From chemistry-request@ccl.net Sun Feb 20 20:45:22 2005 Received: from rouge.phys.lsu.edu (reef.phys.lsu.edu [130.39.182.96]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id j1L1jMpT026536 for ; Sun, 20 Feb 2005 20:45:22 -0500 Received: from localhost (vani@localhost) by rouge.phys.lsu.edu (8.9.2/8.9.2) with ESMTP id SAA29410 for ; Sun, 20 Feb 2005 18:49:44 -0600 (CST) Date: Sun, 20 Feb 2005 18:49:44 -0600 (CST) From: Vemparala Satyavani To: chemistry-.at.-server.ccl.net Subject: autodock3 on Linux 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: I have been having problems trying to compile autodock on Linux machine..are there any suggestions? any particular flags i need to have/omit Thanks Vani From chemistry-request@ccl.net Sun Feb 20 22:52:16 2005 Received: from server.ccl.net (t157 [127.0.0.1]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id j1L3qFpT030929 for ; Sun, 20 Feb 2005 22:52:15 -0500 Received: (from apache@localhost) by server.ccl.net (8.12.8/8.12.8/Submit) id j1L3qFc8030927 for chemistry.-at-.ccl.net; Sun, 20 Feb 2005 22:52:15 -0500 Date: Sun, 20 Feb 2005 22:52:15 -0500 Message-Id: <200502210352.j1L3qFc8030927.-at-.server.ccl.net> X-Authentication-Warning: server.ccl.net: apache set sender to chemistry-request.-at-.ccl.net using -f From: "venkat, , arunachalam" To: chemistry.-at-.ccl.net X-Web-Message-Number: 050220225011-30878 Subject: W:failed drugs database X-Spam-Status: No, hits=2.5 required=7.5 tests=FROM_ENDS_IN_NUMS, FROM_HAS_ULINE_NUMS 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 subscribers, I am interested to know whether there is any database (either public domain or commercial) for the failed drug candidates? Regards, Venkat sara_venkat_2004.-at-.yahoo.co.in From chemistry-request@ccl.net Sun Feb 20 16:18:43 2005 Received: from web51301.mail.yahoo.com (web51301.mail.yahoo.com [206.190.38.167]) by server.ccl.net (8.12.8/8.12.8) with SMTP id j1KLIgpT020057 for ; Sun, 20 Feb 2005 16:18:42 -0500 Received: (qmail 77252 invoked by uid 60001); 20 Feb 2005 21:18:41 -0000 Comment: DomainKeys? See http://antispam.yahoo.com/domainkeys DomainKey-Signature: a=rsa-sha1; q=dns; c=nofws; s=s1024; d=yahoo.com; b=b++tSbYAHHpbsxVUdZUfI3LH484q3IGoLZJUR1z0hOjvQGZDD8OidFSUv20IL6RiZiwEGqW2rTCY+82qUaQLoc9DJjiZNpO9MWi5uoGJYFXbguTDvjzE8UlZ7Db5aSBIs8pS1PwVKi4NI69F9HamwyLTXCcsNuIrEVc97AFe3pM= ; Message-ID: <20050220211841.77250.qmail:at:web51301.mail.yahoo.com> Received: from [24.152.169.181] by web51301.mail.yahoo.com via HTTP; Sun, 20 Feb 2005 13:18:41 PST Date: Sun, 20 Feb 2005 13:18:41 -0800 (PST) From: Sengen Sun Subject: CCL: more references on orbitals and reality To: chemistry:at:ccl.net In-Reply-To: <20050220200851.243.qmail:at:web51306.mail.yahoo.com> 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 accept some arguments by Wai-To Chan on my comment ["against the main stream of the misled community"], which might not be appropriate to describe the reality. I take such a responsibility if I am wrong. But the controversy is clear in the understanding of orbitals via electron density, which has been remained as a historical problem. It is not a responsible scientist to deny the existence of this controversy. This severe controversy has been ignored by the top scientific journals such as Nature, which only allows one-sided stories. In fact, I am supported by many CCL members, who has found this thread very interesting. I got more responses off-line than on-line so that I don't have enough time to reply to each of them. Many people are shy to argue anything in the public. But I would sacrifice myself to stimulate this discussion even with severe languages I have ever used. If I (- a small guy) am not willing to sacrifice myself, who else should be for such an important scientific issue? I certainly don't quite understand the remaining arguments by Wai-To Chan, which seem to me logically self-contradictory. Are orbitals arbitory and made by humans, and still physically measurable? Sengen > From: Wai-To Chan > Date: Sat, 19 Feb 2005 03:39:35 -0500 (EST) > Subject: more references on orbitals and reality > > > > I realize that no one ever stated where Professor > Richard Bader > would stand in this discussion/debate over the > reality > of orbitals. I > somehow got the impression that perhaps to you Bader > is the kind of 'non-mainstream' researcher you may > aspire to. > > Let me point out that Bader has always > disseminated > his ideas > just like the others in the 'mainstreadm'. > His work has long gained acceptance by > the 'mainstream'. Some of this former students went > on > to join > the developers of Gaussian and Gamess which have > been > interaced with > AIMPAC a program Bader made available to the > 'mainstream'. > If you pick a computation paper from one of the many > 'mainstream' journals > > from the last decade randomly there is a good > chance > you will run > into a study applying Bader's program > as an alternate or supplementary tool to the MO > theory > in j phys chem, jacs, j chem phys and many others. > > > Professor Bader himself is ready to argue > people he does not agree with. > I can't remember how many times Bader > has pointed out works of others he considered > erroneous > according to his theory. Just off the top of my head > I can recall him taking on Parr, Mezey, Cioslowski > and > many > others whose name escaped me. Perhaps this is what > made Bader > somewhat 'non-mainstream'. But then Bader invariably > presented > his view in refereed which means 'mainstream' > journals. > > Bader's AIM theory is many ways non-arbitray and > hence > more theoretically sound than qualitative MO theory. > I > don't remember > Bader ever criticising experiments purported to > measure orbitals or raving about AIM as a better > theory. > I doubt he will appreciate the > kind of venomus attacks waged by John Ogilvie on > researchers > applying electron momentum spectrocsopy to measure > MOs > and later > even Linus Pauling from the early 90s. If a theorist > of > the calibre of Richard Bader were to provide an > analysis on this subject I trust that I could gain a > much > better understanding > of what those experiments debated over in this > thread > is about. > > May I suggest that you could also make a real > contribution > to science by publishing in the > mainstream journal. Give a try to sending an essay > to > perhaps > J Chem Edu as the first step to educate the > manstream if writing an original research > article is too difficult. > > Wai-To Chan > __________________________________ Do you Yahoo!? Read only the mail you want - Yahoo! Mail SpamGuard. http://promotions.yahoo.com/new_mail From chemistry-request@ccl.net Mon Feb 21 02:49:26 2005 Received: from sungod.ccs.yorku.ca (mailrelay.yorku.ca [130.63.236.104]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id j1L7nPpT006856 for ; Mon, 21 Feb 2005 02:49:26 -0500 Received: from curl.gkcl.yorku.ca (curl.gkcl.yorku.ca [130.63.232.224]) by sungod.ccs.yorku.ca (8.12.10/8.12.8) with ESMTP id j1L7nP9N025113 for ; Mon, 21 Feb 2005 02:49:25 -0500 (EST) Received: (from chan@localhost) by curl.gkcl.yorku.ca (8.10.0/8.10.0) id j1L7bxi07333 for chemistry:at:ccl.net; Mon, 21 Feb 2005 02:37:59 -0500 (EST) From: Wai-To Chan Message-Id: <200502210737.j1L7bxi07333:at:curl.gkcl.yorku.ca> Subject: Re: Request: DFT methods for silica nanoparticles To: chemistry:at:ccl.net Date: Mon, 21 Feb 2005 02:37:58 -0500 (EST) X-Mailer: ELM [version 2.5 PL3] MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii 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 The page number of the reference cited in my previous message, 933--92, should be corrected to 933-42. Wai-To Chan From chemistry-request@ccl.net Sun Feb 20 21:32:10 2005 Received: from CLEMSON.EDU (mail.clemson.edu [130.127.28.87]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id j1L2W8pT027714 for ; Sun, 20 Feb 2005 21:32:08 -0500 Received: from rh6.clemson.edu (rh6.clemson.edu [130.127.69.70]) by CLEMSON.EDU (8.13.1/8.13.1) with ESMTP id j1KNjtZX020046 for ; Sun, 20 Feb 2005 18:45:55 -0500 (EST) Received: (from apache@localhost) by rh6.clemson.edu (8.11.6/8.11.6) id j1KNjxX14977; Sun, 20 Feb 2005 18:45:59 -0500 X-Authentication-Warning: rh6.clemson.edu: apache set sender to sun/at/clemson.edu using -f Received: from 205.232.74.228 (SquirrelMail authenticated user sun); by rh6.clemson.edu with HTTP; Sun, 20 Feb 2005 18:45:59 -0500 (EST) Message-ID: <3870.205.232.74.228.1108943159.squirrel@205.232.74.228> Date: Sun, 20 Feb 2005 18:45:59 -0500 (EST) Subject: QM software to calculate interaction energy From: "Yu Sun (Denis)" To: chemistry/at/ccl.net User-Agent: SquirrelMail/1.4.3a X-Mailer: SquirrelMail/1.4.3a MIME-Version: 1.0 Content-Type: text/plain;charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Priority: 3 (Normal) Importance: Normal X-Spam-Level: X-Scanned-By: mail MIMEDefang 2.43 X-Spam-Status: No, hits=0.3 required=7.5 tests=FVGT_s_OBFU_Q1 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, We've done MM calculation of interaction energy between a series of short peptides and model polymer surfaces with different implicit solvent models. The systems are about 500 ~ 1000 atoms. Now we want to compare these results with higher level QM model. However, I've known little about QM software and QM itself. I was told I can consider: - Schrodingers Jaguar with SCRF calculations to handle solvation effects. - DFT with COSMO-RS (included in TURBOMOLE). - MOPAC in BioCache I really know little about this software. I would appreciate someone can help me to choose appropriate software or suggest others ( We have thousands dollar budgt for this software). I would expect in our system solvation effect must be considered. Thanks ! Yu From chemistry-request@ccl.net Mon Feb 21 04:52:53 2005 Received: from chemaxon.hu (90.156-228-195.hosting.adatpark.hu [195.228.156.90]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id j1L9qput012393 for ; Mon, 21 Feb 2005 04:52:52 -0500 Received: from a84-0-128-223.adsl-pool.axelero.hu ([84.0.128.223] helo=[10.0.0.139]) by chemaxon.hu with esmtpsa (Exim 4.44 #1 (Debian)) id 1D39Dn-0000rI-CL TLS Cipher TLSv1:AES256-SHA:256; Mon, 21 Feb 2005 09:47:15 +0100 Message-ID: <42199FD8.3040709*at*chemaxon.com> Date: Mon, 21 Feb 2005 09:46:16 +0100 From: Szabolcs Csepregi Organization: Chemaxon Ltd. User-Agent: Mozilla Thunderbird 1.0 (Windows/20041206) X-Accept-Language: en-us, en MIME-Version: 1.0 To: "Asif, , Rahaman" CC: chemistry*at*ccl.net Subject: CCL:Re:W:Free conformational search/analysis software References: <200502182346.j1INkAc2021770*at*server.ccl.net> In-Reply-To: <200502182346.j1INkAc2021770*at*server.ccl.net> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=3.9 required=7.5 tests=MY_DSL,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 Hello Asif, Check out molconvert from ChemAxon's Marvin package: http://www.chemaxon.com/marvin/doc/user/molconvert.html You should have a look at the help for the 3D generation options: molconvert -H3D You can also access the functionality from Java API. All ChemAxon tools are free for academia: http://www.chemaxon.hu/forum/ftopic193.html All the best, Szabolcs Asif, , Rahaman wrote: > Hi, > > Could you please tell me if there is free software for conformational search/analysis? > > Thank you in advance, Asif -- Szabolcs Csepregi, PhD ChemAxon Ltd. Maramaros koz 3/A, Budapest, 1037 Hungary http://www.chemaxon.com Cell: +3620 4219863 Tel: +361 4532661 Fax: +361 4532659 mailto:scsepregi*at*chemaxon.com From chemistry-request@ccl.net Mon Feb 21 08:00:19 2005 Received: from rouge.phys.lsu.edu (reef.phys.lsu.edu [130.39.182.96]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id j1LD0Hut020084 for ; Mon, 21 Feb 2005 08:00:17 -0500 Received: from localhost (vani@localhost) by rouge.phys.lsu.edu (8.9.2/8.9.2) with ESMTP id GAA02337; Mon, 21 Feb 2005 06:11:15 -0600 (CST) Date: Mon, 21 Feb 2005 06:11:15 -0600 (CST) From: Vemparala Satyavani To: "D.BIO- Gerard Pujadas" cc: CHEMISTRY #%# ccl.net Subject: Re: CCL:autodock3 on Linux In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=X-UNKNOWN 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 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from QUOTED-PRINTABLE to 8bit by server.ccl.net id j1LD0Jut020089 Gerard: Thanks for the Makefile.. I could compile it.. but sadly when i try to execute it, it fails giving a segmentation fault.. Vani On Mon, 21 Feb 2005, D.BIO- Gerard Pujadas wrote: > > Dear Vani, > > > > >I have been having problems trying to compile autodock on Linux > >machine..are there any suggestions? > >any particular flags i need to have/omit > > > > probably the problem is that you need a Makefile > adapted for a compilation in a Linux machine. I > am running AutoDock in a PC with Mandrake and I > did the following: > > 1) make clean > 2) make > > and that's all > > Please, use the Makefile I attached here and > replace with it the existing Makefile in > src/autodock folder. > > Hope this helps > > Gerard > -- > ======================== NOTE: NEW ADDRESS AND E-MAIL ======================== > Dr. Gerard Pujadas > Grup de recerca en "Vi i Salut" > Dept. Bioqummica i Biotecnologia room 106 > Campus de Sant Pere Sescelades e-mail: gerard.pujadas #%# urv.net > Univ. Rovira i Virgili phone: 34-977 559565 > C/ Marcel7lm Domingo fax: 34-977 559597 > 43007 Tarragona (CATALONIA) > State: Spain (European Union) > =========================================================================== > From chemistry-request@ccl.net Mon Feb 21 04:57:44 2005 Received: from gvedoh01.emea.givaudan.com (mail-external3.givaudan.com [57.66.141.4]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id j1L9vcut012694; Mon, 21 Feb 2005 04:57:39 -0500 To: "Asif, , Rahaman" Cc: chemistry #%# ccl.net, "Computational Chemistry List" Subject: Re: CCL:W:Free conformational search/analysis software MIME-Version: 1.0 X-Mailer: Lotus Notes Release 5.0.11 July 24, 2002 Message-ID: From: andras.borosy #%# givaudan.com Date: Mon, 21 Feb 2005 10:57:53 +0100 X-MIMETrack: Serialize by Router on gvedoh01/H/Givaudan(Release 6.5.3|September 14, 2004) at 21/02/2005 10:57:38, Serialize complete at 21/02/2005 10:57:38 Content-Type: text/plain; charset="iso-8859-1" X-Spam-Status: No, hits=2.0 required=7.5 tests=IMPRONONCABLE_1,NO_REAL_NAME 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 j1L9viut012705 Dear Mr. Rahaman For academic users MOLOC is free (www.moloc.ch). This is is a molecular modeling package designed with emphasis on high interactivity and contains almost everything what is needed in computer-aided molecular design. Best regards, Dr. Andras Borosy Seniour Scientist Delivery Systems, Fragrance Research Givaudan Schweiz AG Ueberlandstr. 138 8600 D|bendorf Switzerland tel: + 41-1-8242164 fax: +41-1-8242926 e-mail: andras.borosy #%# givaudan.com "Asif, , Rahaman" Sent by: "Computational Chemistry List" 19.02.2005 00:46 To: chemistry #%# ccl.net cc: Subject: CCL:W:Free conformational search/analysis software Hi, Could you please tell me if there is free software for conformational search/analysis? Thank you in advance, Asif -= 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 #%# ccl.net Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST #%# 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 #%# nd.edu (read about it on CCL Home Page) -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ From chemistry-request@ccl.net Mon Feb 21 15:35:48 2005 Received: from casbah.it.northwestern.edu (casbah.it.northwestern.edu [129.105.16.52]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id j1LKZlut002963 for ; Mon, 21 Feb 2005 15:35:47 -0500 Received: (from mailnull@localhost) by casbah.it.northwestern.edu (8.12.10/8.12.10) id j1LKZl9P023119 for ; Mon, 21 Feb 2005 14:35:47 -0600 (CST) Received: from chief.chem-eng.northwestern.edu (chief.chem-eng.northwestern.edu [129.105.205.171]) by casbah.it.northwestern.edu via smap (V2.0) id xma022557; Mon, 21 Feb 05 14:35:33 -0600 Subject: Problems with gaussian 03 and freqchk From: Jim Pfaendtner To: chemistry-.at.-ccl.net Content-Type: text/plain Message-Id: <1109018200.24046.32.camel-.at.-chief.chem-eng.northwestern.edu> Mime-Version: 1.0 X-Mailer: Ximian Evolution 1.4.5 (1.4.5-9) Date: Mon, 21 Feb 2005 14:36:41 -0600 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 Hi all, I have Gaussian 03 installed on a PIII with 32-bit binaries and an AMD Opteron with 64-bit binaries. Both machines run redhat enterprise r3 for their OS. If I run freqchk on the 64-bit computers I can use it no problem and there are no errors. Running freqchk on the 32-bit computers gives results like this: E (Thermal) CV S KCal/Mol Cal/Mol-Kelvin Cal/Mol-Kelvin Total nan nan nan Electronic 0.000 0.000 1.377 Translational 0.889 2.981 34.068 Rotational 0.889 2.981 11.812 Vibrational nan nan nan Vibration 1 nan nan nan Has anyone had any experience with this? The 32-bit machines have g98 and g03 installed, but we have a simple script which sources the right login file/directories to switch between the two installations. Freqchk with g98 works on 32-bit, but I don't think it's an issue with the dual-install. thanks a lot, Jim