) >> >> >> >> >> >> -- Dr. Nicolas Ferre' Laboratoire de Chimie Theorique et de Modelisation Moleculaire UMR 6517 - CNRS Universite' de Provence Case 521 - Faculte' de Saint-Jerome Av. Esc. Normandie Niemen 13397 MARSEILLE Cedex 20 (FRANCE) Tel : (+33)4.91.28.27.33 Fax : (+33)4.91.28.87.58 Please avoid sending me Word or PowerPoint attachments. See http://www.gnu.org/philosophy/no-word-attachments.html From chemistry-request@ccl.net Wed Jun 23 13:04:24 2004 Received: from glaurung.gpcc.itd.umich.edu (glaurung.gpcc.itd.umich.edu [141.211.2.181]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i5NI4OlW012678 for ; Wed, 23 Jun 2004 13:04:24 -0500 Received: from asteroids.gpcc.itd.umich.edu (asteroids.gpcc.itd.umich.edu [141.211.2.218]) by glaurung.gpcc.itd.umich.edu (8.9.3p2/4.3-mailhub) with ESMTP id OAA23804; Wed, 23 Jun 2004 14:09:12 -0400 (EDT) Received: from localhost (weishi@localhost) by asteroids.gpcc.itd.umich.edu (8.9.3p2/5.1-client) with ESMTP id OAA18816; Wed, 23 Jun 2004 14:09:11 -0400 (EDT) Precedence: first-class Date: Wed, 23 Jun 2004 14:09:11 -0400 (EDT) From: Wei Shi X-X-Sender: weishi-.at.-asteroids.gpcc.itd.umich.edu To: Rick Venable cc: chemistry-.at.-ccl.net Subject: Re: CCL:protein cross the boundary of the box in PBC In-Reply-To: Message-ID: References: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, Rick, Thanks for your help. All the best, Wei Shi On Wed, 23 Jun 2004, Rick Venable wrote: > First, I'd like to suggest using the CHARMM discussion Forums at > www.charmm.org; people from several of the development groups regularly > read and answer posts, and the message threads are searchable. > > N.B. CHARMM == academic, CHARMm == commercial > > There's an arcane feature known as image patching (IMPATCH; see > images.doc) which allows creating a bond to an image molecule; > historically, I believe DNA simulations were attempted using this. > There are a number of restrictions and requirements: > > [1] IMAGE facility only, not CRYSTal > [2] must create the image patch > [3] must account for ANGLE, DIHEDRAL terms in the patch > [4] must prepare image transformation list > [5] cannot use Ewald or CPT methods (both require CRYSTal) > > > On Tue, 22 Jun 2004, Wei Shi wrote: > > I am planning to do MD simulations for a pretty large system. The > > system is composed of several protein molecules. I want to apply > > periodic boundary condition in the Z direction for the system. > > However, one of the protein will cross the boundary of the PBC box I > > am going to use. How does the CHARMm (academic cersion) deal with this > > kind of probelm? Can I just simply truncate the part out of the > > primary box and put it back into the image position in the primary > > box? Based on my experience for small molecule simulations, this needs > > carefulness to deal with the inter and intra interactions. I am not > > sure how CHARMm deal with it. > > > =+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+= > Rick Venable 29/500 > FDA/CBER/OVRR Biophysics Lab > 1401 Rockville Pike HFM-419 > Rockville, MD 20852-1448 U.S.A. > (301) 496-1905 Rick_Venable-.at.-nih.gov > ALT email: rvenable-.at.-speakeasy.org > ------------------------------------- > "Don't blame me, I voted for Kang." > Homer > =+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+= > From chemistry-request@ccl.net Wed Jun 23 09:57:39 2004 Received: from mail.ic.sunysb.edu (mail.ic.sunysb.edu [129.49.1.4]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i5NEvclW005743 for ; Wed, 23 Jun 2004 09:57:38 -0500 Received: from postal.ic.sunysb.edu (mail [129.49.1.4]) by mail.ic.sunysb.edu (8.12.10/8.12.10) with SMTP id i5NF2Kjh019060; Wed, 23 Jun 2004 11:02:25 -0400 (EDT) Received: from smtp.ic.sunysb.edu ([129.49.1.24]) by postal.ic.sunysb.edu (SAVSMTP 3.1.5.43) with SMTP id M2004062311022515481 ; Wed, 23 Jun 2004 11:02:25 -0400 Received: from sparky.ic.sunysb.edu (sparky.ic.sunysb.edu [129.49.1.3]) by smtp.ic.sunysb.edu (8.12.10/8.12.10) with ESMTP id i5NF2P7Q019104; Wed, 23 Jun 2004 11:02:25 -0400 (EDT) Received: from localhost (yonyang@localhost) by sparky.ic.sunysb.edu (8.12.10/8.12.9) with ESMTP id i5NF2Pv1007934; Wed, 23 Jun 2004 11:02:25 -0400 (EDT) Date: Wed, 23 Jun 2004 11:02:25 -0400 (EDT) From: Yong Liang Yang To: chemistry:at:ccl.net cc: zliang:at:cs.sunysb.edu Subject: Mopac7 under IRIX Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed X-Spam-Status: No, hits=3.0 required=7.5 tests=NO_RDNS2 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 CCL users: I tried to compile mopac7 under IRIX6.5 using GCC compiler, however I always get the error message as below: **Error code 1 (bug 21) Too many arguments passed to intrinsic 'SECOND' at (^) ---------------------------------- The commnad line in Makefile is as below: g77 -w -O -static *.f -o $(EXE) Does anybody know how to fix this bug? I downloaed the binary from Webmo website. Any suggestion is highly appreciated. Thanks in advance. Cheers Yong.LY. Stony Brook --------------------- From chemistry-request@ccl.net Wed Jun 23 09:58:23 2004 Received: from mm02snlnto.son.sandia.gov (mm02snlnto.sandia.gov [132.175.109.21]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i5NEwMlW005781 for ; Wed, 23 Jun 2004 09:58:22 -0500 Received: from 132.175.109.1 by mm02snlnto.son.sandia.gov with ESMTP ( Tumbleweed MMS SMTP Relay 01 (MMS v5.6.1)); Wed, 23 Jun 2004 09:03:02 -0600 X-Server-Uuid: 8A37177F-35F9-47CF-80CF-3627B2E578DE Received: from sandia.gov (s848769.sandia.gov [134.253.246.160]) by sass165.sandia.gov (8.12.10/8.12.10) with ESMTP id i5NF31vE007055 for ; Wed, 23 Jun 2004 09:03:01 -0600 (MDT) Date: Wed, 23 Jun 2004 09:03:28 -0600 MIME-Version: 1.0 Subject: parameter files for pm5 or pm3(tm) From: "Rick Muller" To: chemistry/at/ccl.net Message-ID: <7BF3ACE3-C526-11D8-BB77-000A95823962/at/sandia.gov> X-Mailer: Apple Mail (2.553) X-PMX-Version: 4.6.0.99824, Antispam-Core: 4.6.0.101390, Antispam-Data: 2004.6.22.104791 X-WSS-ID: 6CC7442C1CW215145-01-01 Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=0.0 required=7.5 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 Can anyone point me to parameter files for pm5 or pm3(tm) suitable for using in mopac7 via the EXTERNAL flag? Thanks in advance. Rick Muller rmuller/at/sandia.gov From chemistry-request@ccl.net Wed Jun 23 12:17:26 2004 Received: from mx5.net.nih.gov (mailfwd.nih.gov [165.112.130.36]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i5NHHPlW011245 for ; Wed, 23 Jun 2004 12:17:25 -0500 Received: from mx5.net.nih.gov (localhost [127.0.0.1]) by mx5.net.nih.gov (8.12.10/8.12.8p1) with ESMTP id i5NHMGqB023480 for ; Wed, 23 Jun 2004 13:22:16 -0400 Received: from pollux.cber.nih.gov (pollux.cber.nih.gov [128.231.52.5]) by mx5.net.nih.gov (8.12.10/8.12.8p1) with ESMTP id i5NHMEd3023446; Wed, 23 Jun 2004 13:22:14 -0400 Date: Wed, 23 Jun 2004 13:22:00 -0400 From: Rick Venable To: Wei Shi cc: chemistry^at^ccl.net Subject: Re: CCL:protein cross the boundary of the box in PBC In-Reply-To: Message-ID: References: ReplyTo: Rick_Venable^at^nih.gov MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Spam-Status: No, hits=0.0 required=7.5 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 First, I'd like to suggest using the CHARMM discussion Forums at www.charmm.org; people from several of the development groups regularly read and answer posts, and the message threads are searchable. N.B. CHARMM == academic, CHARMm == commercial There's an arcane feature known as image patching (IMPATCH; see images.doc) which allows creating a bond to an image molecule; historically, I believe DNA simulations were attempted using this. There are a number of restrictions and requirements: [1] IMAGE facility only, not CRYSTal [2] must create the image patch [3] must account for ANGLE, DIHEDRAL terms in the patch [4] must prepare image transformation list [5] cannot use Ewald or CPT methods (both require CRYSTal) On Tue, 22 Jun 2004, Wei Shi wrote: > I am planning to do MD simulations for a pretty large system. The > system is composed of several protein molecules. I want to apply > periodic boundary condition in the Z direction for the system. > However, one of the protein will cross the boundary of the PBC box I > am going to use. How does the CHARMm (academic cersion) deal with this > kind of probelm? Can I just simply truncate the part out of the > primary box and put it back into the image position in the primary > box? Based on my experience for small molecule simulations, this needs > carefulness to deal with the inter and intra interactions. I am not > sure how CHARMm deal with it. =+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+= Rick Venable 29/500 FDA/CBER/OVRR Biophysics Lab 1401 Rockville Pike HFM-419 Rockville, MD 20852-1448 U.S.A. (301) 496-1905 Rick_Venable^at^nih.gov ALT email: rvenable^at^speakeasy.org ------------------------------------- "Don't blame me, I voted for Kang." Homer =+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+= From chemistry-request@ccl.net Wed Jun 23 10:04:55 2004 Received: from camdmail01.cam.accelrys.com (gate1.cam.accelrys.com [212.44.43.190]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i5NF4slW005991 for ; Wed, 23 Jun 2004 10:04:54 -0500 To: chemistry)at(ccl.net Subject: Pharmacophore Datamining Competition MIME-Version: 1.0 X-Mailer: Lotus Notes Release 6.0.1 February 07, 2003 Message-ID: From: Katalin Nadassy Date: Wed, 23 Jun 2004 16:09:43 +0100 X-MIMETrack: Serialize by Router on camdmail01/Server/Accelrys(Release 6.0.2CF1|June 9, 2003) at 23/06/2004 15:09:45, Serialize complete at 23/06/2004 15:09:45 Content-Type: multipart/alternative; boundary="=_alternative 005349BD80256EBC_=" X-Spam-Status: No, hits=0.3 required=7.5 tests=HTML_MESSAGE,MK_BAD_HTML_04 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 005349BD80256EBC_= Content-Type: text/plain; charset="US-ASCII" Dear CCL members, Accelrys is delighted to invite you to participate in our first Pharmacophore Datamining Competition in 2004. This is a competition for Catalyst users to develop a pharmacophore best able to retrieve a subset of known actives from a database, given an initial dataset. Our ambition is to challenge you to explore new ideas and directions in the arena of pharmacophore perception and design. Our hope is that this will be a springboard to a broader competition encompassing all methods and avenues of datamining. More information about the competition can be found at the following URL http://www.accelrys.com/usergroups/catalyst/2004/eu/competition/details.html Prize winning entries will be made publicly available on our webpages at the conclusion of the competition. We invite you to take part in this challenge and look forward to the great pharmacophore models derived from this competition. For any further questions or comments please contact pharmacophore)at(accelrys.com --=_alternative 005349BD80256EBC_= Content-Type: text/html; charset="US-ASCII"

Dear CCL members,

Accelrys is delighted to invite you to participate in our first Pharmacophore Datamining Competition in 2004.

This is a competition for Catalyst users to develop a pharmacophore best able to retrieve a subset of known actives > from a database, given an initial dataset.

Our ambition is to challenge you to explore new ideas and directions in the arena of pharmacophore perception and design.  Our hope is that this will be a springboard to a broader competition encompassing all methods and avenues of datamining.

More information about the competition can be found at the following URL

http://www.accelrys.com/usergroups/catalyst/2004/eu/competition/details.html

Prize winning entries will be made publicly available on our webpages at the conclusion of the competition.

We invite you to take part in this challenge and look forward to the great pharmacophore models derived from this competition.

For any further questions or comments please contact pharmacophore)at(accelrys.com

--=_alternative 005349BD80256EBC_=-- From chemistry-request@ccl.net Wed Jun 23 10:27:56 2004 Received: from web21508.mail.yahoo.com (web21508.mail.yahoo.com [66.163.169.19]) by server.ccl.net (8.12.8/8.12.8) with SMTP id i5NFRtlW007165 for ; Wed, 23 Jun 2004 10:27:55 -0500 Message-ID: <20040623153245.69923.qmail!at!web21508.mail.yahoo.com> Received: from [147.8.148.109] by web21508.mail.yahoo.com via HTTP; Wed, 23 Jun 2004 08:32:45 PDT Date: Wed, 23 Jun 2004 08:32:45 -0700 (PDT) From: zhao cunyuan Subject: G03-B05/linda parallel for large system and multiple-processors To: chemistry!at!ccl.net MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="0-217673524-1088004765=:66448" X-Spam-Status: No, hits=2.5 required=7.5 tests=HTML_MESSAGE,MK_BAD_HTML_04, MK_YAHOO_REDIR_01,WLS_URI_OPT_150 autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net --0-217673524-1088004765=:66448 Content-Type: text/plain; charset=us-ascii Dear CCLers, I am having some troubles in using many processors, %NProcLinda= 8 or more, for large molecular systems (more than than 60 atoms) for G03/linda. In those cases, only one node work and other nodes assigned to are idle all the time. But for small jobs(less atoms) with less CPU procesors, like %NProcLinda=4 or less, the job is paralleling well. Does anybody have any experience about this G03/linda parallel problem? Our computer system are PC clusters with 128 Dual-Xeon Nodes. The details are shown in the following pages. We are using PBS for job sumitting. http://www.hku.hk/cc_news/ccnews106/hpcpower.htm http://www.hku.hk/cc/ccsystem/hpcpower Thanks in advance. P.S. Our administrator can not solve the problem right now and wish to get a solution from the vendor. Dr. Cunyuan Zhao Department of Chemistry The University of Hong Kong, Hong Kong Email: zhaocy!at!hkucc.hku.hk Tel:(852)2859 8947 --------------------------------- Do you Yahoo!? New and Improved Yahoo! Mail - Send 10MB messages! --0-217673524-1088004765=:66448 Content-Type: text/html; charset=us-ascii
Dear CCLers,

I am having some troubles in using many processors, %NProcLinda= 8 or more,
for large molecular systems (more than than 60 atoms) for G03/linda. In those
cases, only one node work and other nodes assigned to are idle all the time.
But for small jobs(less atoms) with less CPU procesors, like %NProcLinda=4 or
less, the job is paralleling well. Does anybody have any experience about this
G03/linda parallel problem? Our computer system are PC clusters with 128
Dual-Xeon Nodes. The details are shown in the following pages. We are using
PBS for job sumitting.

http://www.hku.hk/cc_news/ccnews106/hpcpower.htm
http://www.hku.hk/cc/ccsystem/hpcpower

Thanks in advance.

P.S. Our administrator can not solve the problem right now and wish to get a
solution from the vendor.

Dr. Cunyuan Zhao
Department of Chemistry
The University of Hong Kong, Hong Kong
Email: zhaocy!at!hkucc.hku.hk
Tel:(852)2859 8947

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New and Improved Yahoo! Mail - Send 10MB messages! --0-217673524-1088004765=:66448-- From chemistry-request@ccl.net Wed Jun 23 15:19:44 2004 Received: from acomp.usf.edu (nova.acomp.usf.edu [131.247.100.22]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i5NKJgkp017136 for ; Wed, 23 Jun 2004 15:19:42 -0500 Received: from [131.247.209.78] (HELO WillsToy) by acomp.usf.edu (CommuniGate Pro SMTP 4.1.5) with ESMTP id 6362122 for chemistry!at!ccl.net; Wed, 23 Jun 2004 16:24:30 -0400 From: "will" To: Subject: hyperchem in tandem with autodock Date: Wed, 23 Jun 2004 16:24:20 -0400 Message-ID: <036401c45960$14001a20$4ed1f783@WillsToy> MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0365_01C4593E.8CEE7A20" X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook, Build 10.0.2616 Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1409 X-Spam-Status: No, hits=2.2 required=7.5 tests=HTML_60_70,HTML_MESSAGE, NO_EXPERIENCE 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 multi-part message in MIME format. ------=_NextPart_000_0365_01C4593E.8CEE7A20 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit I'm a biochemistry grad student who has recently been given the task of learning basic molecular modeling independently. I have learned the basics of hyperchem and autodock, and, having no experience in computational chemistry, have blindly moved forward and my dockings. It was recently suggested to me that although hyperchem can be used to find docking/binding energies through geometry optimizations, I should just use it to assign charges to my substrates (which are rather small 10-15 C) and use these substrates for my autodock dockings. However, I was under the impression that charges were assigned through autodock without having to use hyperchem. Please correct me if I'm wrong. Also, .hin files are not compatible with autodock and must somehow be converted to .pdbq files if this method is indeed useful. I've found a python script hin2pdbq.py, but don't know how to use it since I have no real knowledge of how to use linux/python. I managed to get autodock up and running on cygwin with some help from the members of this board (thanks). Any input would be greatly appreciated. On a side note, I'm very interested in learning how to screen a database of possible substrate/inhibitors with autodock. I have no idea if an additional program is needed or what changes to make. Thanks a lot for the help in advance. Will University of south florida ewlowe!at!helios.acomp.usf.edu ------=_NextPart_000_0365_01C4593E.8CEE7A20 Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

I’m a biochemistry grad student who has = recently been given the task of learning basic molecular modeling independently.  I have learned the basics of = hyperchem and autodock, and, having no experience in computational chemistry, have blindly moved = forward and my dockings.  It was = recently suggested to me that although hyperchem can = be used to find docking/binding energies through geometry optimizations, I = should just use it to assign charges to my substrates (which are rather small 10-15 = C) and use these substrates for my autodock = dockings.  However, I was under the = impression that charges were assigned through autodock = without having to use hyperchem.  Please correct me if I’m wrong.  Also, .hin files are not compatible with autodock and = must somehow be converted to .pdbq files if this = method is indeed useful.  I’ve = found a python script hin2pdbq.py, but don’t know how to use it since I = have no real knowledge of how to use linux/python.  I managed to get autodock up and running on cygwin with some help from = the members of this board (thanks).  = Any input would be greatly appreciated.  On a side note, I’m very interested in learning how to = screen a database of possible substrate/inhibitors with autodock.  I have no idea if an additional = program is needed or what changes to make.  Thanks a lot for the help in advance.

 

Will

University of south = florida=

ewlowe!at!helios.acomp.usf.edu

------=_NextPart_000_0365_01C4593E.8CEE7A20-- From chemistry-request@ccl.net Wed Jun 23 17:21:00 2004 Received: from kff1.uchicago.edu (kff1.uchicago.edu [128.135.160.87]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i5NMKxkp022060 for ; Wed, 23 Jun 2004 17:20:59 -0500 Received: from kff1.uchicago.edu (localhost [127.0.0.1]) by kff1.uchicago.edu (8.12.3/8.12.3/Debian-6.6) with ESMTP id i5NMPpMs001730 for ; Wed, 23 Jun 2004 17:25:51 -0500 Received: from localhost (cmtaylor@localhost) by kff1.uchicago.edu (8.12.3/8.12.3/Debian-6.6) with ESMTP id i5NMPppc001726 for ; Wed, 23 Jun 2004 17:25:51 -0500 Date: Wed, 23 Jun 2004 17:25:51 -0500 (CDT) From: caroline taylor To: CCL list Subject: ifc8.0 error: THANKS Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Spam-Status: No, hits=0.0 required=7.5 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 everyone. Thank you to all you who replied with suggestions for solving my problem with the ifc8 compiler. The LD_LIBRARY_PATH variable was fine, but /etc/ld.so.conf needed to be updated, as many of you suggested. Thanks again for the help! Regards, Caroline > At 03:37 PM 6/21/2004, you wrote: > >I'm trying to get version 8 of the intel fortran compiler working (ifc7 > >is fine), and everything runs fine if I do a static build of some > >program. The compiler appears to build/install correctly, and will build a > >(dynamic) executable, but I get the following error when I try to run that > >executable: > > > > >./a.out: error while loading shared libraries: libcxa.so.5: cannot open > >shared object file: No such file or directory > > > >Does anyone out there have a solution to this? > --------------------------------------------- Dr. Caroline M. Taylor Department of Chemistry University of Chicago, James Franck Institute 5640 S. Ellis Avenue Chicago, Illinois 60637 (773) 702-7223 http://kff1.uchicago.edu/~cmtaylor --------------------------------------------- From chemistry-request@ccl.net Wed Jun 23 22:30:19 2004 Received: from smtp.goldrush.com (smtp.goldrush.com [206.171.171.11]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i5O3UIkp000300 for ; Wed, 23 Jun 2004 22:30:18 -0500 Received: from COMPAQ1800T (x2-04b-70.goldrush.com [64.162.11.70]) by smtp.goldrush.com (8.12.8/8.12.8) with SMTP id i5O3Z6e3021122 for ; Wed, 23 Jun 2004 20:35:11 -0700 From: "Steve Bowlus" To: Subject: CCL: Orient molecule Date: Wed, 23 Jun 2004 20:42:27 -0700 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 V5.50.4927.1200 X-MailScanner: Found to be clean X-MailScanner-SpamCheck: X-MailScanner-From: chezbowlus)at(goldrush.com X-Spam-Status: No, hits=0.0 required=7.5 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 I am frantically searching for a simple piece of code that will allow me to: Read a standard file (mol, pdb, Sybyl ...) select an atom to put at the Cartesian origin select an atom to put on the X axis select an atom to put in the XY plane Do a rigid rotation Do sequential rigid rotations about Cartesian axes Freeze the molecule in the new orientation Output the NEW, transformed coordinates. This is equivalent to the Sybyl "orient" command, plus rigid rotations, plus "Freeze molecule". But I have not found a free (or even cheap) package that will freeze a molecule in the new coordinates before output. Thanks in advance for any pointers, Steve