From chemistry-request@server.ccl.net Mon Oct 7 06:23:52 2002 Received: from pcserver.iqm.unicamp.br ([143.106.51.10]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g97ANqu00359 for ; Mon, 7 Oct 2002 06:23:52 -0400 Received: from localhost (localhost.iqm.unicamp.br [127.0.0.1]) by pcserver.iqm.unicamp.br (Postfix) with ESMTP id B38EC3EFA for ; Mon, 7 Oct 2002 07:23:50 -0300 (BRT) Received: from iqm.unicamp.br (luxor.iqm.unicamp.br [143.106.51.146]) by pcserver.iqm.unicamp.br (Postfix) with ESMTP id EEDC43EF7 for ; Mon, 7 Oct 2002 07:23:48 -0300 (BRT) Message-ID: <3DA16090.7010307@iqm.unicamp.br> Date: Mon, 07 Oct 2002 07:23:12 -0300 From: Milton Taidi Sonoda User-Agent: Mozilla/5.0 (X11; U; Linux i386; en-US; rv:1.0rc2) Gecko/20020508 X-Accept-Language: en-us, en MIME-Version: 1.0 To: chemistry ccl Subject: dna molecular building Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit X-Virus-Scanned: by AMaViS perl-11 Hi all I would like to know if there is any dna molecular building free program that, providing the nucleotide sequence, it outputs a first approximation to dna molecular moldel, in PDB format, if possible. Thank you all Milton Taidi Sonoda From chemistry-request@server.ccl.net Mon Oct 7 07:23:21 2002 Received: from donjuan.stud.chemie.tu-muenchen.de (root@[129.187.245.122]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g97BNJu01516 for ; Mon, 7 Oct 2002 07:23:20 -0400 Received: from donjuan.stud.chemie.tu-muenchen.de (smmsp@localhost [127.0.0.1]) by donjuan.stud.chemie.tu-muenchen.de (8.12.3/8.12.3/Debian -4) with ESMTP id g97BNJqE011173 for ; Mon, 7 Oct 2002 13:23:19 +0200 Received: (from banck@localhost) by donjuan.stud.chemie.tu-muenchen.de (8.12.3/8.12.3/Debian -4) id g97BNIZ7011171 for chemistry@ccl.net; Mon, 7 Oct 2002 13:23:18 +0200 From: Michael Banck Date: Mon, 7 Oct 2002 13:23:18 +0200 To: chemistry@ccl.net Subject: Re: CCL:dna molecular building Message-ID: <20021007112318.GA11157@stud.ch.tum.de> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline In-Reply-To: <3DA16090.7010307@iqm.unicamp.br> User-Agent: Mutt/1.3.28i Hi, > I would like to know if there is any dna molecular building free > program that, providing the nucleotide sequence, it outputs > a first approximation to dna molecular moldel, in PDB format, > if possible. have a look at http://rutchem.rutgers.edu/~xiangjun/software.html or http://rutchem.rutgers.edu/~xiangjun/3DNA/index.html hope that helps, Michael From chemistry-request@server.ccl.net Mon Oct 7 09:30:45 2002 Received: from facstaff.wesleyan.edu ([129.133.1.61]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g97DUju04588 for ; Mon, 7 Oct 2002 09:30:45 -0400 Received: from wesleyan.edu (ion.chem.wesleyan.edu [129.133.89.89]) by facstaff.wesleyan.edu (8.11.2/8.10.2) with ESMTP id g97DUXd28989; Mon, 7 Oct 2002 09:30:33 -0400 (EDT) Message-ID: <3DA18BE8.5070507@wesleyan.edu> Date: Mon, 07 Oct 2002 09:28:08 -0400 From: Surjit Dixit Reply-To: sdixit@wesleyan.edu Organization: Wesleyan University User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.0.0) Gecko/20020529 X-Accept-Language: en-us, en MIME-Version: 1.0 To: Milton Taidi Sonoda CC: chemistry ccl Subject: Re: CCL:dna molecular building References: <3DA16090.7010307@iqm.unicamp.br> Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit X-ECS-MailScanner: Found to be clean Hi, You could try the web based server at http://ludwig.chem.wesleyan.edu/dna/ You have the option of using different dinucleotide models to build your model. You can download the predicted structure in PDB format. Surjit Milton Taidi Sonoda wrote: > Hi all > I would like to know if there is any > dna molecular building free program > that, providing the nucleotide sequence, it > outputs a first approximation to dna molecular > moldel, in PDB format, if possible. > Thank you all > Milton Taidi Sonoda > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To > Admins > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: > jkl@ccl.net > > > > > > > From chemistry-request@server.ccl.net Mon Oct 7 00:51:53 2002 Received: from mx2.elte.hu ([157.181.151.9]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g974pqu26919 for ; Mon, 7 Oct 2002 00:51:53 -0400 Received: from theopzs.chem.elte.hu (theopzs.chem.elte.hu [157.181.193.147]) by mx2.elte.hu (Postfix) with ESMTP id 5A00F48755; Mon, 7 Oct 2002 06:51:42 +0200 (CEST) Date: Mon, 7 Oct 2002 06:47:30 +0200 (CEST) From: Zsolt Szekeres To: Yi Gao Cc: chemistry@ccl.net Subject: Re: CCL:question on gamess In-Reply-To: <20021007032501.70019.qmail@web21304.mail.yahoo.com> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, you probably received an I/O error because the partition which you used as a scratch got full. You may want to reset your scratch directory/ directories in the rungms script or delete unnecessary files stored there. Zsolt From chemistry-request@server.ccl.net Mon Oct 7 07:41:44 2002 Received: from shardagate.mahindrabt.com ([203.124.158.2]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g97Bfdu01923 for ; Mon, 7 Oct 2002 07:41:41 -0400 Received: from thisdomain (mailscan.sharda.mahindrabt.com [10.5.0.97]) by shardagate.mahindrabt.com (8.9.3/8.9.3/SuSE Linux 8.9.3-0.1) with ESMTP id RAA28988 for ; Mon, 7 Oct 2002 17:11:22 +0530 Received: from intranet.sharda.mahindrabt.com by mahindrabt.com ; Mon, 07 Oct 2002 17:03:25 +0530 Date: Mon, 07 Oct 2002 17:03:25 +0530 X-Originating-IP: 10.5.0.15 X-Auth-User: sudhirk@mahindrabt.com Received: from mahindrabt.com ([10.5.12.195]) by intranet.sharda.mahindrabt.com (8.9.3/8.9.3) with ESMTP id RAA32061 for ; Mon, 7 Oct 2002 17:11:16 +0530 Message-ID: <3DA17242.5975F177@mahindrabt.com> Date: Mon, 07 Oct 2002 17:08:43 +0530 From: "Dr. Sudhir A. Kulkarni" Organization: Mahindra British Telecom Limited X-Mailer: Mozilla 4.7 [en] (Win95; I) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: H-bonded clusters Content-Type: multipart/mixed; boundary="------------5ACFC16B37FC64872ED827F5" This is a multi-part message in MIME format. --------------5ACFC16B37FC64872ED827F5 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hello, We are working H-bonded clusters of some small molecules using Gaussian 98. We found that clusters up to n=2-4 are quite easy to get and are optimized at both RHF and MP2 level (using 6-31++G** and CC-pVTZ basis). However for n=5 or 6 we face a peculiar problem: we find several structures that are true minima (all frequencies positive) at RHF level, however when we optimize these structures using MP2 method they have more than 5 negative frequencies. I would like to know if anyone else has such experience & whether there is any solution to this problem. Thanks. Sudhir ********************************************************* Disclaimer This message (including any attachments) contains confidential information intended for a specific individual and purpose, and is protected by law. If you are not the intended recipient, you should delete this message and are hereby notified that any disclosure, copying, or distribution of this message, or the taking of any action based on it, is strictly prohibited. ********************************************************* Visit us at http://www.mahindrabt.com --------------5ACFC16B37FC64872ED827F5 Content-Type: text/x-vcard; charset=us-ascii; name="sudhirk.vcf" Content-Transfer-Encoding: 7bit Content-Description: Card for Dr. Sudhir A. Kulkarni Content-Disposition: attachment; filename="sudhirk.vcf" begin:vcard n:Kulkarni;Dr. Sudhir A. tel;fax:+91-20-542-4466 tel;work:+91-20-401-8350 x-mozilla-html:FALSE url:www.mahindrabt.com org:Mahindra British Telecom Limited;Research and Development version:2.1 email;internet:sudhirk@MahindraBT.com title:Consultant adr;quoted-printable:;;Sharda Center, Off Karve Road=0D=0AErandwane;Pune;Maharashtra;411 004;India x-mozilla-cpt:;32608 fn:Dr. Sudhir A. Kulkarni end:vcard --------------5ACFC16B37FC64872ED827F5-- From chemistry-request@server.ccl.net Mon Oct 7 07:42:28 2002 Received: from yangtze.hku.hk (IDENT:root@[147.8.148.244]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g97BgQu01942 for ; Mon, 7 Oct 2002 07:42:27 -0400 Received: from localhost (lhhu@localhost) by yangtze.hku.hk (8.11.6/8.9.3) with ESMTP id g97Bpeq26312 for ; Mon, 7 Oct 2002 19:51:40 +0800 Date: Mon, 7 Oct 2002 19:51:40 +0800 (HKT) From: Hu LiHong To: chemistry@ccl.net Subject: on calculation of protein Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear all, I have three questions, if someone can give me an answer or suggestion, I greatly appreciate your kind help. 1. How to deal with the charge of protein (the crystal stucture of protein > from protein data bank)? Should I keep it or change it to zero or change it to any charges? 2 I want to know if I want to investigate the interaction between protein and inhibitors, should I optimize the structure of protein? 3 How to find the binding energy in the qmmm output file calculated by CHARMM standalone version? Sincerely yours, Carol From chemistry-request@server.ccl.net Mon Oct 7 04:41:51 2002 Received: from websmtp03.sohu.com ([61.135.145.13]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g978fou30680 for ; Mon, 7 Oct 2002 04:41:51 -0400 Received: from mail.sohu.com (unknown [192.168.41.208]) by websmtp03.sohu.com (Postfix) with ESMTP id A39D366DF9 for ; Mon, 7 Oct 2002 16:41:33 +0800 (CST) Message-ID: <3060413.1033980096844.JavaMail.postfix@srv23.mail.sohu.com> Date: Mon, 7 Oct 2002 16:41:36 +0800 (CST) From: To: Subject: how to deal with the metal ion in autodock? Mime-Version: 1.0 Content-Type: text/plain; charset="GB2312" Content-Transfer-Encoding: 8bit X-Mailer: Sohu Web Mail 2.0.13 X-SHIP: 134.157.24.81 Dear CCLers, Hi. Who knows that how to deal with the ligand contained metal ion in autodock? For example, the Fe(III) in heme, I can't add gastager charge on it in sybyl. Who has done it, can you tell me? How to prepare the input file about metal ion? Thank you very much! Li Qiang Shanghai Institute of Organic Chemistry Chinese Academy of Science No. 354, Road Fenglin Shanghai, 200032, China Tel: 0862164163300-2735 Fax: 0862164166128 E-mail: chem_liqiang@sohu.com From chemistry-request@server.ccl.net Mon Oct 7 12:56:44 2002 Received: from trivial.uchicago.edu (IDENT:root@[128.135.160.75]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g97Guiu10746 for ; Mon, 7 Oct 2002 12:56:44 -0400 Received: from localhost (cmtaylor@localhost) by trivial.uchicago.edu (8.9.3/8.9.3) with ESMTP id LAA21599 for ; Mon, 7 Oct 2002 11:56:44 -0500 Date: Mon, 7 Oct 2002 11:56:44 -0500 (CDT) From: Caroline Taylor To: CCL list Subject: R^2 values in Molden? Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi. Does anybody know if Molden can calculate the R^2 values of an orbital? Thanks! -Caroline --------------------------------------------- Caroline M. Taylor Department of Chemistry University of Chicago, James Franck Institute 5640 S. Ellis Avenue Chicago, Illinois 60637 (773) 702-7223 http://home.uchicago.edu/~cmtaylor --------------------------------------------- From chemistry-request@server.ccl.net Mon Oct 7 14:04:32 2002 Received: (from root@localhost) by server.ccl.net (8.11.6/8.11.0) id g97I4WA12465 for chemistry@ccl.net; Mon, 7 Oct 2002 14:04:32 -0400 Date: Mon, 7 Oct 2002 14:04:32 -0400 Message-Id: <200210071804.g97I4WA12465@server.ccl.net> From: Robert Flight To: Computational Chemistry List Cc: Ghislain Deslongchamps , Larry Calhoun Subject: Compiling Autodock 3.05 on Unix Fellow CCL'ers, I'm trying to compile a new Autodock binary on my Unix machine (SGI O2, running Irix 6.5, MIPSPRO C++ compiler). I'm trying to add extra atom types (16 vs the default 8) and change the maximum number of runs. This should be fairly simple, I've managed it under linux and I didnt think it would be too much more difficult under Unix. I've modified the "autocomm.h" and "constants.h" files appropriately, and then changed the "Makefile" to reflect my machine. Unfortunately, it doesnt want to work. I've modified the Makefile numerous times tyring a few different combinations, but nothing works. Any help would or suggestions would be appreciated. Below is the present error that comes up during the compile. Thanks, Robert CC -DNOSQRT -o autodock3 main.o -L. -lad -lm ld32: ERROR 146: Expecting relocatable objects: main.o is IPA intermediate object; You must specify -IPA on link line. ******************************** Robert Flight Masters Student Department of Chemistry University of New Brunswick Fredericton, NB Canada E3B 6E2 e-mail: L72K6@unb.ca ********************************