From chemistry-request@ccl.net Fri Jun 17 04:31:50 2005 Received: from distrib2.mail.u-psud.fr (distrib2.mail.u-psud.fr [129.175.34.154]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j5H8Vi7H003860 for ; Fri, 17 Jun 2005 04:31:44 -0400 Received: from intfiltre3.mail.u-psud.fr (intfiltre3.mail.u-psud.fr [129.175.34.151]) by distrib2.mail.u-psud.fr (8.12.10/8.12.0.Beta10) with ESMTP id j5H8VfC5008460 for ; Fri, 17 Jun 2005 10:31:41 +0200 Received: from post1.mail.u-psud.fr (post1.mail.u-psud.fr [129.175.34.87]) by intfiltre3.mail.u-psud.fr (8.12.10/8.12.0.Beta10) with ESMTP id j5H8Uewp029690 for ; Fri, 17 Jun 2005 10:31:40 +0200 Received: from ext.lcp.u-psud.fr (ext.lcp.u-psud.fr [129.175.100.5]) by post1.mail.u-psud.fr (8.12.10/8.12.0.Beta10) with ESMTP id j5H8TKRf016776 for ; Fri, 17 Jun 2005 10:29:21 +0200 Received: from lcp.u-psud.fr (pc7.lcp.u-psud.fr [129.175.101.37]) by ext.lcp.u-psud.fr (8.13.1/8.13.1) with ESMTP id j5H8TMSh008949 for ; Fri, 17 Jun 2005 10:29:23 +0200 Message-ID: <42B289E2.4030103 [] lcp.u-psud.fr> Date: Fri, 17 Jun 2005 10:29:22 +0200 From: Pierre Archirel User-Agent: Mozilla/5.0 (X11; U; Linux i686; fr; rv:1.4.1) Gecko/20031114 X-Accept-Language: fr, en MIME-Version: 1.0 To: chemistry [] ccl.net Subject: CCL: NDDO code Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 8bit X-Scanned: by amavis X-Spam-Status: No, score=0.0 required=5.0 tests=none autolearn=failed version=3.0.3 X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net Dear collegue, The AMPAC package (by Holder, Liotard et al.) uses the NDDO postulate: the integrals are calculated with a STO-3G basis, and then weighted with a geometry dependent factor. The source is not free. Best wishes, P.A. __________________________________________________________ Pierre Archirel Groupe de Chimie Thiorique Laboratoire de Chimie Physique Tel: 01 69 15 63 86 Bat 349 Fax: 01 69 15 61 88 91405 Orsay Cedex France pierre.archirel [] lcp.u-psud.fr __________________________________________________________ From chemistry-request@ccl.net Fri Jun 17 05:51:03 2005 Received: from mailhost.u-strasbg.fr (mailhost.u-strasbg.fr [130.79.200.155]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j5H9owFk011725 for ; Fri, 17 Jun 2005 05:50:58 -0400 Received: from sokaris.u-strasbg.fr (sokaris.u-strasbg.fr [IPv6:2001:660:2402::101]) by mailhost.u-strasbg.fr (8.13.1/jtpda-5.5pre1) with ESMTP id j5H8x9sW067933 for ; Fri, 17 Jun 2005 10:59:09 +0200 (CEST) Received: from hit11 (pcf-b315a-hit3.u-strasbg.fr [130.79.85.33]) by sokaris.u-strasbg.fr (8.12.9/jtpda-5.5pre1) with ESMTP id j5H8x7tv061899 for ; Fri, 17 Jun 2005 10:59:09 +0200 (CEST) Received: from [127.0.0.1] by hit11 (PGP Universal service); Fri, 17 Jun 2005 10:55:01 +0100 X-PGP-Universal: processed; by hit11 on Fri, 17 Jun 2005 10:55:01 +0100 Message-ID: <42B28FE5.30205 ^^^ pharma.u-strasbg.fr> Date: Fri, 17 Jun 2005 10:55:01 +0200 From: Mireille Krier User-Agent: Mozilla Thunderbird 1.0 (Windows/20041206) X-Accept-Language: fr, en MIME-Version: 1.0 To: chemistry ^^^ ccl.net Subject: Alpha Helix kink Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 8bit X-Greylist: Sender IP whitelisted, not delayed by milter-greylist-1.6 (mailhost.u-strasbg.fr [IPv6:2001:660:2402::155]); Fri, 17 Jun 2005 10:59:09 +0200 (CEST) X-Antivirus: scanned by sophos at u-strasbg.fr X-Spam-Status: No, score=0.0 required=5.0 tests=none autolearn=failed version=3.0.3 X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net Dear CCLers, we are looking for a tool that can detect (because not always induced by proline) and measure the angle of an kink in an alpha helix. Any suggestions? We found in the literature SWINK, (Cordes et al., Sansom Group) was developed to estimate the kink and swivel angle of TM small alpha, Greek-helices. Any ideas, if this is available? Many thanks in advance to the community for the any help provided. Mireille Krier -- ----------------------------------------------------------------------- Bioinformatique du midicament, Equipe 5 du Laboratoire de Pharmacochimie et de la communication cellulaire UMR 7081 ULP-CNRS Faculti de Pharmacie 74, route du Rhin - B.P. 60024 F-67401 Illkirch CEDEX, France ----------------------------------------------------------------------- From chemistry-request@ccl.net Fri Jun 17 04:29:08 2005 Received: from mserv6.dl.ac.uk (mserv6.dl.ac.uk [148.79.80.137]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j5H8T4TQ003577 for ; Fri, 17 Jun 2005 04:29:05 -0400 X-DL-MFrom: X-DL-Connect: Received: from dl.ac.uk (csevig7.dl.ac.uk [193.62.112.97]) by mserv6.dl.ac.uk (8.12.10/8.12.8/[ref postmaster ## dl.ac.uk]) with ESMTP id j5H7m8nj006184 for ; Fri, 17 Jun 2005 08:48:09 +0100 Message-ID: <42B28038.4000606 ## dl.ac.uk> Date: Fri, 17 Jun 2005 08:48:08 +0100 From: Huub van Dam Organization: CCLRC Daresbury Laboratory User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.6) Gecko/20040113 X-Accept-Language: en, en-us MIME-Version: 1.0 To: chemistry ## ccl.net Subject: Re: CCL:CRYSTAL03 - Help needed References: In-Reply-To: Content-Type: text/plain; charset=windows-1252; format=flowed Content-Transfer-Encoding: 7bit X-CCLRC-SPAM-report: 0 : X-Scanned-By: MIMEDefang 2.37 X-Spam-Status: No, score=0.0 required=5.0 tests=URG_BIZ autolearn=failed version=3.0.3 X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net Hi, I have been informed by our local CRYSTAL experts that most likely your input geometry is wrong. Alternatively you may have a very diffuse function in your basis set. LIM007 refers to the number of lattice vectors needed to describe your system correctly. This number can get exceedingly big if some atoms are too close together, or likewise if you use too diffuse functions for crystal calculations in your basis set. Let me know if this does not solve your problems and I will progress it further. Best wishes, Huub Ojwang, J.G.O. wrote: >Dear CCLnetters, >Has anyone had experience with Crystal03? I've tried to run a system but I get error messages to the effect that: >(i) increase LIM007 >(ii) neighbour list too big increase LIMBEC >Any idea how I can do this. >Futrther when I try to run a supercel I get an error message that 'file size limit exceed'. How can i increase the limit of the file size. >Waiting for an urgent response from any Crystal03 informed netter. > >Best Regards, >Ojwang' JGO > >Eindhoven University of Technology, >The Netherlands. > > > >-= 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 is mail bouncing from ccl.net domain due to spam filters, please >use the Web based form from CCL Home Page >-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > > > > > -- ========================================================== Huub van Dam email: h.j.j.vandam ## dl.ac.uk CCLRC Daresbury Laboratory phone: +44-1925-603933 Daresbury, Warrington fax: +44-1925-603634 Cheshire, UK WA4 4AD ========================================================== From chemistry-request@ccl.net Fri Jun 17 12:14:02 2005 Received: from web41210.mail.yahoo.com (web41210.mail.yahoo.com [66.218.93.43]) by server.ccl.net (8.13.1/8.13.1) with SMTP id j5HGDwhH013943 for ; Fri, 17 Jun 2005 12:13:58 -0400 Received: (qmail 79961 invoked by uid 60001); 17 Jun 2005 15:13:56 -0000 DomainKey-Signature: a=rsa-sha1; q=dns; c=nofws; s=s1024; d=yahoo.com; h=Message-ID:Received:Date:From:Subject:To:MIME-Version:Content-Type:Content-Transfer-Encoding; b=ONs/sx3+kFemjX/FBLtgRXGG4Op24/+3NovpgH48OZ9ZMyx+N1gRGH62EeFBCZ1Ke3bnaoqa5wtisuUZSm7p0Lh7O5UF3LgkIzo2veIcObNlZQB4/Vd8Q2MC2fpo34ebGHWF7hVDCiJ2pnNO4Kh4HY01OSdJJX/37k/Yh8rMLE4= ; Message-ID: <20050617151356.79959.qmail ^^^ web41210.mail.yahoo.com> Received: from [157.182.90.41] by web41210.mail.yahoo.com via HTTP; Fri, 17 Jun 2005 08:13:56 PDT Date: Fri, 17 Jun 2005 08:13:56 -0700 (PDT) From: Robyn Ayscue Subject: autodock3 dies upon launch with multiple errors To: autodock ^^^ scripps.edu, chemistry ^^^ ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Spam-Status: No, score=1.8 required=5.0 tests=DNS_FROM_RFC_ABUSE, DNS_FROM_RFC_POST autolearn=no version=3.0.3 X-Spam-Level: * X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net All, Sorry for the cross-post. I'm running AutoDockTools using autodock/autogrid version 3.05 on an SGI machine with IRIX 6.5.24. I'm trying to dock an effector molecule in the active site of an enzyme (p450 2c9) with a substrate molecule also present. Autogrid finishes out with no problems, but autogrid dies immediately upon launch with the following errors: Can't find ".dpf" in the dock-parameter filename. AutoDock needs the extension of the grid parameter file to be ".gpf" and that of the docking parameter file to be ".dpf". /disk02/usr/local/autodock/dist305/bin/sgi4D.IRIX64_6.5_R10000/autodock3: Wrong number of x grid-points in grid-map file "2c9q_HEMq_FLPq.A.map". /disk02/usr/local/autodock/dist305/bin/sgi4D.IRIX64_6.5_R10000/autodock3: Use either 32 or 1129013060 throughout! /disk02/usr/local/autodock/dist305/bin/sgi4D.IRIX64_6.5_R10000/autodock3: ERROR: Using wrong grid-map file. /disk02/usr/local/autodock/dist305/bin/sgi4D.IRIX64_6.5_R10000/autodock3: Aborting... /disk02/usr/local/autodock/dist305/bin/sgi4D.IRIX64_6.5_R10000/autodock3: Unsuccessful Completion. First it complains about not being able to find a docking parameter file with .dpf as the suffix, but the file DOES have a .dpf suffix and it is listed as having one in the command that is typed in the command line used to launch autodock. The .dpf file looks fine as far as I can tell, compared to other .dpf files I've used for other docking runs that have completed successfully. The next thing it complains about is the differing number of grid points. It keeps referring to the number "1129013060" but I can't find that number in any of the grid-map files. The number of x- grid points in all grid-map files is the same. Autodock comes to the conclusion that I'm using the wrong grid-map files, but the files I'm using ARE the correct files (I checked and double-checked). If anyone has had experience with this kind of error message and knows how to resolve it, I'd appreciate any input. Thanks much! Robyn Ayscue rayscue ^^^ hsc.wvu.edu kajsicat ^^^ yahoo.com ____________________________________________________ Yahoo! Sports Rekindle the Rivalries. Sign up for Fantasy Football http://football.fantasysports.yahoo.com From chemistry-request@ccl.net Fri Jun 17 11:52:16 2005 Received: from smtp3.libero.it (smtp3.libero.it [193.70.192.127]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j5HFqBO8012025 for ; Fri, 17 Jun 2005 11:52:12 -0400 Message-Id: <200506171552.j5HFqBO8012025 ^^^ server.ccl.net> Received: from localhost (172.16.1.84) by smtp3.libero.it (7.0.027-DD01) id 428B9D5C00692A56 for chemistry ^^^ ccl.net; Fri, 17 Jun 2005 16:55:53 +0200 Received: from rcmdaspire (151.41.207.129) by smtp1.libero.it (7.0.027-DD01) id 41BF654A085A2343 for chemistry ^^^ ccl.net; Fri, 17 Jun 2005 16:08:14 +0200 From: "Rino Ragno" To: Subject: 3D pharmacophore searching free program Date: Fri, 17 Jun 2005 16:08:11 +0200 MIME-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit X-Mailer: Microsoft Office Outlook, Build 11.0.6353 In-Reply-To: <755a1e3b050616095744fae9e2 ^^^ mail.gmail.com> X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2900.2527 Thread-Index: AcVyursxxRvYrj3cTFi2QEU0GqFRZwAit//A X-Virus-Scanned: by amavisd-new at libero.it serv6 X-Spam-Status: No, score=1.8 required=5.0 tests=DNS_FROM_RFC_ABUSE, DNS_FROM_RFC_POST autolearn=no version=3.0.3 X-Spam-Level: * X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net Dear all, I am looking for free downloadable software to perform 3D pharmacophore searching. Any information received will be summarized. Thank Rino ++------------------------------------------++ || Dr. Rino Ragno || || || || Dip. Studi Farmaceutici || || Facolta' di Farmacia || || Universita' "La Sapienza" || || P.le Aldo Moro, 5 - 00185 || || Roma/Italia || || PO BOX 36 ROMA 62 || || || || Phone: 39-06-49913152 || || || || Fax: 39-06-491491 || || || || E-mail: rino.ragno ^^^ uniroma1.it || || WWW: http://w3.uniroma1.it/rcmd || ++------------------------------------------++ _____ << ella for Spam Control >> has removed 817 Spam messages and set aside 1045 Newsletters for me You can use it too - and it's FREE! www.ellaforspam.com From chemistry-request@ccl.net Fri Jun 17 12:48:03 2005 Received: from pastinakel.tue.nl (pastinakel.tue.nl [131.155.2.7]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j5HGlwIO016584 for < ccl.net>; Fri, 17 Jun 2005 12:47:59 -0400 Received: from pastinakel.tue.nl ([127.0.0.1]) by localhost (pastinakel.tue.nl [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id 38609-05 for < ccl.net>; Fri, 17 Jun 2005 18:47:55 +0200 (CEST) Received: from stex2.campus.tue.nl (stex2.campus.tue.nl [131.155.81.192]) by pastinakel.tue.nl (Postfix) with ESMTP for < ccl.net>; Fri, 17 Jun 2005 18:47:55 +0200 (CEST) X-MimeOLE: Produced By Microsoft Exchange V6.0.6487.1 content-class: urn:content-classes:message MIME-Version: 1.0 Subject: CRYSTAL03 - Date: Fri, 17 Jun 2005 18:47:55 +0200 Message-ID: < stex2.campus.tue.nl> From: "Ojwang, J.G.O." < tue.nl> To: < ccl.net> Hi. I somehow sorted out the LIM007 case for a different system. The geometry was not correct! What now bothers me about the present structure is that using a visualisation package I see something not resembling crystal at all! Reasons why the geometry inputs cannot be wrong are: (i) I've used different sets of well documented theoretical and experimental geometrical inputs with the same result (ii) other geometries for other different structures, other space groups, are very much perfect and gives me the right crystals. My guess is (i) there is a bug in the crystal03 code as pertains to space group 11, but I've been assured that crystal03 code space group is bugfree (ii) maybe the structure(Na3AlH6) was assigned the wrong space group. The geometry I used are as follows: (a =5.33, b=5.53, c=7.68, beta=90.103)(space group(P21/n) 11) Al 0.0 0.0 0.0 Na 0.0 0.0 0.5 H 0.9897 0.4532 0.2535 H 0.2281 0.3307 0.5437 H 0.1608 0.2673 0.9366 I tried other different sets of geometrical inputs(experimental and theoretical) with the same results. The program calculates alright but the structure does not resemble a crystal at all. (Al should be six coordinates in H) Well, let me hear your opinion. Best Regards, Ojwang' BTW: What bothers me is (i) was the wrong space group assigned to Na3AlH6 or is there a bug in crystal03 code in so far as space group 11 is concerned. -----Original Message----- From: Computational Chemistry List on behalf of Huub van Dam Sent: Fri 6/17/2005 9:48 AM To: chemistry >< ccl.net Cc: Subject: CCL:CRYSTAL03 - Help needed Hi, I have been informed by our local CRYSTAL experts that most likely your input geometry is wrong. Alternatively you may have a very diffuse function in your basis set. LIM007 refers to the number of lattice vectors needed to describe your system correctly. This number can get exceedingly big if some atoms are too close together, or likewise if you use too diffuse functions for crystal calculations in your basis set. Let me know if this does not solve your problems and I will progress it further. Best wishes, Huub Ojwang, J.G.O. wrote: >Dear CCLnetters, >Has anyone had experience with Crystal03? I've tried to run a system but I get error messages to the effect that: >(i) increase LIM007 >(ii) neighbour list too big increase LIMBEC >Any idea how I can do this. >Futrther when I try to run a supercel I get an error message that 'file size limit exceed'. How can i increase the limit of the file size. >Waiting for an urgent response from any Crystal03 informed netter. > >Best Regards, >Ojwang' JGO > >Eindhoven University of Technology, >The Netherlands. > Huub van Dam email: h.j.j.vandam >< dl.ac.uk CCLRC Daresbury Laboratory phone: +44-1925-603933 Daresbury, Warrington fax: +44-1925-603634 Cheshire, UK WA4 4AD From chemistry-request@ccl.net Fri Jun 17 12:52:11 2005 Received: from nsuncom2.rz.hu-berlin.de (nsuncom2.rz.hu-berlin.de [141.20.1.28]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j5HGq2O7016721 for < ccl.net>; Fri, 17 Jun 2005 12:52:03 -0400 Received: from localhost (suncom3.cms.hu-berlin.de [141.20.1.71]) by nsuncom2.rz.hu-berlin.de (8.12.11/8.12.11) with ESMTP id j5GGlUYZ000660; Thu, 16 Jun 2005 18:47:30 +0200 (MEST) Received: from suncom3.cms.hu-berlin.de ([127.0.0.1]) by localhost (suncom3 [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id 08353-30; Thu, 16 Jun 2005 18:47:27 +0200 (CEST) Received: from impact1.chemie.hu-berlin.de (impact1.chemie.hu-berlin.de [141.20.72.25]) by suncom3.cms.hu-berlin.de (8.13.1/8.13.1) with ESMTP id j5GGk7M1010305; Thu, 16 Jun 2005 18:46:07 +0200 (CEST) Received: from impact1.chemie.hu-berlin.de (localhost [127.0.0.1]) by impact1.chemie.hu-berlin.de (SGI-8.12.5/8.12.5) with ESMTP id j5GGk7hR286374; Thu, 16 Jun 2005 18:46:07 +0200 (MESZ) Received: (from ah@localhost) by impact1.chemie.hu-berlin.de (SGI-8.12.5/8.12.5/Submit) id j5GGk4Cf285986; Thu, 16 Jun 2005 18:46:04 +0200 (MESZ) Date: Thu, 16 Jun 2005 18:46:03 +0200 From: "Dr. Alexander Hofmann" < chemie.hu-berlin.de> To: "Ojwang, J.G.O." < tue.nl> Cc: chemistry >< ccl.net Subject: CRYSTAL03 - Help needed Message-ID: <20050616164603.GS166999 >< chemie.hu-berlin.de> Reply-To: ah >< chemie.hu-berlin.de References: < stex2.campus.tue.nl> Mime-Version: 1.0 Content-Type: multipart/mixed; boundary="OrT4iOlIQZp3kw4S" Content-Disposition: inline In-Reply-To: < stex2.campus.tue.nl> User-Agent: Mutt/1.4i X-Virus-Scanned: by amavisd-new at cms.hu-berlin.de X-Spam-Status: No, score=0.0 required=5.0 tests=none autolearn=failed version=3.0.3 X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net --OrT4iOlIQZp3kw4S Content-Type: text/plain; charset=us-ascii Content-Disposition: inline Hello, I've tested the monoclinic structure with your setting (and PW instead of B3LYP) and it did not work, too. However I made some changes and it started calculating ... I checked the geometry and it looks a little weird, I found bond distances of 0.67 A, which is even for hydrides small. So I'd suggest have a close look what crystal is doing with your input. This can be (easily) achieved by giving COORPRT in the geometry section. Have a look at the modified input. Anyway it only started after modifying the k-points ( to 4 4 4 ). TOLINTEG is also worth a look, the settings I use are converged for my cases (less than 0.1 kJ difference in total energy to the better setting) The other input (ccl1.in) works just fine, but I've got a 64 bit filesystem. The integrals (channel 44) are growing beyond your limit (probably 2GB). Maybe it's a good idea to do direct scf in your case to avoid large files for the start. Or use a modern filesystem for larger files. Hth Alex -- Dr. Alexander Hofmann Humboldt-Universitaet zu Berlin Institut fuer Chemie Arbeitsgruppe Quantenchemie Post: Unter den Linden 6 10099 Berlin Visitors: Brook-Taylor-Strasse 2 12489 Berlin ah >< chemie.hu-berlin.de Tel.: +49-30-2093-7138 Fax.: +49-30-2093-7136 http://www.chemie.hu-berlin.de/ag_sauer/index.html PGP-Key: wwwkeys.de.pgp.net ID: D9D62D35 --OrT4iOlIQZp3kw4S Content-Type: text/plain; charset=us-ascii Content-Disposition: attachment; filename="ccl1.in" AlH4 SUPERCELL CRYSTAL 0 0 0 88 5.021 11.346 3 11 0.0 0.25 0.125 13 0.0 0.25 0.625 1 0.2335 0.3918 0.5439 SUPERCEL 2 0 0 0 2 0 0 0 2 COORPRT ENDG 11 4 0 0 8 2. 1. 56700. 0.000225 8060. 0.00191 1704. 0.01105 443.6 0.05006 133.1 0.1691 45.8 0.3658 17.75 0.3998 7.38 0.1494 0 1 5 8. 1. 119.0 -0.00673 0.00803 25.33 -0.0798 0.0639 7.80 -0.0793 0.2074 3.00 0.3056 0.3398 1.289 0.5639 0.3726 0 1 1 0. 1. 0.578 1. 1. 0 1 1 0. 1. 0.323 1. 1. 13 5 0 0 8 2. 1. 70510.0 0.000226 10080.0 0.0019 2131.0 0.0110 547.5 0.0509 163.1 0.1697 54.48 0.3688 19.05 0.3546 5.402 0.0443 0 1 5 8. 1. 139.6 -0.01120 0.0089 32.53 -0.1136 0.0606 10.23 -0.0711 0.1974 3.810 0.5269 0.3186 1.517 0.7675 0.2995 0 1 1 0. 1. 0.59 1. 1. 0 1 1 0. 1. 0.35 1. 1. 0 3 1 0. 1. 0.51 1. 1. 1 4 0 0 5 2.0 1.0 120.0 0.000267 40.0 0.002249 12.8 0.006470 3.98 0.03291 1.21 0.09551 0 0 1 0.0 1.0 0.47 1.0 0 0 1 0.0 1.0 0.14 1.0 0 2 1 0.0 1.0 0.30 1.0 99 0 PRINT ENDBS BIPOSIZE 3103200 DFT EXCHANGE PWGGA CORRELAT PWGGA END END 8 0 8 FMIXING 30 MAXCYCLE 50 PPAN ENDSCF --OrT4iOlIQZp3kw4S Content-Type: text/plain; charset=us-ascii Content-Disposition: attachment; filename="ccl2.in" AlH4 SUPERCELL CRYSTAL 0 0 0 11 5.33 5.53 7.68 90.103 6 13 0.0 0.0 0.0 11 0.0 0.0 0.5 11 0.9897 0.4532 0.2535 1 0.1000 0.0481 0.2164 1 0.2281 0.3307 0.5437 1 0.1608 0.2673 0.9366 SUPERCEL 2 0 0 0 2 0 0 0 2 COORPRT ENDG 11 4 0 0 8 2. 1. 56700. 0.000225 8060. 0.00191 1704. 0.01105 443.6 0.05006 133.1 0.1691 45.8 0.3658 17.75 0.3998 7.38 0.1494 0 1 5 8. 1. 119.0 -0.00673 0.00803 25.33 -0.0798 0.0639 7.80 -0.0793 0.2074 3.00 0.3056 0.3398 1.289 0.5639 0.3726 0 1 1 0. 1. 0.578 1. 1. 0 1 1 0. 1. 0.323 1. 1. 13 5 0 0 8 2. 1. 70510.0 0.000226 10080.0 0.0019 2131.0 0.0110 547.5 0.0509 163.1 0.1697 54.48 0.3688 19.05 0.3546 5.402 0.0443 0 1 5 8. 1. 139.6 -0.01120 0.0089 32.53 -0.1136 0.0606 10.23 -0.0711 0.1974 3.810 0.5269 0.3186 1.517 0.7675 0.2995 0 1 1 0. 1. 0.59 1. 1. 0 1 1 0. 1. 0.35 1. 1. 0 3 1 0. 1. 0.51 1. 1. 1 4 0 0 5 2.0 1.0 120.0 0.000267 40.0 0.002249 12.8 0.006470 3.98 0.03291 1.21 0.09551 0 0 1 0.0 1.0 0.47 1.0 0 0 1 0.0 1.0 0.14 1.0 0 2 1 0.0 1.0 0.30 1.0 99 0 PRINT ENDBS BIPOSIZE 3103200 DFT EXCHANGE PWGGA CORRELAT PWGGA END TOLINTEG 8 8 8 8 16 END 4 4 4 FMIXING 30 MAXCYCLE 50 PPAN ENDSCF --OrT4iOlIQZp3kw4S-- From chemistry-request@ccl.net Fri Jun 17 13:18:48 2005 Received: from smtp1.Stanford.EDU (smtp1.Stanford.EDU [171.67.16.123]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j5HHIiMp017990 for ; Fri, 17 Jun 2005 13:18:44 -0400 Received: from [171.65.23.152] (B157-PowerBookG4.Stanford.EDU [171.65.23.152]) by smtp1.Stanford.EDU (8.12.11/8.12.11) with ESMTP id j5HHIgah013851 for ; Fri, 17 Jun 2005 10:18:43 -0700 Message-ID: <42B305F2.4040302 %x% stanford.edu> Date: Fri, 17 Jun 2005 10:18:42 -0700 From: Xavier Deupi User-Agent: Mozilla Thunderbird 1.0.2 (Macintosh/20050317) X-Accept-Language: en-us, en MIME-Version: 1.0 To: chemistry %x% ccl.net Subject: Re: CCL:Alpha Helix kink References: <42B28FE5.30205 %x% pharma.u-strasbg.fr> In-Reply-To: <42B28FE5.30205 %x% pharma.u-strasbg.fr> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit X-Spam-Status: No, score=0.0 required=5.0 tests=none autolearn=failed version=3.0.3 X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net Hi Mireille, You can also use HelAnal (Bansal et al. J Biomol Struct Dyn. 2000 Apr;17(5):811-9) to detect and measure local distortions of the helical structure, in terms of local (i.e. per residue) bend and twist angles. You can see an application to Pro-kinked alpha-helices in Deupi et al., Biophys J. 2004 Jan;86(1 Pt 1):105-15. Hope this helps, xavi Mireille Krier wrote: > Dear CCLers, > > we are looking for a tool that can detect (because not always induced > by proline) > and measure the angle of an kink in an alpha helix. > Any suggestions? > We found in the literature SWINK, (Cordes et al., Sansom Group) > was developed to estimate the kink and swivel angle of TM small alpha, > Greek-helices. > Any ideas, if this is available? > > Many thanks in advance to the community for the any help provided. > > Mireille Krier > -- Xavier Deupi, Ph.D. Department of Molecular and Cellular Physiology Beckman Center for Molecular and Genetic Medicine (B161) 279 Campus Drive, Stanford University School of Medicine Stanford, CA 94305 (USA) E-mail: Xavier.Deupi %x% stanford.edu Phone: +1 (650) 725-6497 Fax : +1 (650) 725-8021 From chemistry-request@ccl.net Fri Jun 17 15:09:07 2005 Received: from ithnet.com (mail-a03.ithnet.com [217.64.83.98]) by server.ccl.net (8.13.1/8.13.1) with SMTP id j5HJ8xG4022028 for ; Fri, 17 Jun 2005 15:09:03 -0400 Received: (qmail 31626 invoked by uid 0); 17 Jun 2005 19:08:57 -0000 Received: from rer.-at-.panet.de by heather-ng (Processed in 1.944338 secs); 17 Jun 2005 19:08:57 -0000 X-Spam-Status: No, score=0.1 required=5.0 tests=FORGED_RCVD_HELO autolearn=failed version=3.0.3 X-Virus-Status: No Received: from unknown (HELO panet.de) (84.145.241.201) by heather-ng.ithnet.com with SMTP; 17 Jun 2005 19:08:55 -0000 X-Sender-Authentication: SMTP AUTH verified Message-ID: <42B31FF5.F6C57FC.-at-.panet.de> Date: Fri, 17 Jun 2005 20:09:41 +0100 From: rer X-Mailer: Mozilla 4.75 [de]C-CCK-MCD QXW0325a (Win98; U) X-Accept-Language: de,en MIME-Version: 1.0 To: chemistry.-at-.ccl.net Subject: Gaussian98W memory requirements Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net Hello together, there are actually two questions. The first relates to an observation made by scanning the CCL archive. In almost regular time spans the question appears what to with the error codes given by Gaussian after a link dies. Surprisingly (at leat so me), a summuray of responses to these questions is apparently never posted. Does it mean that these error codes are only for the specialists > from Gaussian Inc., because no member of this list (THE experts, I suppose) has an answer to these questions so that no summary can be given? The second question relates to a hard (and unpleasant fact). A calculation is running on GAUSSIAN98W on a 3.4 GHz Pentium IV with 1 GByte working memory and 100 GByte disk space. Following the use of internal memory during a run it is found that the code never uses the internal memory to more than 20%. The calculation is a point optimisation of a lanthanide molecule with 8 water molecules (other ligand combinations were tested, the observation is the same - it seems to depend on the fact that a lanthanide ion is used). SDD pseudo cores with SDD basis sets is used for the lanthanide ion, the basis set for the light elements were successively reduced to 3-21G* (with no effect). The algorithm converges. Upon going into the next 'round', it dies with the following message: Compute integral first derivatives. Integral derivatives from FoFDir, PRISM(SPDF). Symmetry not used in FoFDir. MinBra= 0 MaxBra= 3 Meth= 1. IRaf= 0 NMat= 1 IRICut= 1 DoRegI=T DoRafI=F ISym2E= 0 JSym2E=0. Insufficient memory for a single shell combination in PrsMar called from PRISM: LenV= 57934341 MaxCom= 0 Error termination via Lnk1e in d:\gaussian98w\l703.exe. Any suggestion to get around this nasty problem is highly welcome - as is contact to other CCL members doing Gaussian calculations with lanthanides. Best regards and thanks in advance Guenther Passau, Freiberg & Toronto From chemistry-request@ccl.net Fri Jun 17 13:52:43 2005 Received: from mail.ic.sunysb.edu (mail.ic.sunysb.edu [129.49.1.4]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j5HHqcfI019593 for ; Fri, 17 Jun 2005 13:52:38 -0400 Received: from postal.ic.sunysb.edu (mail [129.49.1.4]) by mail.ic.sunysb.edu (8.13.1/8.13.1) with SMTP id j5HH8N50029494 for ; Fri, 17 Jun 2005 13:08:26 -0400 (EDT) Received: from smtp.ic.sunysb.edu ([129.49.1.24]) by postal.ic.sunysb.edu (SMSSMTP 4.1.5.31) with SMTP id M2005061713082602919 for ; Fri, 17 Jun 2005 13:08:26 -0400 Received: from sparky.ic.sunysb.edu (daemon.-at-.sparky.ic.sunysb.edu [129.49.1.3]) by smtp.ic.sunysb.edu (8.13.1/8.13.1) with ESMTP id j5HH8QEf029511 for ; Fri, 17 Jun 2005 13:08:26 -0400 (EDT) Received: from localhost (yonyang@localhost) by sparky.ic.sunysb.edu (8.12.10/8.12.9) with ESMTP id j5HH8L4X009231 for ; Fri, 17 Jun 2005 13:08:25 -0400 (EDT) Date: Fri, 17 Jun 2005 13:08:21 -0400 (EDT) From: Yong Liang Yang To: chemistry.-at-.ccl.net Subject: Re: CCL:autodock3 dies upon launch with multiple errors In-Reply-To: <20050617151356.79959.qmail.-at-.web41210.mail.yahoo.com> Message-ID: References: <20050617151356.79959.qmail.-at-.web41210.mail.yahoo.com> MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed X-Spam-Status: No, score=0.0 required=5.0 tests=none autolearn=failed version=3.0.3 X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net Dear Robyn: In a command window in IRIX, try, # mkdpf3 .pdbq .pdbqs this will produce a ..dpf file, then try # autodock3 -p ..dpf -l ..dlg& This might work if ADT could not launch the job. Cheers Yong On Fri, 17 Jun 2005, Robyn Ayscue wrote: > All, > > Sorry for the cross-post. > > I'm running AutoDockTools using autodock/autogrid > version 3.05 on an SGI machine with IRIX 6.5.24. I'm > trying to dock an effector molecule in the active site > of an enzyme (p450 2c9) with a substrate molecule also > present. Autogrid finishes out with no problems, but > autogrid dies immediately upon launch with the > following errors: > > > Can't find ".dpf" in the dock-parameter filename. > > AutoDock needs the extension of the grid parameter > file to be ".gpf" > and that of the docking parameter file to be ".dpf". > > /disk02/usr/local/autodock/dist305/bin/sgi4D.IRIX64_6.5_R10000/autodock3: > Wrong number of x grid-points in grid-map file > "2c9q_HEMq_FLPq.A.map". > /disk02/usr/local/autodock/dist305/bin/sgi4D.IRIX64_6.5_R10000/autodock3: > Use either 32 or 1129013060 throughout! > /disk02/usr/local/autodock/dist305/bin/sgi4D.IRIX64_6.5_R10000/autodock3: > ERROR: Using wrong grid-map file. > > /disk02/usr/local/autodock/dist305/bin/sgi4D.IRIX64_6.5_R10000/autodock3: > Aborting... > > /disk02/usr/local/autodock/dist305/bin/sgi4D.IRIX64_6.5_R10000/autodock3: > Unsuccessful Completion. > > > First it complains about not being able to find a > docking parameter file with .dpf as the suffix, but > the file DOES have a .dpf suffix and it is listed as > having one in the command that is typed in the command > line used to launch autodock. The .dpf file looks fine > as far as I can tell, compared to other .dpf files > I've used for other docking runs that have completed > successfully. > > The next thing it complains about is the differing > number of grid points. It keeps referring to the > number "1129013060" but I can't find that number in > any of the grid-map files. The number of x- grid > points in all grid-map files is the same. > > Autodock comes to the conclusion that I'm using the > wrong grid-map files, but the files I'm using ARE the > correct files (I checked and double-checked). > > If anyone has had experience with this kind of error > message and knows how to resolve it, I'd appreciate > any input. Thanks much! > > Robyn Ayscue > rayscue.-at-.hsc.wvu.edu > kajsicat.-at-.yahoo.com > > > > > > > ____________________________________________________ > Yahoo! Sports > Rekindle the Rivalries. Sign up for Fantasy Football > http://football.fantasysports.yahoo.com > > > -= 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 is mail bouncing from ccl.net domain due to spam filters, please > use the Web based form from CCL Home Page > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > > From chemistry-request@ccl.net Fri Jun 17 13:45:45 2005 Received: from smtpgw.sud-chemieinc.com (smtpgw.sud-chemieinc.com [208.23.162.5]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j5HHjclC019254 for ; Fri, 17 Jun 2005 13:45:38 -0400 Received: from localhost (localhost.localdomain [127.0.0.1]) by localhost.sud-chemieinc.com (Postfix) with ESMTP id 6B23A324171 for ; Fri, 17 Jun 2005 13:31:26 -0400 (EDT) Received: from smtpgw.sud-chemieinc.com ([127.0.0.1]) by localhost (smtpgw.sud-chemieinc.com [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id 22789-01 for ; Fri, 17 Jun 2005 13:31:24 -0400 (EDT) Received: from srvkyec1.americas.sc-world.com (srvkyec1.americas.sc-world.com [10.16.100.11]) by smtpgw.sud-chemieinc.com (Postfix) with ESMTP id 6B4953241A1 for ; Fri, 17 Jun 2005 13:31:18 -0400 (EDT) Received: from srvkyem1.americas.sc-world.com ([10.16.100.68]) by srvkyec1.americas.sc-world.com with Microsoft SMTPSVC(5.0.2195.6713); Fri, 17 Jun 2005 13:44:37 -0400 x-mimeole: Produced By Microsoft Exchange V6.0.6556.0 content-class: urn:content-classes:message MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Subject: RE: Force Constants Date: Fri, 17 Jun 2005 13:44:37 -0400 Message-ID: <9DD56492790889439F731F5BD6DACA0007D78B22~at~srvkyem1.americas.sc-world.com> X-MS-Has-Attach: X-MS-TNEF-Correlator: Thread-Topic: Force Constants Thread-Index: AcVyvH4glacHDmj7SvWXeso8YXT+UAApVIuA From: "Shobe, David" To: X-OriginalArrivalTime: 17 Jun 2005 17:44:37.0737 (UTC) FILETIME=[3B37E590:01C57364] X-Spam-Status: No, score=0.0 required=5.0 tests=none autolearn=failed version=3.0.3 X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id j5HHjjlC019297 1 eV = 1.60218 x 10^-19 J thus 1 eV/A = (1.60218 x 10^-19 J)/(10^-10 m) = 1.60218 x 10^-9 N and 1 N = 6.2415 x 10^8 eV/A 1 dyne = 10^-5 N thus 1 mDyne = 10^-11 N So the conversion factor is 1 mdyne/A = 6.2415 x 10^-3 eV/A^2. --David Shobe, Ph.D., M.L.S. S|d-Chemie, Inc. phone (502) 634-7409 fax (502) 634-7724 Don't bother flaming me: I'm behind a firewall. -----Original Message----- From: Computational Chemistry List [mailto:chemistry-request~at~ccl.net] On Behalf Of Pradyumna Shaakuntal Singh Sent: Thursday, June 16, 2005 12:58 PM To: chemistry~at~ccl.net Subject: CCL:Force Constants Hello, Could someone on this list please suggest how I could obtain a force-constant for a diatomic and triatomic molecule in eV/A^2 instead of mDyne/A. I am using Gaussian at the B3LYP/MP2 level. Thanks, Pradyumna -= 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 is mail bouncing from ccl.net domain due to spam filters, please use the Web based form from CCL Home Page -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ From chemistry-request@ccl.net Fri Jun 17 20:32:39 2005 Received: from mail.ic.sunysb.edu (mail.ic.sunysb.edu [129.49.1.4]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j5I0WXmh003401 for ; Fri, 17 Jun 2005 20:32:33 -0400 Received: from postal.ic.sunysb.edu (mail [129.49.1.4]) by mail.ic.sunysb.edu (8.13.1/8.13.1) with SMTP id j5I0WW6u010709 for ; Fri, 17 Jun 2005 20:32:32 -0400 (EDT) Received: from smtp.ic.sunysb.edu ([129.49.1.24]) by postal.ic.sunysb.edu (SMSSMTP 4.1.5.31) with SMTP id M2005061720323213672 for ; Fri, 17 Jun 2005 20:32:32 -0400 Received: from sparky.ic.sunysb.edu (daemon = sparky.ic.sunysb.edu [129.49.1.3]) by smtp.ic.sunysb.edu (8.13.1/8.13.1) with ESMTP id j5I0WWpm010703 for ; Fri, 17 Jun 2005 20:32:32 -0400 (EDT) Received: from localhost (yonyang@localhost) by sparky.ic.sunysb.edu (8.12.10/8.12.9) with ESMTP id j5I0WVsr016669 for ; Fri, 17 Jun 2005 20:32:32 -0400 (EDT) Date: Fri, 17 Jun 2005 20:32:31 -0400 (EDT) From: Yong Liang Yang To: chemistry = ccl.net Subject: Autodock_3.0.5 Makefile for Linux Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed X-Spam-Status: No, score=0.0 required=5.0 tests=none autolearn=failed version=3.0.3 X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net hello CCLers: I am wondering if anybody could kindly send me a copy of Makefile for autodock and autogrid under Linux OS. I am kind of stuck by modifying the Makefile. Thanks very much. Cheers Yong From chemistry-request@ccl.net Fri Jun 17 17:28:16 2005 Received: from wproxy.gmail.com (wproxy.gmail.com [64.233.184.198]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j5HLSD3P027993 for ; Fri, 17 Jun 2005 17:28:13 -0400 Received: by wproxy.gmail.com with SMTP id 63so178930wri for ; Fri, 17 Jun 2005 14:28:12 -0700 (PDT) DomainKey-Signature: a=rsa-sha1; q=dns; c=nofws; s=beta; d=gmail.com; h=received:message-id:date:from:reply-to:to:subject:mime-version:content-type:content-transfer-encoding:content-disposition; b=TCJsDPHXN27Nq4P2wKfP1zgIHYMvaJhjZ9Q7CEWETJdBQoF1prYWZxRiTuPbD/3sbVpVrSxhIXdeFhT/Dd/q9TAmLqbisbakIZTQIEw07PHe/BxZq8MtjNedKeqqtWNgRkeLBd/+3y+wajKXjoaPY9TzB3g2dEWsIPAC7BlGtGw= Received: by 10.54.19.75 with SMTP id 75mr52655wrs; Fri, 17 Jun 2005 14:28:12 -0700 (PDT) Received: by 10.54.20.63 with HTTP; Fri, 17 Jun 2005 14:28:12 -0700 (PDT) Message-ID: <755a1e3b050617142875d94e96 = mail.gmail.com> Date: Fri, 17 Jun 2005 14:28:12 -0700 From: Pradyumna Shaakuntal Singh Reply-To: pradyu = u.arizona.edu To: chemistry = ccl.net Subject: Force Constants Mime-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Disposition: inline X-Spam-Status: No, score=0.0 required=5.0 tests=RCVD_BY_IP autolearn=failed version=3.0.3 X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id j5HLSG3P027997 Hi, I'm trying to compute the force constant for the superoxide ion (O2-) using MP2/6-31G*. using Gaussian 03. The value I get after running a frequency calculation is 11.03 mDyne/A. This converts to 68.9 eV/A^2. The experimental value (using spectroscopic constants) is about 37.8 eV/A^2. Clealy, I am quite off the mark. I suspect I am not interpreting the gaussian results correctly. Could anyone throw some light on whether I'm doign something wrong, and if so, what ? Any help is will be appreciated. Thanks, Pradyumna