From chemistry-request@server.ccl.net Mon Mar 24 10:37:20 2003 Received: from web15202.mail.bjs.yahoo.com ([61.135.128.132]) by server.ccl.net (8.11.6/8.11.0) with SMTP id h2OFbJr28316 for ; Mon, 24 Mar 2003 10:37:19 -0500 Message-ID: <20030324153717.43283.qmail@web15202.mail.bjs.yahoo.com> Received: from [202.119.32.49] by web15202.mail.bjs.yahoo.com via HTTP; Mon, 24 Mar 2003 23:37:17 CST Date: Mon, 24 Mar 2003 23:37:17 +0800 (CST) From: =?gb2312?q?Jinsong=20Zhao?= Subject: How to make a executable MOPAC To: chemistry@ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=gb2312 Content-Transfer-Encoding: 8bit Dear all, I have some problems to make a executable MOPAC on a Linux PC (RetHat 8.0). Is there anyone who makes a excutable MOPAC on such machine? Would you please give me some instruction, or email me your Makefile? Alternatively, please tell me where I could get the complied MOPAC7 and/or MOPAC6 (static). Thank you very much in advance! Sincerely yours, Jinsong _________________________________________________________ Do You Yahoo!? 更多惊喜，同样精彩，NetVista A30 热卖 http://ad.cn.doubleclick.net/clk;5313999;7930402;p?http://www.ibm.com/cn/promotion/pc/netvista_a30/index.shtml From chemistry-request@server.ccl.net Mon Mar 24 18:44:16 2003 Received: from ks.uiuc.edu ([130.126.120.73]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h2ONiGr05075 for ; Mon, 24 Mar 2003 18:44:16 -0500 Received: from ks.uiuc.edu (dhcp31.ks.uiuc.edu [130.126.120.231]) by ks.uiuc.edu (8.12.8/8.11.2) with ESMTP id h2ONiGEF025747; Mon, 24 Mar 2003 17:44:16 -0600 (CST) Date: Mon, 24 Mar 2003 17:44:11 -0600 Reply-To: biocore@ncsa.uiuc.edu Subject: BioCoRE@NCSA Collaborative Research Environment Content-Type: text/plain; charset=US-ASCII; format=flowed Mime-Version: 1.0 (Apple Message framework v551) From: Robert Brunner To: chemistry@ccl.net Content-Transfer-Encoding: 7bit Message-Id: <83721C70-5E52-11D7-ACAD-0030654E438A@ks.uiuc.edu> X-Mailer: Apple Mail (2.551) March 24, 2003: Urbana, Illinois - The Theoretical and Computational Biophysics (TCB) Group at the University of Illinois is proud to announce the initial public release of BioCoRE@NCSA, a collaborative research environment at the National Center for Supercomputer Applications. The TCB Group develops BioCoRE with support from the NIH's National Center for Research Resources. The BioCoRE@NCSA effort is also funded by the NSF. BioCoRE is a collaborative work environment for biomedical research, research management and training. A resource-centered platform, BioCoRE offers scientists, working together or alone, a seamless interface to a broad range of local and remote technologies such as discipline-specific and general tools, data, and visualization solutions. In creating unprecedented proximity to colleagues' expertise and knowledge, BioCoRE empowers scientists everywhere, establishing equal access to research and training opportunities. To harness and streamline collaborative capabilities across temporal and physical boundaries in research and training, BioCoRE builds on the transparent use of and communication between technological resources (hardware and software) and databases. BioCoRE features powerful yet easy-to-use tools, among them co-authoring papers and other documents, running applications on supercomputers, sharing molecular visualization over the Internet, notifying project team members of recent project changes by email, chatting, keeping a lab book, and other practical features. For additional information, please visit the BioCoRE@NCSA website at http://biocore.ncsa.uiuc.edu/ The TCB Group encourages BioCoRE@NCSA users to be closely involved in the development process through reporting bugs, contributing fixes, regular feedback mechanisms, periodic surveys and via other means. Questions or comments may be directed to biocore@ncsa.uiuc.edu. We are eager to hear from you, and thank you for using our software! From chemistry-request@server.ccl.net Mon Mar 24 13:00:37 2003 Received: from bureau6.utcc.utoronto.ca ([128.100.132.16]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h2OI0br31538 for ; Mon, 24 Mar 2003 13:00:37 -0500 Received: from mditdell.mdit.utoronto.ca ([128.100.251.12] HELO MditDell ident: IDENT-NOT-QUERIED [port 1166]) by bureau6.utcc.utoronto.ca with SMTP id <238444-8250>; Mon, 24 Mar 2003 13:00:22 -0500 From: "William Wei" To: "Amber List" , "CCLers" Subject: Protein-Inhibitor binding afinity Date: Mon, 24 Mar 2003 13:02:04 -0500 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 V6.00.2600.0000 Hi , I want to calculate the binding affinity of protein complex with inhibitors. Could anyone give me some suggestion? Except molecular dynamics simulation in amber, what other software is good at it? Or some reference. Thanks. Have a good day, William ------------------------- William Wei Faculty of Pharmacy 19 Russell Street Toronto, ON. M5S 2S2 Tel: 1-416-946-8469 Fax: 1-416-978-8511 Email: william@phm.utoronto.ca william.wei@utoronto.ca From chemistry-request@server.ccl.net Mon Mar 24 15:49:09 2003 Received: from sal.ahpcrc.org ([144.34.1.1]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h2OKn9r01830 for ; Mon, 24 Mar 2003 15:49:09 -0500 Received: from mycroft.ahpcrc.org (mycroft.ahpcrc.org [144.34.9.34]) by sal.ahpcrc.org (8.11.6/8.11.6) with ESMTP id h2OKn9v08601 for ; Mon, 24 Mar 2003 14:49:09 -0600 Received: from ahpcrc.org (GULL.dhcp.famu.ahpcrc.org [144.34.131.114]) by mycroft.ahpcrc.org (8.11.6/8.11.6) with ESMTP id h2OKn4932494 for ; Mon, 24 Mar 2003 14:49:04 -0600 Message-ID: <3E7F6F3F.A937427C@ahpcrc.org> Date: Mon, 24 Mar 2003 15:49:03 -0500 From: Genzo Tanaka X-Mailer: Mozilla 4.79 [en] (Windows NT 5.0; U) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: Optimization of 2D molecules Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi all, I encountered several times the floating point exception (signal 8) error for optimization of linear and/or flat molecules (CO2, naphthalene analogs) in Gaussian 98 on Cray T3E. Methods included PM3 as well as DFT (b3lyp/6-31G*). For CO2, we can fix the angle to 179.999..., but it is not a good idea. Does anybody know how to work around this? Your suggestions are welcome. Thanks, Genzo Tanaka From chemistry-request@server.ccl.net Mon Mar 24 00:36:40 2003 Received: from web15212.mail.bjs.yahoo.com ([61.135.128.142]) by server.ccl.net (8.11.6/8.11.0) with SMTP id h2O5adr07543 for ; Mon, 24 Mar 2003 00:36:39 -0500 Message-ID: <20030324053637.50877.qmail@web15212.mail.bjs.yahoo.com> Received: from [61.240.111.196] by web15212.mail.bjs.yahoo.com via HTTP; Mon, 24 Mar 2003 13:36:37 CST Date: Mon, 24 Mar 2003 13:36:37 +0800 (CST) From: =?gb2312?q?Jinsong=20Zhao?= Subject: maximum replicated memory of GAMESS To: chemistry@ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=gb2312 Content-Transfer-Encoding: 8bit Dear all, I have one questions about the maximum replicated memory which my job can use. I do the GAMESS calculation on one PC (LINUX). The total physic memory is 256M. I can allocate 2/3 of total memory to GAMESS. How do I define this in $SYSTEM group? And in general, how do you define it in your job? Thank you very much in advance! Sincerely yours, Jinsong Zhao zh_jinsong@yahoo.com.cn _________________________________________________________ Do You Yahoo!? 更多惊喜，同样精彩，NetVista A30 热卖 http://ad.cn.doubleclick.net/clk;5313999;7930402;p?http://www.ibm.com/cn/promotion/pc/netvista_a30/index.shtml From chemistry-request@server.ccl.net Mon Mar 24 18:22:07 2003 Received: from gate-sl1.mdli.com ([208.200.221.2]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h2ONM6r04815 for ; Mon, 24 Mar 2003 18:22:06 -0500 Received: (from smap@localhost) by gate-sl1.mdli.com (8.8.8/8.8.8) id PAA06475 for ; Mon, 24 Mar 2003 15:22:06 -0800 (PST) Received: from puffin.mdli.com(172.16.1.12) by gate-sl1 via smap (V2.1) id xmaa06473; Mon, 24 Mar 03 15:22:06 -0800 Received: from exch-sl02.mdli.com by puffin.mdli.com (980427.SGI.8.8.8/BCH1.0) id PAA84791; Mon, 24 Mar 2003 15:22:05 -0800 (PST) Received: by exch-sl02.mdli.com with Internet Mail Service (5.5.2653.19) id ; Mon, 24 Mar 2003 15:22:06 -0800 Message-ID: From: Terry Wright To: "'chemistry@ccl.net'" Subject: Request for papers - CINF session on Advances in Reaction Searchi ng - ACS New York, September 7-11, 2003 Date: Mon, 24 Mar 2003 15:22:02 -0800 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-Type: text/plain; charset="iso-8859-1" Hello I would like to invite you or your colleagues to submit abstracts for a CINF session entitled "Advances in Reaction Searching", to be held at the next National ACS in New York, Sept. 7-11, 2003. Reaction Databases and related reaction information sources have greatly helped synthesis chemists in recent years. Now, however, there is so much electronic information available, from so many sources, it is often difficult to efficiently search for the "relevant information". This session will focus on advances in tools, techniques, and technology for more efficient searching and organization of reaction information for the organic chemists. Example topics are listed, but not limited to, those below: * New searching applications and functionality for reaction retrieval * Reaction registration and building of "in-house" databases * New types of data sources for reaction information * New database models and integration of different types of data sources. * Tools or methods for classification or organization of reaction information - either at the database level or post-search handling The format will be 30-minute talks (this includes question time). The online submission system (OASYS) for New York is now active, at: To submit an abstract, please go to this website and select the "advances in reaction searching". Anyone without web access who wishes to submit an abstract can contact me. I look forward to receiving submissions to this symposium. Please contact me if you have any questions on this symposium. Terry Wright, Ph.D. MDL Information Systems, Inc. 14600 Catalina Street San Leandro, CA 94577 Phone: 510-357-2222, ext. 1392 Fax: 510-614-3652 terryw@mdl.com From chemistry-request@server.ccl.net Tue Mar 25 04:28:16 2003 Received: from century.fen.bilkent.edu.tr ([139.179.97.100]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h2P9SDN24421 for ; Tue, 25 Mar 2003 04:28:14 -0500 Received: from fen.bilkent.edu.tr (fenII-124.fen.bilkent.edu.tr [139.179.97.239]) by century.fen.bilkent.edu.tr (8.12.8/8.12.8) with ESMTP id h2P9Mhga003570 for ; Tue, 25 Mar 2003 11:22:49 +0200 (EET) Message-ID: <3E802213.5040205@fen.bilkent.edu.tr> Date: Tue, 25 Mar 2003 11:32:03 +0200 From: Ulrike Salzner Organization: Bilkent University User-Agent: Mozilla/5.0 (Windows; U; Win98; en-US; rv:0.9.4) Gecko/20011128 Netscape6/6.2.1 X-Accept-Language: en-us MIME-Version: 1.0 To: chemistry@ccl.net Subject: MPA in G98 Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit Hello, is it possible to print individual summations of the Mulliken populations with G98 like in Mullikens 1955 paper? In particular, I would need the populations of basis functions in a given MO. Thanks, Uli Salzner From chemistry-request@server.ccl.net Tue Mar 25 10:53:14 2003 Received: from mailserv.unb.ca ([131.202.3.23]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h2PFrEN19700 for ; Tue, 25 Mar 2003 10:53:14 -0500 Received: from pop.unb.ca (root@newpop.unb.ca [131.202.3.46]) by mailserv.unb.ca (8.12.6/8.12.6) with ESMTP id h2PFnQWw023116; Tue, 25 Mar 2003 11:49:26 -0400 Received: from webmail1 (webmail1.unb.ca [131.202.130.26]) by pop.unb.ca (8.11.6+Sun/8.11.6) with ESMTP id h2PFnPY22024; Tue, 25 Mar 2003 11:49:25 -0400 (AST) X-WebMail-UserID: l72k6 Date: Tue, 25 Mar 2003 11:49:25 -0400 Sender: Robert Flight From: Robert Flight To: AutoDockList , Computational Chemistry List X-EXP32-SerialNo: 00003025, 00003442 Subject: ADT error message - "No Atom records" Message-ID: <3E97A363@webmail1> Mime-Version: 1.0 Content-Type: text/plain; charset="US-ASCII" Content-Transfer-Encoding: 7bit X-Mailer: WebMail (Hydra) SMTP v3.61.08 X-UNB-VirusScanner: Found to be clean X-UNB-SpamDetails: Hi All, I have been using AutoDockTools in Windows for a long time, and have had very few problems with it. One of the major tasks I use it for is the conversion of my receptor Mol2 files to PDBQS files. I am trying to use ADT in Linux, and I am getting the following error message: The file /mnt/d_win/autodock/test_set/1gpn/tacl.gr3/02.1gpn.mol2 doesn't have Atom records, molecules can't be built ERROR ************************************************ Traceback (innermost last): File "/usr/local/mgltools/rel.1.1beta/share/lib/python1.5/site-packages/ViewerFrame work/VF.py", line 571, in tryto result = apply( command, args, kw ) File "/usr/local/mgltools/rel.1.1beta/share/lib/python1.5/site-packages/AutoDockToo ls/autogpfCommands.py", line 851, in doit mol = mols[0] File "/usr/local/mgltools/rel.1.1beta/share/lib/python1.5/UserList.py", line 18, in __getitem__ def __getitem__(self, i): return self.data[i] IndexError: list index out of range I have never seen the message "doesn't have Atom records" before, and as far as I can tell my Mol2 files look the exact same in Linux as they did in Windows, and I am using the same program to prepare them. Any help or suggestions are very much appreciated. I will summarise the responses to the list. Thanks, -Robert ******************************** Robert Flight Masters Student Department of Chemistry University of New Brunswick Fredericton, NB Canada E3B 6E2 e-mail: robert.flight@unb.ca ******************************** "A computer terminal is not some clunky old television with a typewriter in front of it. It is an interface where the mind and body can connect with the universe and move bits of it about." -- Hitch Hikers Guide to the Galaxy From chemistry-request@server.ccl.net Tue Mar 25 12:15:39 2003 Received: from mxout5.cac.washington.edu ([140.142.32.135]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h2PHFdN25715 for ; Tue, 25 Mar 2003 12:15:39 -0500 Received: from smtp.washington.edu (smtp.washington.edu [140.142.33.9]) by mxout5.cac.washington.edu (8.12.1+UW03.03/8.12.1+UW02.12) with ESMTP id h2PHFcNr001394; Tue, 25 Mar 2003 09:15:38 -0800 Received: from u.washington.edu (konga.chem.washington.edu [128.95.128.222]) (authenticated bits=0) by smtp.washington.edu (8.12.1+UW03.03/8.12.1+UW02.12) with ESMTP id h2PHFcwa025958 (version=TLSv1/SSLv3 cipher=RC4-MD5 bits=128 verify=NOT); Tue, 25 Mar 2003 09:15:38 -0800 Message-ID: <3E808EC5.3010009@u.washington.edu> Date: Tue, 25 Mar 2003 09:15:49 -0800 From: Carsten Detering User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.0.2) Gecko/20030208 Netscape/7.02 X-Accept-Language: en-us, en MIME-Version: 1.0 To: aldo jongejan , chemistry@ccl.net Subject: Re: CCL:autogrid/dock + segmentation fault on Redhat8 References: <3E7F86CC.6060305@u.washington.edu> <3E801ED3.AEEF764D@few.vu.nl> Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit Hi Aldo, right, I looked into this. In an older version of AutoDock (I believe it is 3.04) the specification of atom types is given in the autogrid.h, whereas in the latest version, it is given in the autocomm.h, and exactly this piece of code is responsible for the number of atom types; it is actually the same source code simply pasted into autocomm.h. Thanks anyway for your reply. Carsten aldo jongejan wrote: > Hi Carsten, > > Probably you already looked into this, but what about fx "autogrid.h" in the > autogrid-source directory. Here I see that onlt 7 atom types have been > declared. > If you play around with this, would it read more types?? > I see fx a : > > #define ATOMTYPE "CNOSHXM" > > #define NATOMTYPES 7 /* Number of atom types for atomic interactions > */ > #define MAX_TYPES 8 /* Maximum number of atom types used. > */ > > This code is for the macromolecule (I guess) , but something similar probably > holds for the ligand as well... > > hope it helps a little, > > aldo > > Carsten Detering wrote: > > >>Hi fellow AutoDockers and CClers, >> >>Unfortunately I still couldn't fix the problem of AutoDock not being >>able to take more than ten atom types, although I think I did everything >>according to the guidance. I used the autocomm.h-extra-maps as >>autocomm.h, and at least I didn't have trouble compiling both programs. >>I changed the Makefile according to the Linux AutoDock HOWTO. But >>everytime I call autogrid, I get a segmentation fault, even if I use >>less than ten atom types. I think the problem arises when the program >>starts to calculate the grids, since the gpf file was read in without >>problems (according to glg). I also set the stacksize to unlimited, so >>this cannot cause the problem either (I use bash, so I have ulimit -s >>unlimited). >> >>Is there anyone who experienced similar problems and could help me with >>this? I honestly don't know why this doen't work. >> >>Thanks a lot in advance, >> >>Carsten >> >>-- >> >>Carsten Detering, Ph.D. >>University of Washington >>Seattle, WA 98195 >>Fon 206.543.5081 >>Fax 206.685.8665 >> >>-= 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 > > > -- > ########################################### > > Aldo Jongejan > Molecular Modeling Group > Dept. of Pharmacochemistry > Free University of Amsterdam > De Boelelaan 1083 > 1081 HV Amsterdam > The Netherlands > > e-mail: jongejan@chem.vu.nl > tlf: +31 (0)20 4447612 > fax: +31 (0)20 4447610 > > ########################################### > > > -- Carsten Detering University of Washington Seattle, WA 98195 Fon 206.543.5081 Fax 206.685.8665 From chemistry-request@server.ccl.net Tue Mar 25 16:04:53 2003 Received: from mailserv.unb.ca ([131.202.3.23]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h2PL4rN11006 for ; Tue, 25 Mar 2003 16:04:53 -0500 Received: from pop.unb.ca (root@newpop.unb.ca [131.202.3.46]) by mailserv.unb.ca (8.12.6/8.12.6) with ESMTP id h2PL4AWw011811; Tue, 25 Mar 2003 17:04:10 -0400 Received: from webmail1 (webmail1.unb.ca [131.202.130.26]) by pop.unb.ca (8.11.6+Sun/8.11.6) with ESMTP id h2PL4BY05135; Tue, 25 Mar 2003 17:04:11 -0400 (AST) X-WebMail-UserID: l72k6 Date: Tue, 25 Mar 2003 17:04:10 -0400 Sender: Robert Flight From: Robert Flight To: AutoDockList , Computational Chemistry List X-EXP32-SerialNo: 00003025, 00003442 Subject: ADT error message - "No Atom records" - solution Message-ID: <3E9929F7@webmail1> Mime-Version: 1.0 Content-Type: text/plain; charset="US-ASCII" Content-Transfer-Encoding: 7bit X-Mailer: WebMail (Hydra) SMTP v3.61.08 X-UNB-VirusScanner: Found to be clean X-UNB-SpamDetails: Thanks to everyone to tried to help me with this, your suggestions were appreciated. I did figure out what was wrong, or at least a solution. I am running a dual boot machine with RHLinux7.3 and WindowsXP. I have a FAT32 drive partition so I can write and read it in both Linux and XP. It turns out that ADT in Linux does not like mol2 files that were created in XP, it gives me the error message I reported below. If I create the Mol2 file in Linux, ADT gives me no problems. I guess I should have tried that first, but I could not find any obvious differences between files that worked and files that didnt. A good lesson to work in one operating system or the other, not both. -Robert Hi All, I have been using AutoDockTools in Windows for a long time, and have had very few problems with it. One of the major tasks I use it for is the conversion of my receptor Mol2 files to PDBQS files. I am trying to use ADT in Linux, and I am getting the following error message: The file /mnt/d_win/autodock/test_set/1gpn/tacl.gr3/02.1gpn.mol2 doesn't have Atom records, molecules can't be built ERROR ************************************************ Traceback (innermost last): File "/usr/local/mgltools/rel.1.1beta/share/lib/python1.5/site-packages/ViewerFrame work/VF.py", line 571, in tryto result = apply( command, args, kw ) File "/usr/local/mgltools/rel.1.1beta/share/lib/python1.5/site-packages/AutoDockToo ls/autogpfCommands.py", line 851, in doit mol = mols[0] File "/usr/local/mgltools/rel.1.1beta/share/lib/python1.5/UserList.py", line 18, in __getitem__ def __getitem__(self, i): return self.data[i] IndexError: list index out of range I have never seen the message "doesn't have Atom records" before, and as far as I can tell my Mol2 files look the exact same in Linux as they did in Windows, and I am using the same program to prepare them. Any help or suggestions are very much appreciated. I will summarise the responses to the list. Thanks, -Robert ******************************** Robert Flight Masters Student Department of Chemistry University of New Brunswick Fredericton, NB Canada E3B 6E2 e-mail: robert.flight@unb.ca ******************************** "A computer terminal is not some clunky old television with a typewriter in front of it. It is an interface where the mind and body can connect with the universe and move bits of it about." -- Hitch Hikers Guide to the Galaxy -- ADL: AutoDock List --- http://www.scripps.edu/pub/olson-web/doc/autodock/ --- From chemistry-request@server.ccl.net Tue Mar 25 16:55:05 2003 Received: from 01mail.PghMail.com ([216.151.83.18]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h2PLt4N14614 for ; Tue, 25 Mar 2003 16:55:05 -0500 Received: from DJM.gaussian.com (unverified [63.113.39.56]) by 01mail.PghMail.com (Vircom SMTPRS 5.3.232) with ESMTP id for ; Tue, 25 Mar 2003 16:55:00 -0500 Message-Id: <5.1.0.14.2.20030325165531.00b85ab8@mail.pghmail.com> X-Sender: tripletdad@mail.pghmail.com (Unverified) X-Mailer: QUALCOMM Windows Eudora Version 5.1 Date: Tue, 25 Mar 2003 16:57:21 -0500 To: chemistry@ccl.net From: Gaussian Subject: Announcing Gaussian 03 Mime-Version: 1.0 Content-Type: multipart/alternative; boundary="=====================_18669640==_.ALT" --=====================_18669640==_.ALT Content-Type: text/plain; charset="us-ascii"; format=flowed Gaussian, Inc. is proud to announce the latest release in the Gaussian series, Gaussian 03, and our graphical interface GaussView 3.0. These products are available on a wide range of platforms and operating systems including parallel execution on shared memory systems and distributed systems using TCP Linda. Gaussian 03 continues the tradition of providing a combination of new and enhanced methods which increase both the size and the type of systems which an be studied. Of note are a more mature implementation of the ONIOM facility, a number of new properties which can be computed in either gas or solution phase and initial implementations of methods using periodic boundary conditions and ADMP ab initio molecular dynamics. For pricing, available platforms, system requirements and other information, please visit our website at www.gaussian.com, or contact us via email (info@gaussian.com), phone or fax (given below). We look forward to providing you with the latest versions of Gaussian, GaussView and Linda. Sincerely, David Moses ---------- David J. Moses, Ph.D. Vice President, C.O.O. Gaussian, Inc. Carnegie Office Park Building Six Pittsburgh, PA 15106 412-279-6700 (Voice) 412-279-2118 (FAX) moses@gaussian.com http://www.gaussian.com --=====================_18669640==_.ALT Content-Type: text/html; charset="us-ascii" Gaussian, Inc. is proud to announce the latest release in the Gaussian series,
Gaussian 03, and our graphical interface GaussView 3.0. These products are
available on a wide range of platforms and operating systems including parallel
execution on shared memory systems and distributed systems using TCP Linda.

Gaussian 03 continues the tradition of providing a combination of new and
enhanced methods which increase both the size and the type of systems which
an be studied. Of note are a more mature implementation of the ONIOM facility,
a number of new properties which can be computed in either gas or solution phase
and initial implementations of methods using periodic boundary conditions and
ADMP ab initio molecular dynamics.

For pricing, available platforms, system requirements and other information, please
visit our website at www.gaussian.com, or contact us via email (info@gaussian.com),
phone or fax (given below). We look forward to providing you with the latest versions
of Gaussian, GaussView and Linda.

Sincerely,
David Moses
David J. Moses, Ph.D.
Vice President, C.O.O.
Gaussian, Inc.
Carnegie Office Park
Building Six
Pittsburgh, PA 15106

412-279-6700 (Voice)
412-279-2118 (FAX)
moses@gaussian.com
http://www.gaussian.com --=====================_18669640==_.ALT-- From chemistry-request@server.ccl.net Tue Mar 25 17:41:36 2003 Received: from bioboss.bio.ucalgary.ca ([136.159.234.204]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h2PMfZN17846 for ; Tue, 25 Mar 2003 17:41:36 -0500 Received: from bioboss.bio.ucalgary.ca (bobcat.bio.ucalgary.ca [136.159.234.168]) by bioboss.bio.ucalgary.ca (SGI-8.9.3/8.9.3) with ESMTP id PAA55151; Tue, 25 Mar 2003 15:41:24 -0700 (MST) Message-ID: <3E80DB3F.6090008@bioboss.bio.ucalgary.ca> Date: Tue, 25 Mar 2003 15:42:07 -0700 From: Craig Shepherd User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.3b) Gecko/20030210 X-Accept-Language: en-us, en MIME-Version: 1.0 To: autodock@scripps.edu, chemistry@ccl.net Subject: Re: CCL:ADT error message - "No Atom records" - solution References: <3E9929F7@webmail1> In-Reply-To: <3E9929F7@webmail1> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Hi there, Sounds like you don't have a problem any more, but I think I know what MIGHT have caused it. Text files created on a Windows operating system contain both "newlines" and "carriage returns" at the end of lines, whereas those made on *nix OS's have just newlines. I first noticed this with PostScript files I opened up in Emacs on my linux partition (I had made them with Illustrator). In this case, you'll see a "^M" at the end of every line. You can interconvert text files between DOS and *nix if you install the package "tofrodos" on your linux partition. It provides the program "fromdos", which will strip (or add) the carriage returns as needed. You can find the package at http://rpmfind.net Hope that helps if you ever face this kind of thing again. Craig Shepherd Robert Flight wrote: >Thanks to everyone to tried to help me with this, your suggestions were >appreciated. I did figure out what was wrong, or at least a solution. I am >running a dual boot machine with RHLinux7.3 and WindowsXP. I have a FAT32 >drive partition so I can write and read it in both Linux and XP. > >It turns out that ADT in Linux does not like mol2 files that were created in >XP, it gives me the error message I reported below. If I create the Mol2 file >in Linux, ADT gives me no problems. I guess I should have tried that first, >but I could not find any obvious differences between files that worked and >files that didnt. A good lesson to work in one operating system or the other, >not both. > >-Robert > > > > From chemistry-request@server.ccl.net Tue Mar 25 16:47:35 2003 Received: from hal.netbox.cz ([212.96.166.1]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h2PLlYN14119 for ; Tue, 25 Mar 2003 16:47:34 -0500 Received: from lubos (r10s01p08.home.nbox.cz [212.96.184.72]) by hal.netbox.cz (Postfix) with SMTP id 34F88171D38; Tue, 25 Mar 2003 22:47:33 +0100 (CET) Message-ID: <007601c2f316$4da84a60$d200a8c0@mshome.net> Reply-To: "Lubos Vrbka" From: "Lubos Vrbka" To: "Robert Flight" Cc: References: <3E9929F7@webmail1> Subject: Re: CCL:ADT error message - "No Atom records" - solution Date: Tue, 25 Mar 2003 22:34:23 +0100 Organization: NCBR MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="----=_NextPart_000_0073_01C2F31E.AF18C600" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2800.1106 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1106 This is a multi-part message in MIME format. ------=_NextPart_000_0073_01C2F31E.AF18C600 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit hi, try using unix shell scripts that are attached - to_dos converts unix text files to windows text files; to_unix does the opposite conversion - it just removes ^M characters that are appended to the end of line in all text files in dos/windows... syntax is to_dos unix_file_name dos_file_name to_unix dos_file_name unix_file_name the problem could be in these ^M characters... vi should display them, but i'm not sure about other editors/viewers... and a question is if they are/aren't interpreted in autodock somehow... try, it could help and surely won't hurt... :o) regards, lubos - ################################################# Lubos Vrbka National Centre for Biomolecular Research Masaryk university, Brno, Czech Republic shnek@chemi.muni.cz http://www.chemi.muni.cz/~shnek tel. +420 541 129 508 ################################################# ------=_NextPart_000_0073_01C2F31E.AF18C600 Content-Type: application/octet-stream; name="to_unix" Content-Transfer-Encoding: quoted-printable Content-Disposition: attachment; filename="to_unix" #! /bin/sh -e #Tag 1538 # # convert a DOS ASCII file to a UNIX ASCII file by removing trailing ^M = at the # end of each line and ^Z at the end of the file TMPFILE=3D/tmp/to_unix$$ if [ $# -gt 2 ] then echo "usage: to_unix [ []]" exit 1 fi # First strip out all carriage-return and ctrl-Z's if [ $# -gt 0 ] then tr -d '\015\032' < "$1" > $TMPFILE else tr -d '\015\032' > $TMPFILE fi if [ $# -eq 2 ] then mv -f $TMPFILE "$2" else cat $TMPFILE rm $TMPFILE fi ------=_NextPart_000_0073_01C2F31E.AF18C600 Content-Type: application/octet-stream; name="to_dos" Content-Transfer-Encoding: quoted-printable Content-Disposition: attachment; filename="to_dos" #! /bin/sh -e #Tag 1538 # # convert a UNIX ASCII file to a DOS ASCII file by appending ^M at the # end of each line and ^Z at the end of the file TMPFILE=3D/tmp/to_dos$$ if [ $# -gt 2 ] then echo "usage: to_dos [ []]" exit 1 fi if [ $# -gt 0 ] then awk '{printf("%s\r\n", $0);}' "$1" > $TMPFILE else awk '{printf("%s\r\n", $0);}' > $TMPFILE fi # Stick on the EOF character echo '=1A' >> $TMPFILE if [ $# -eq 2 ] then mv -f $TMPFILE "$2" else cat $TMPFILE rm $TMPFILE fi ------=_NextPart_000_0073_01C2F31E.AF18C600-- From chemistry-request@server.ccl.net Tue Mar 25 23:45:39 2003 Received: from ns1.scripps.edu ([192.42.82.59]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h2Q4jcN32588 for ; Tue, 25 Mar 2003 23:45:39 -0500 Received: from antigen.scripps.edu (antigen.scripps.edu [137.131.200.100]) by ns1.scripps.edu (8.11.6/TSRI-4.1rx) with SMTP id h2Q4jcL00671 for ; Tue, 25 Mar 2003 20:45:38 -0800 (PST) Received: from relay2.scripps.edu(137.131.200.30) by antigen.scripps.edu via csmap id 5682; Tue, 25 Mar 2003 20:36:37 -0800 (PST) Received: from hermes.scripps.edu (hermes.scripps.edu [137.131.140.49]) by relay2.scripps.edu (8.11.6/TSRI-4.2rAV) with ESMTP id h2Q4jbv05665 for ; Tue, 25 Mar 2003 20:45:37 -0800 (PST) Received: from scripps.edu (samson-arpt [137.131.108.37]) by hermes.scripps.edu (8.12.8/8.12.8/TSRI-4.0.2h) with ESMTP id h2Q4jaOt413248; Tue, 25 Mar 2003 20:45:36 -0800 (PST) Date: Tue, 25 Mar 2003 20:45:37 -0800 Subject: NCI diversity set Content-Type: text/plain; charset=US-ASCII; format=flowed Mime-Version: 1.0 (Apple Message framework v551) From: "Garrett M. Morris" To: autodock@scripps.edu, chemistry@ccl.net Content-Transfer-Encoding: 7bit Message-Id: X-Mailer: Apple Mail (2.551) Hi Carsten All rotatable bonds were allowed to rotate. Most of these molecules have a small number of rotatable bonds, though. Hope this helps, Garrett > From owner-autodock@spiderweb.scripps.edu Mon Mar 10 14:27:49 2003 > From: "Carsten Detering" > To: > Cc: > Subject: ADL: NCI diversity set > MIME-Version: 1.0 > X-Priority: 3 > X-MSMail-Priority: Normal > X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1106 > > Hi again, > > > Did somebody work already with the recently released NCI-diversity Set > for AutoDock (to be found on the AutoDock web site)? How are the > rotatable bonds treated in this approach?? Of course, it is impossible > to edit 2000 files regarding rotatable bonds, let alone the treatment > of the hydrogen rotors -OH, -NH2 etc. Is this to be neglected until a > promising molecule is found and then redocked with the correct > > number?? > > Thanks for helpful suggestions/comments. > > Carsten > > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > Carsten Detering, Ph.D. > University of Washington > Seattle, WA 98195 > Fon 206-543-5081 > Fax 206-865-8665 > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -- Dr Garrett M. Morris, MA, DPhil The Scripps Research Institute, tel: (858) 784-2292 Dept. Molecular Biology, MB-5, fax: (858) 784-2860 10550 North Torrey Pines Road, email: garrett@scripps.edu La Jolla, CA 92037-1000, USA. www.scripps.edu/pub/olson-web/gmm