From jerzy@fqs.fujitsu.co.jp Tue Jan 24 07:39:17 1995 Received: from fgwmail.fujitsu.co.jp for jerzy@fqs.fujitsu.co.jp by www.ccl.net (8.6.9/930601.1506) id HAA13738; Tue, 24 Jan 1995 07:19:02 -0500 Received: from fdmmail.fujitsu.co.jp by fgwmail.fujitsu.co.jp (8.6.9+2.4W/3.3W5-MX941209-Fujitsu Mail Gateway) id VAA21776; Tue, 24 Jan 1995 21:18:44 +0900 Received: from fqs.fujitsu.co.jp by fdmmail.fujitsu.co.jp (8.6.9+2.4W/3.3W5-MX941219-Fujitsu Domain Mail Master) id VAA20363; Tue, 24 Jan 1995 21:18:43 +0900 Received: from localhost (jerzy@localhost) by fqs.fujitsu.co.jp (8.6.4/3.3Wb-) id VAA19721 for CHEMISTRY@ccl.net; Tue, 24 Jan 1995 21:15:59 +0900 Date: Tue, 24 Jan 1995 21:15:59 +0900 From: Jerzy Rudzinski Message-Id: <199501241215.VAA19721@fqs.fujitsu.co.jp> To: CHEMISTRY@ccl.net Subject: science teacher position Dear all, please excuse me for this single missuse of the list. I do not know other place to post the below given ad and that is why I ask you for help. Thank you. I hope the coordinator will not put me on the black list! Should you know anyone interested in, please pass it around. Thank you, Jerzy. ------------------------------------------------------------------------------ SCIENCE TEACHER POSITION FUKUOKA INTERNATIONAL SCHOOL 18-50, Momochi 3-chome, Sawara-ku, Fukuoka 814, Japan TEL(092)841-7601 FAX(092)841-7602 Fukuoka International School (FIS) is accepting applications from candidates of all nationalities for a science teacher with the department head responsi- bilities. Applicants must have degree in science and teaching credentials, be fluent in English and capable of interacting with students, parents and staff in a multicultural environment. Send credentials and resume to FIS Principal, Mr.Dennis Wm Clark at the above address and/or (for e-mail reference) via internet to jerzy@fqs.fujitsu.co.jp (Jerzy Rudzinski, FIS Personnel Committee) before February 10, 1995. ------------------------------------------------------------------------------ Dr Jerzy M Rudzinski, Fujitsu Kyushu System Engineering (FQS) Ltd Hakata Eki Mae 1-5-1, Hakata-ku, Fukuoka 812, Japan Tel +81 (92) 472-0714; Fax +81 (92) 483-0663 jerzy@fqs.fujitsu.co.jp ------------------------------------------------------------------------------ From ch11mh@surrey.ac.uk Tue Jan 24 08:03:43 1995 Received: from mail-server.surrey.ac.uk for ch11mh@surrey.ac.uk by www.ccl.net (8.6.9/930601.1506) id HAA13712; Tue, 24 Jan 1995 07:09:50 -0500 Received: from central.surrey.ac.uk by mail-server.surrey.ac.uk with SMTP (PP); Tue, 24 Jan 1995 11:59:49 +0000 Received: by central.surrey.ac.uk (1.37.109.8/16.2) id AA26441; Tue, 24 Jan 1995 11:58:31 GMT Date: Tue, 24 Jan 1995 11:58:31 +0000 (GMT) From: Mr Martin J Hargreaves To: chemistry@ccl.net Subject: Re: Security breach? Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII I don't think there will be any loss of network freedom, any more than there was when the "packet sniffing" stuff was in the papers. Here is the CIAC advisory. Further discussion on this topic should not be addresses to CCL, but I'm sending this as a reply and including the official info so hopefully that will be an end to it. There is dicussion of this on bugtraq (mail to bugtraq-request@fc.net). Sorry about th off-topic posting. Regards, Martin ---------------------------------------------------------------- | Martin Hargreaves, ch11mh@surrey.ac.uk| | Undergraduate Computational Chemist | | WWW Server Admin http://www.chem.surrey.ac.uk| ---------------------------------------------------------------- ---------- Forwarded message ---------- Date: Mon, 23 Jan 1995 11:32:28 -0800 From: Steve Weeber To: ch11mh@surrey.ac.uk Subject: CIAC Advisory F-08: IP Address Spoofing and Hijacked Session Attacks _____________________________________________________ The U.S. Department of Energy Computer Incident Advisory Capability ___ __ __ _ ___ / | /_\ / \___ __|__ / \ \___ _____________________________________________________ ADVISORY NOTICE Internet Address Spoofing and Hijacked Session Attacks January 23, 1994 1100 PST Number F-08 _____________________________________________________________________________ PROBLEM: Sophisticated new attacks on Internet systems based on forged IP packets and hijacked login sessions. PLATFORMS: Primarily Unix systems connected to the Internet, although all systems that support session authentication based on IP addresses are potentially vulnerable. Systems protected by packet filtering firewalls may also be vulnerable. DAMAGE: Unauthorized privileged access to systems. SOLUTION: Enable router packet filtering on inbound Internet traffic, and protect systems against root compromise. _____________________________________________________________________________ VULNERABILITY These attacks represent a significant new threat to Internet ASSESSMENT: systems. Without proactive measures in place, these attacks are very difficult to detect or defend against. CIAC strongly recommends sites implement the solutions described below as soon as is possible. _____________________________________________________________________________ Critical Information about the Internet Attacks CIAC has received information regarding a new attack technique on systems connected to the Internet. These attacks are based on the exploitation of two separate vulnerabilites: forging or spoofing the source address of IP packets and hijacking already established login sessions. Although these vulnerabilities are currently being used together to attack systems, each may also be used on its own. Both of these vulnerabilities must be addressed in order to keep systems secure. IP Spoofing Attacks ------------------- Description ----------- The first vulnerability, spoofing IP packets, allows an intruder on the Internet to effectively impersonate a local system's IP address. If other local systems perform session authentication based on the IP address of a connection (e.g. rlogin with .rhosts or /etc/hosts.equiv files under Unix), they will believe incoming connections from the intruder actually originate from a local "trusted host" and will not require a password. This technique is especially damaging when root connections are permitted with no password. Services that are vulnerable to forged IP packets include: SunRPC & NFS BSD Unix "r" commands, including rlogin Services secured by TCP Wrappers using source address access control X Windows It is possible for forged packets to penetrate firewalls based on filtering routers if the router is not configured to block incoming packets with source addresses in the local domain. It is important to note that this attack is possible even if no session packets can be routed back to the attacker. Note also that this attack is not based on the source routing option of the IP protocol. The IP spoofing attacks are very similar to those described in section 2 of "Security Problems in the TCP/IP Protocol Suite" by Steve Bellovin. This paper was published in _Computer Communication Review_ vol. 19, no. 2 (April 1989), pages 32-48. It is also available via anonymous FTP from research.att.com in the file /dist/internet_security/ipext.ps.Z. Additional information is available in the paper "A Weakness in the 4.2BSD Unix TCP/IP Software," by Robert T. Morris. It is also available via anonymous FTP from research.att.com in the file /dist/internet_security/117.ps.Z. Detection --------- IP spoofing attacks are currently very difficult to detect. If your site has the ability to monitor network traffic on the external interface of your Internet router, examine incoming traffic for packets with both a source and destination address in your local domain. Such packets should never be found entering your site from the Internet and are a strong indicator that an IP spoofing attack is in progress. Users within the Deparment of Energy (DOE) and Department of Defense (DOD) communities may obtain a new version of the Network Intrusion Detector (NID) with added features allowing the detection of IP spoofing attacks. Please contact Bob Palasek, NID Project Leader, at (510) 422-8527 or palasek@llnl.gov, for more information. Additionally, two freely available software tools are known to allow this type of packet monitoring on Unix systems: tcpdump and netlog. The tcpdump package is available via anonymous FTP from ftp.ee.lbl.gov in the file /tcpdump.tar.Z (MD5 checksum 4D8975B18CAD40851F382DDFC9BD638F). When built and installed, the command # tcpdump src net X.Y and dst net X.Y will print all packets found that claim to have both a source and destination IP address on the X.Y network. The netlog package, developed at Texas A&M University, is available via anonymous FTP at coast.cs.purdue.edu in the file /pub/tools/unix/TAMU/netlog-1.2.tar.gz (MD5 checksum 1DD62E7E96192456E8C75047C38E994B). When built and installed, it may be invoked with the command # tcplogger -b | extract -U -e 'srcnet=X.Y.0.0 && dstnet=X.Y.0.0 {print}' to scan for packets with a source and destination address on the same network. Prevention ---------- Currently, the best defense against IP spoofing attacks is to filter packets as they enter your router from the Internet, blocking any packet that claims to have originated inside your local domain. This feature, known as an input filter, is currently known to be supported by several brands of routers: Bay Networks/Wellfleet, version 5 and later Cabletron with LAN Secure Cisco, RIS software version 9.21 and later Livingston NSC If your current router hardware does not support packet filtering on inbound traffic, a second router may be installed between the existing router and the Internet connection. This second router may then be used to filter spoofed IP packets with an output filter. Hijacked Session Attacks ------------------------ Description ----------- The second attack currently being observed involves the use of a tool called "tap" to take over existing login sessions on a system. This tool allows an intruder with root access to gain control of any other session currently active on the system, executing commands as if they had been typed by the owner of the session. If the user session has previously performed a telnet or rlogin to another system, then the intruder may gain access to the remote system as well, bypassing any authentication normally required for access. Currently, the tap tool is only known to affect SunOS 4.1.x systems, although the system features that allow the attack are not unique to Sun systems. Detection --------- The owner of the hijacked session may notice unusual activity, including the appearance of commands typed by the intruder. Users should be notified of this possibility and encouraged to report any suspicious activity. Prevention ---------- The primary defense against this attack is to prevent root compromise through careful system management, installation of security patches, and network controls such as firewalls. The tap tool currently in use makes use of SunOS loadable module support to dynamically modify the operation of the running Unix kernel. CIAC recommends that sites not requiring loadable modules disable this feature on their SunOS 4.1.x systems. To do so, edit the kernel configuration file found in the /sys/`arch -k`/conf directory and comment out the following line with a "#" character: options VDDRV # loadable modules Then build and install the new kernel: # /etc/config CONFIG_NAME # cd ../CONFIG_NAME # make # cp /vmunix /vmunix.orig # cp vmunix / # sync; sync; sync Finally, reboot the system to activate the new kernel. Note that intruders have been known to regenerate their own kernels and reboot systems to install the functionality they desire. The authenticity of the running kernel should be verified after any unexplained system reboots. _____________________________________________________________________________ CIAC wishes to acknowledge the contributions of the CERT Coordination Center, Eric Allman, Steve Bellovin, Keith Bostic, Bill Cheswick, Mike Karels, and Tsutomu Shimomura for their assistance in the construction of this bulletin. _____________________________________________________________________________ For emergencies and off-hour assistance, DOE and DOE contractor sites can contact CIAC 24-hours a day via an integrated voicemail and SKYPAGE number. To use this service, dial 1-510-422-8193 or 1-800-759-7243 (SKYPAGE). The primary SKYPAGE PIN number, 8550070 is for the CIAC duty person. A second PIN, 8550074 is for the CIAC Project Leader. CIAC's FAX number is 510-423-8002, and the STU-III number is 510-423-2604. Send E-mail to ciac@llnl.gov. Previous CIAC notices, anti-virus software, and other information are available on the Internet via anonymous FTP from ciac.llnl.gov (IP address 128.115.19.53). CIAC has several self-subscribing mailing lists for electronic publications: 1. CIAC-BULLETIN for Advisories, highest priority - time critical information, and Bulletins, important computer security information; 2. CIAC-NOTES for Notes, a collection of computer security articles; 3. SPI-ANNOUNCE for official news about Security Profile Inspector (SPI) software updates, new features, distribution and availability; 4. SPI-NOTES, for discussion of problems and solutions regarding the use of SPI products. Our mailing lists are managed by a public domain software package called ListProcessor, which ignores E-mail header subject lines. To subscribe (add yourself) to one of our mailing lists, send requests of the following form: subscribe list-name LastName, FirstName PhoneNumber as the E-mail message body, substituting CIAC-BULLETIN, CIAC-NOTES, SPI-ANNOUNCE or SPI-NOTES for "list-name" and valid information for "LastName" "FirstName" and "PhoneNumber." Send to: ciac-listproc@llnl.gov not to: ciac@llnl.gov e.g., subscribe ciac-notes O'Hara, Scarlett 404-555-1212 x36 subscribe ciac-bulletin O'Hara, Scarlett 404-555-1212 x36 You will receive an acknowledgment containing address and initial PIN, and information on how to change either of them, cancel your subscription, or get help. _____________________________________________________________________________ PLEASE NOTE: Many users outside of the DOE and ESnet computing communities receive CIAC bulletins. If you are not part of these communities, please contact your agency's response team to report incidents. Your agency's team will coordinate with CIAC. The Forum of Incident Response and Security Teams (FIRST) is a world-wide organization. A list of FIRST member organizations and their constituencies can be obtained by sending E-mail to first-request@first.org with an empty subject line and a message body containing the line: send first-contacts. This document was prepared as an account of work sponsored by an agency of the United States Government. Neither the United States Government nor the University of California nor any of their employees, makes any warranty, expressed or implied, or assumes any legal liability or responsibility for the accuracy, completeness, or usefulness of any information, product, or process disclosed, or represents that its use would not infringe privately owned rights. Reference herein to any specific commercial products, process, or service by trade name, trademark manufacturer, or otherwise, does not necessarily constitute or imply its endorsement, recommendation, or favoring by the United States Government or the University of California. The views and opinions of authors expressed herein do not necessarily state or reflect those of the United States Government nor the University of California, and shall not be used for advertising or product endorsement purposes. From ch11mh@surrey.ac.uk Tue Jan 24 08:39:21 1995 Received: from mail-server.surrey.ac.uk for ch11mh@surrey.ac.uk by www.ccl.net (8.6.9/930601.1506) id IAA14175; Tue, 24 Jan 1995 08:09:22 -0500 Received: from central.surrey.ac.uk by mail-server.surrey.ac.uk with SMTP (PP); Tue, 24 Jan 1995 11:59:49 +0000 Received: by central.surrey.ac.uk (1.37.109.8/16.2) id AA26441; Tue, 24 Jan 1995 11:58:31 GMT Date: Tue, 24 Jan 1995 11:58:31 +0000 (GMT) From: Mr Martin J Hargreaves To: chemistry@ccl.net Subject: Re: Security breach? Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII I don't think there will be any loss of network freedom, any more than there was when the "packet sniffing" stuff was in the papers. Here is the CIAC advisory. Further discussion on this topic should not be addresses to CCL, but I'm sending this as a reply and including the official info so hopefully that will be an end to it. There is dicussion of this on bugtraq (mail to bugtraq-request@fc.net). Sorry about th off-topic posting. Regards, Martin ---------------------------------------------------------------- | Martin Hargreaves, ch11mh@surrey.ac.uk| | Undergraduate Computational Chemist | | WWW Server Admin http://www.chem.surrey.ac.uk| ---------------------------------------------------------------- ---------- Forwarded message ---------- Date: Mon, 23 Jan 1995 11:32:28 -0800 From: Steve Weeber To: ch11mh@surrey.ac.uk Subject: CIAC Advisory F-08: IP Address Spoofing and Hijacked Session Attacks _____________________________________________________ The U.S. Department of Energy Computer Incident Advisory Capability ___ __ __ _ ___ / | /_\ / \___ __|__ / \ \___ _____________________________________________________ ADVISORY NOTICE Internet Address Spoofing and Hijacked Session Attacks January 23, 1994 1100 PST Number F-08 _____________________________________________________________________________ PROBLEM: Sophisticated new attacks on Internet systems based on forged IP packets and hijacked login sessions. PLATFORMS: Primarily Unix systems connected to the Internet, although all systems that support session authentication based on IP addresses are potentially vulnerable. Systems protected by packet filtering firewalls may also be vulnerable. DAMAGE: Unauthorized privileged access to systems. SOLUTION: Enable router packet filtering on inbound Internet traffic, and protect systems against root compromise. _____________________________________________________________________________ VULNERABILITY These attacks represent a significant new threat to Internet ASSESSMENT: systems. Without proactive measures in place, these attacks are very difficult to detect or defend against. CIAC strongly recommends sites implement the solutions described below as soon as is possible. _____________________________________________________________________________ Critical Information about the Internet Attacks CIAC has received information regarding a new attack technique on systems connected to the Internet. These attacks are based on the exploitation of two separate vulnerabilites: forging or spoofing the source address of IP packets and hijacking already established login sessions. Although these vulnerabilities are currently being used together to attack systems, each may also be used on its own. Both of these vulnerabilities must be addressed in order to keep systems secure. IP Spoofing Attacks ------------------- Description ----------- The first vulnerability, spoofing IP packets, allows an intruder on the Internet to effectively impersonate a local system's IP address. If other local systems perform session authentication based on the IP address of a connection (e.g. rlogin with .rhosts or /etc/hosts.equiv files under Unix), they will believe incoming connections from the intruder actually originate from a local "trusted host" and will not require a password. This technique is especially damaging when root connections are permitted with no password. Services that are vulnerable to forged IP packets include: SunRPC & NFS BSD Unix "r" commands, including rlogin Services secured by TCP Wrappers using source address access control X Windows It is possible for forged packets to penetrate firewalls based on filtering routers if the router is not configured to block incoming packets with source addresses in the local domain. It is important to note that this attack is possible even if no session packets can be routed back to the attacker. Note also that this attack is not based on the source routing option of the IP protocol. The IP spoofing attacks are very similar to those described in section 2 of "Security Problems in the TCP/IP Protocol Suite" by Steve Bellovin. This paper was published in _Computer Communication Review_ vol. 19, no. 2 (April 1989), pages 32-48. It is also available via anonymous FTP from research.att.com in the file /dist/internet_security/ipext.ps.Z. Additional information is available in the paper "A Weakness in the 4.2BSD Unix TCP/IP Software," by Robert T. Morris. It is also available via anonymous FTP from research.att.com in the file /dist/internet_security/117.ps.Z. Detection --------- IP spoofing attacks are currently very difficult to detect. If your site has the ability to monitor network traffic on the external interface of your Internet router, examine incoming traffic for packets with both a source and destination address in your local domain. Such packets should never be found entering your site from the Internet and are a strong indicator that an IP spoofing attack is in progress. Users within the Deparment of Energy (DOE) and Department of Defense (DOD) communities may obtain a new version of the Network Intrusion Detector (NID) with added features allowing the detection of IP spoofing attacks. Please contact Bob Palasek, NID Project Leader, at (510) 422-8527 or palasek@llnl.gov, for more information. Additionally, two freely available software tools are known to allow this type of packet monitoring on Unix systems: tcpdump and netlog. The tcpdump package is available via anonymous FTP from ftp.ee.lbl.gov in the file /tcpdump.tar.Z (MD5 checksum 4D8975B18CAD40851F382DDFC9BD638F). When built and installed, the command # tcpdump src net X.Y and dst net X.Y will print all packets found that claim to have both a source and destination IP address on the X.Y network. The netlog package, developed at Texas A&M University, is available via anonymous FTP at coast.cs.purdue.edu in the file /pub/tools/unix/TAMU/netlog-1.2.tar.gz (MD5 checksum 1DD62E7E96192456E8C75047C38E994B). When built and installed, it may be invoked with the command # tcplogger -b | extract -U -e 'srcnet=X.Y.0.0 && dstnet=X.Y.0.0 {print}' to scan for packets with a source and destination address on the same network. Prevention ---------- Currently, the best defense against IP spoofing attacks is to filter packets as they enter your router from the Internet, blocking any packet that claims to have originated inside your local domain. This feature, known as an input filter, is currently known to be supported by several brands of routers: Bay Networks/Wellfleet, version 5 and later Cabletron with LAN Secure Cisco, RIS software version 9.21 and later Livingston NSC If your current router hardware does not support packet filtering on inbound traffic, a second router may be installed between the existing router and the Internet connection. This second router may then be used to filter spoofed IP packets with an output filter. Hijacked Session Attacks ------------------------ Description ----------- The second attack currently being observed involves the use of a tool called "tap" to take over existing login sessions on a system. This tool allows an intruder with root access to gain control of any other session currently active on the system, executing commands as if they had been typed by the owner of the session. If the user session has previously performed a telnet or rlogin to another system, then the intruder may gain access to the remote system as well, bypassing any authentication normally required for access. Currently, the tap tool is only known to affect SunOS 4.1.x systems, although the system features that allow the attack are not unique to Sun systems. Detection --------- The owner of the hijacked session may notice unusual activity, including the appearance of commands typed by the intruder. Users should be notified of this possibility and encouraged to report any suspicious activity. Prevention ---------- The primary defense against this attack is to prevent root compromise through careful system management, installation of security patches, and network controls such as firewalls. The tap tool currently in use makes use of SunOS loadable module support to dynamically modify the operation of the running Unix kernel. CIAC recommends that sites not requiring loadable modules disable this feature on their SunOS 4.1.x systems. To do so, edit the kernel configuration file found in the /sys/`arch -k`/conf directory and comment out the following line with a "#" character: options VDDRV # loadable modules Then build and install the new kernel: # /etc/config CONFIG_NAME # cd ../CONFIG_NAME # make # cp /vmunix /vmunix.orig # cp vmunix / # sync; sync; sync Finally, reboot the system to activate the new kernel. Note that intruders have been known to regenerate their own kernels and reboot systems to install the functionality they desire. The authenticity of the running kernel should be verified after any unexplained system reboots. _____________________________________________________________________________ CIAC wishes to acknowledge the contributions of the CERT Coordination Center, Eric Allman, Steve Bellovin, Keith Bostic, Bill Cheswick, Mike Karels, and Tsutomu Shimomura for their assistance in the construction of this bulletin. _____________________________________________________________________________ For emergencies and off-hour assistance, DOE and DOE contractor sites can contact CIAC 24-hours a day via an integrated voicemail and SKYPAGE number. To use this service, dial 1-510-422-8193 or 1-800-759-7243 (SKYPAGE). The primary SKYPAGE PIN number, 8550070 is for the CIAC duty person. A second PIN, 8550074 is for the CIAC Project Leader. CIAC's FAX number is 510-423-8002, and the STU-III number is 510-423-2604. Send E-mail to ciac@llnl.gov. Previous CIAC notices, anti-virus software, and other information are available on the Internet via anonymous FTP from ciac.llnl.gov (IP address 128.115.19.53). CIAC has several self-subscribing mailing lists for electronic publications: 1. CIAC-BULLETIN for Advisories, highest priority - time critical information, and Bulletins, important computer security information; 2. CIAC-NOTES for Notes, a collection of computer security articles; 3. SPI-ANNOUNCE for official news about Security Profile Inspector (SPI) software updates, new features, distribution and availability; 4. SPI-NOTES, for discussion of problems and solutions regarding the use of SPI products. Our mailing lists are managed by a public domain software package called ListProcessor, which ignores E-mail header subject lines. To subscribe (add yourself) to one of our mailing lists, send requests of the following form: subscribe list-name LastName, FirstName PhoneNumber as the E-mail message body, substituting CIAC-BULLETIN, CIAC-NOTES, SPI-ANNOUNCE or SPI-NOTES for "list-name" and valid information for "LastName" "FirstName" and "PhoneNumber." Send to: ciac-listproc@llnl.gov not to: ciac@llnl.gov e.g., subscribe ciac-notes O'Hara, Scarlett 404-555-1212 x36 subscribe ciac-bulletin O'Hara, Scarlett 404-555-1212 x36 You will receive an acknowledgment containing address and initial PIN, and information on how to change either of them, cancel your subscription, or get help. _____________________________________________________________________________ PLEASE NOTE: Many users outside of the DOE and ESnet computing communities receive CIAC bulletins. If you are not part of these communities, please contact your agency's response team to report incidents. Your agency's team will coordinate with CIAC. The Forum of Incident Response and Security Teams (FIRST) is a world-wide organization. A list of FIRST member organizations and their constituencies can be obtained by sending E-mail to first-request@first.org with an empty subject line and a message body containing the line: send first-contacts. This document was prepared as an account of work sponsored by an agency of the United States Government. Neither the United States Government nor the University of California nor any of their employees, makes any warranty, expressed or implied, or assumes any legal liability or responsibility for the accuracy, completeness, or usefulness of any information, product, or process disclosed, or represents that its use would not infringe privately owned rights. Reference herein to any specific commercial products, process, or service by trade name, trademark manufacturer, or otherwise, does not necessarily constitute or imply its endorsement, recommendation, or favoring by the United States Government or the University of California. The views and opinions of authors expressed herein do not necessarily state or reflect those of the United States Government nor the University of California, and shall not be used for advertising or product endorsement purposes. From mitchell@bdrc.bd.com Tue Jan 24 10:40:42 1995 Received: from reggae.ncren.net for mitchell@bdrc.bd.com by www.ccl.net (8.6.9/930601.1506) id KAA17137; Tue, 24 Jan 1995 10:38:30 -0500 Received: from bdrc.bd.com by reggae.ncren.net (5.65/tas-reggae/may94) id AA20182; Tue, 24 Jan 95 10:14:15 -0500 Received: from oregano.bdrc.bd.com by bdrc.bdrc.bd.com (5.65/3.02LBDRC/CR/4.1.3) id AA14791; Tue, 24 Jan 95 09:31:09 -0500 Received: by oregano.bdrc.bd.com (931110.SGI/930416.SGI.AUTO) for @bdrc.bdrc.bd.com:chemistry@ccl.net id AA03927; Tue, 24 Jan 95 09:30:42 -0500 Date: Tue, 24 Jan 95 09:30:42 -0500 From: mitchell@bdrc.bd.com (Mike Mitchell) Message-Id: <9501241430.AA03927@oregano.bdrc.bd.com> To: chemistry@ccl.net Subject: Patenting of Molecular Modeling? Cc: mitchell@ncren.net I'm curious as to whether anyone else has read a patent application from Baxter Diagnostics with International Application Number PCT/US91/03009 and titled "High Affinity Antibodies To Small Peptides." From my reading of this patent, Baxter is attempting to patent the use of molecular modeling for predicting mutations which would enhance the affinities of antibodies for antigens. I'm not a patent attorney, but it appears to me that granting of this patent would prohibit anyone else from using molecular modeling to enhance antibody affinities and might be extended to prohibit anyone else from using molecular modeling for predicting any protein mutations that would enhance the performance of that protein. How do others on CCL feel about having to pay Baxter or some other corporate entity a royalty so that one can practice one's scientific craft? Any (All?) opinions can be e-mailed to me directly so as to limit the number of responses on CCL. I'll post a summary of responses. Please get and READ the patent application before responding so as to express an informed opinion. Mike Mitchell Becton Dickinson Research Center RTP, NC 27709 mitchell@bdrc.bd.com From christoph.ehrendorfer@tbi.univie.ac.at Tue Jan 24 11:04:46 1995 Received: from tbi.univie.ac.at for christoph.ehrendorfer@tbi.univie.ac.at by www.ccl.net (8.6.9/930601.1506) id JAA15628; Tue, 24 Jan 1995 09:41:14 -0500 Received: from tiger.tbi.univie.ac.at by tbi.univie.ac.at (8.6.8.1/TBI-Vie(ih)-1.2) id PAA13950; Tue, 24 Jan 1995 15:40:48 +0100 Received: by tiger.tbi.univie.ac.at (4.1/SMI-4.1) id AA28300; Tue, 24 Jan 95 15:40:54 +0100 From: christoph.ehrendorfer@tbi.univie.ac.at (Christoph Ehrendorfer) Message-Id: <9501241440.AA28300@tiger.tbi.univie.ac.at> Subject: summary: g92/dft-rwf-files To: CHEMISTRY@ccl.net Date: Tue, 24 Jan 1995 15:40:53 +0100 (MET) X-Mailer: ELM [version 2.4 PL11] Content-Type: text Content-Length: 2074 Dear CCL-members, Since I got several requests for summaries on my question concerning g92-rwf-files, here it is. I am sorry that the summary comes so late, but first I did not want to make a summary at all, since no REAL solution is offered for my problem. Here is my original question: > I have a question concerning the case of large RWF-files in Gaussian > 92/DFT. Doing analytical > FREQ calculations the RWF-file grows to remarkable size and sometimes > becomes larger than the available diskspace (or the limit of > the file-system specified by the operating system). > > Im am working on a AIX-system and I am thinking about the possibility to > split the RWF-file in two files and to put them on two different > file-systems. So my question is, if this splitting of the RWF-file is > possible (and HOW) ? > > But I would also be happy to get other comments on the possibility to > decrease the amount of necessary diskspace during analytical FREQ > calculations. These are the answers, facts (as i understood them) and rumours: i) It is not possible to split rwf-files using g92/dft. ii) It might be possible that in a future release there will be some option for rwf-file splitting. iii) Using numerical calculation of the second derivative will decrease the need for resources. iv) There are systems (CRAY, DEC ........) where the file system size is larger than on AIX 3.2 systems. But with the AIX 4.x there might also be a higher limit. v) Usage of SCF=DIRECT reduces disk space. And here are my thoughts about these things: ad iii) Since I am working on rather large systems with low symmetry, this option would increase the cpu-time very strong. ad v) I think the 2-e-integrals are stored NOT in the rwf, but in the d2e-file. Thus, this option would reduce the need for disk space, but not reduce the size of the rwf-file. Thanks to all who responded and to all who showed interest in my problem Christoph Ehrendorfer Institut fuer Theoretische Chemie Waehringerstrasse 17 1090 Wien Tel.: +43 1 40480 / 676 FAX: +43 1 402 85 25 From Patrick.Bultinck@rug.ac.be Tue Jan 24 11:39:25 1995 Received: from mserv.rug.ac.be for Patrick.Bultinck@rug.ac.be by www.ccl.net (8.6.9/930601.1506) id KAA17538; Tue, 24 Jan 1995 10:56:34 -0500 Received: from allserv.rug.ac.be by mserv.rug.ac.be with SMTP id AA08543 (5.67b/IDA-1.5 for ); Tue, 24 Jan 1995 16:55:22 +0100 Received: by allserv.rug.ac.be (5.0/SMI-SVR4) id AA01059; Tue, 24 Jan 1995 16:55:45 +0100 Date: Tue, 24 Jan 1995 16:55:44 +0100 (MET) From: Patrick Bultinck To: "comp. chem. list" Subject: Spiro rings, coordinate system to use ? Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Length: 895 Netters, I am currently studying a complex between a metal ion connected to two ethylenediamine type ligands. A major problem here is how to define the coordinates of the atoms, other than in the cartesian system. The two rings are in spiro, and so have only one atom in common. The actual optimization will be done using the Pulay internal natural coordinates for spiro compounds, but in GAMESS I first have to input another type of coordinates (cartesian, Z-matrix etc.) Important here is that I also need a coordinate system that will allow me to make different arrangements of one ligand's plane relative to the other. This is the reason why I don't like the cartesian option not much..., and would like to use something like a Z-matrix, but it is well-known enough that the coupling in the Z-matrices of ring compounds is particularly nasty... Who can help ?? Thanks, Patrick From aholder@CCTR.UMKC.EDU Tue Jan 24 11:43:31 1995 Received: from axp1.umkc.edu for aholder@CCTR.UMKC.EDU by www.ccl.net (8.6.9/930601.1506) id KAA17447; Tue, 24 Jan 1995 10:52:01 -0500 From: Received: by CCTR.UMKC.EDU (MX V4.1 AXP) id 245; Tue, 24 Jan 1995 09:51:58 CST Date: Tue, 24 Jan 1995 09:51:57 CST To: CHEMISTRY@ccl.net Message-ID: <0098AEF8.974D90F4.245@CCTR.UMKC.EDU> Subject: AMPAC 5.0 demonstration versions available. ******************************************************** * Try AMPAC 5.0 FREE and EASY for 30 Days! * ******************************************************** Semichem announces a free thirty day trial - at your site - of its poweful AMPAC 5.0 with Graphical User Interface software package! Why try AMPAC? It is state-of-the-art in semiempirical methods and possses computational capabilities and algorithms not found in other packages. We think that once you use AMPAC in your research, you'll always want to have access to some of the most powerful yet easy to use computational chemistry software available. If after 30 days you are not satisfied with AMPAC, simply erase it from your computer. If, on the other hand, you want to keep it, simply contact us and we will keep you up and running without interuption. To get the demo, either contact us directly as noted below or fill out the form which is available from CCL archives as: /pub/chemistry/info/software-packages/ampac-demo-form. You can retrieve it via anonymous ftp (www.ccl.net), or by sending a message: select chemistry get info/software-packages/ampac-demo-form to the address: MAILSERV@ccl.net Andy Holder Semichem 7128 Summit Shawnee, KS 66216 (913)268-3271 / (913)268-3445 (fax) aholder@cctr.umkc.edu ** Approved as to form and content by the list coordinator. ** From AZHARI@FRCU.EUN.EG Tue Jan 24 12:39:20 1995 Received: from FRCU.EUN.EG for AZHARI@FRCU.EUN.EG by www.ccl.net (8.6.9/930601.1506) id MAA19418; Tue, 24 Jan 1995 12:32:03 -0500 From: Received: from FRCU.EUN.EG by FRCU.EUN.EG (PMDF V4.2-11 #3805) id <01HM8IEC270W000Z0D@FRCU.EUN.EG>; Tue, 24 Jan 1995 19:32:02 O Date: Tue, 24 Jan 1995 19:32:02 +0000 (O) Subject: SPECTRO program To: chemistry@ccl.net Message-id: <01HM8IEC39LU000Z0D@FRCU.EUN.EG> X-VMS-To: IN%"chemistry@ccl.net" MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Content-transfer-encoding: 7BIT Dear Netters: I posted a question about three weaks ago that I was looking for the SPECTRO program. I was able to get in touch with Prof. Andrew Willetts and he kindly offered me a copy of the prgoram. Further more he informed me that anyone is interested to have a copy of the program may contact him at aw118@cus.cam.ac.uk Too many thanks for everyone helped me to get a copy of the SPECTRO program. Adel El-Azhary Chemistry Department Cairo University From FS300627@Sol.YorkU.CA Tue Jan 24 12:39:23 1995 Received: from Sol.YorkU.CA for FS300627@Sol.YorkU.CA by www.ccl.net (8.6.9/930601.1506) id LAA18910; Tue, 24 Jan 1995 11:56:12 -0500 From: Received: from Sol.YorkU.CA by Sol.YorkU.CA (PMDF V4.3-7 #6007) id <01HM82GME9OW8WW4QT@Sol.YorkU.CA>; Tue, 24 Jan 1995 11:55:56 EST Date: Tue, 24 Jan 1995 11:55:56 -0500 (EST) Subject: Internet Structure searches To: chemistry@ccl.net Message-id: <01HM82GMGOHU8WW4QT@Sol.YorkU.CA> X-Envelope-to: chemistry@ccl.net X-VMS-To: IN%"chemistry@ccl.net" MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Content-transfer-encoding: 7BIT Greetings, I would like to know which 3D databases can be searched for possible structurally similair compounds. I am not interested in buying a whole database but I am willing to pay for a 'search fee' and possibly an 'entry fee' to do the search via the internet. If anyone has knowledge of this could they please mail me the information as well as where I could apply, and what software I need (using a PC) I will, if there is interest, summarize for the net. Regards, Patrick ************************************************************************** ** Patrick van der Valk | It is a capital mistake to theorize * ** BioMimic | before one has data. Insensibly one * ** | begins to twist facts to suit theories * ** e-mail:FS300627@Sol.YorkU.Ca | instead of theories to suit facts. * ** Phone: (416) 736-5747 | * ** Fax: (416) 650-3558 | -Sherlock Holmes- * ************************************************************************** From georgia@Huckel.chem.uga.edu Tue Jan 24 13:40:20 1995 Received: from Huckel.chem.uga.edu for georgia@Huckel.chem.uga.edu by www.ccl.net (8.6.9/930601.1506) id MAA19617; Tue, 24 Jan 1995 12:45:54 -0500 Received: by Huckel.chem.uga.edu (931110.SGI/901025.SGI.UNSUPPORTED.PROTOTYPE) (for chemistry@ccl.net) id AA13358; Tue, 24 Jan 95 12:45:54 -0500 From: georgia@Huckel.chem.uga.edu (Georgia McGaughey) Message-Id: <9501241745.AA13358@Huckel.chem.uga.edu> Subject: How many enzymes are known? To: chemistry@ccl.net Date: Tue, 24 Jan 95 12:45:54 EST X-Mailer: ELM [version 2.3 PL11] Does anyone know how many enzymes are 'known'? Then, what percentage of these enzymes have had their 3D structure determined via x-ray crystallography or nmr methods (ie how many structures are in the Brookhaven Protein Database?)? You can respond to me directly and I'll summarize for the net. georgia@Huckel.chem.uga.edu -- From lrbu00@xd88.kodak.com Tue Jan 24 14:39:45 1995 Received: from Kodak.COM for lrbu00@xd88.kodak.com by www.ccl.net (8.6.9/930601.1506) id OAA20414; Tue, 24 Jan 1995 14:03:05 -0500 From: Received: from euler.kodak.com by Kodak.COM (5.61+/2.1-Eastman Kodak) id AA17537; Tue, 24 Jan 95 13:58:19 -0500 Reply-To: lrbu00@xd88.kodak.com Received: from xd88.kodak.com by euler.kodak.com via SMTP (931110.SGI/931108.SGI.ANONFTP) for @kodakr.Kodak.COM:chemistry@ccl.net id AA04130; Tue, 24 Jan 95 13:30:45 -0500 Received: by xd88.kodak.com (AIX 3.2/UCB 5.64/4.03) id AA11307; Tue, 24 Jan 1995 13:17:33 -0500 Date: Tue, 24 Jan 1995 13:17:33 -0500 Message-Id: <9501241317.ZM13353@xd88.kodak.com> X-Mailer: Z-Mail (3.0.0 15dec93) To: chemistry@ccl.net Subject: VI editor for DOS/PC Content-Type: text/plain; charset=us-ascii Mime-Version: 1.0 Netters: Is anyone aware of a unix-like VI editor for DOS/PC's ? Thanks in advance! Regards, John McKelvey -- John M. McKelvey email: mckelvey@Kodak.COM Computational Science Laboratory phone: (716) 477-3335 2nd Floor, Bldg 83, RL Eastman Kodak Company Rochester, NY 14650-2216 -- From thuber@Physik.TU-Muenchen.DE Tue Jan 24 15:01:14 1995 Received: from srv.cip.physik.tu-muenchen.de for thuber@Physik.TU-Muenchen.DE by www.ccl.net (8.6.9/930601.1506) id OAA20418; Tue, 24 Jan 1995 14:03:51 -0500 Received: from ss1.cip.physik.tu-muenchen.de by srv.cip.physik.tu-muenchen.de with SMTP id AA18862 for (5.67a/IDA-1.5/bs04); Tue, 24 Jan 1995 19:54:19 +0100 Received: by ss1.cip.physik.tu-muenchen.de (4.1/SMI-4.1) id AA11710; Tue, 24 Jan 95 19:54:18 +0100 Date: Tue, 24 Jan 95 19:54:18 +0100 From: Thomas.Huber@Physik.TU-Muenchen.DE Message-Id: <9501241854.AA11710@ss1.cip.physik.tu-muenchen.de> To: CHEMISTRY@ccl.net Subject: van der Waals parameters from ab initio calc? Hi netters! Could you please tell me how to derive van der Waals parameters from ab initio calculations! Any suggestions are wellcome (references, principles,...). I'm interested in practical as well as theoretical approaches to this problem. If I got interesting response, I'll collect them and post it to this group! Thank you for help! Thomas Thomas Huber Institut fuer Physikalische Biochemie der Universitaet Muenchen Schillerstrasse 44 80336 Muenchen Germany email: thuber@physik.tu-muenchen.de From ghislain@unb.ca Tue Jan 24 16:39:29 1995 Received: from unb.ca for ghislain@unb.ca by www.ccl.net (8.6.9/930601.1506) id QAA27150; Tue, 24 Jan 1995 16:22:58 -0500 Received: from jupiter.sun.csd.unb.ca by unb.ca (8.6.9/941220-22:07) id RAA11284; Tue, 24 Jan 1995 17:22:49 -0400 Received: from [131.202.47.1] by jupiter.sun.csd.unb.ca (8.6.9/950124-14:07) id RAA27746; Tue, 24 Jan 1995 17:22:22 -0400 X-Sender: ghislain@pop.unb.ca Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Tue, 24 Jan 1995 17:26:55 -0400 To: CHEMISTRY@ccl.net From: ghislain@unb.ca (Ghislain Deslongchamps) Subject: RasMol output --> Quicktime movie? Dear CCLers, We are looking for a (relatively) painless way of capturing rotating RasMol pictures (or other molecular modeling apps) as Quicktime movies. These are to be pasted into multimedia Word documents covering topics such as protein secondary, supersecondary and tertiary structure. We tried the ScreenMovie shareware with RasMol but with little success. My personal preference would be to capture a MacroModel session (on SGI) as a Quicktime movie but this may be too complicated. Any suggestions? Thanks -Ghislain +++++++++++++++++++++++++++++++++++++++++++++++++++++ + Ghislain Deslongchamps, Assistant Professor + + Department of Chemistry + + University of New Brunswick + + Fredericton, N.B. CANADA E3B 5A3 + + e-mail: GHISLAIN@UNB.CA + + phone: 506-453-4795 + + FAX: 506-453-4981 + +++++++++++++++++++++++++++++++++++++++++++++++++++++ From lrbu00@xd88.kodak.com Tue Jan 24 17:39:24 1995 Received: from Kodak.COM for lrbu00@xd88.kodak.com by www.ccl.net (8.6.9/930601.1506) id RAA28321; Tue, 24 Jan 1995 17:37:50 -0500 From: Received: from euler.kodak.com by Kodak.COM (5.61+/2.1-Eastman Kodak) id AA17508; Tue, 24 Jan 95 13:57:31 -0500 Reply-To: lrbu00@xd88.kodak.com Received: from xd88.kodak.com by euler.kodak.com via SMTP (931110.SGI/931108.SGI.ANONFTP) for @kodakr.Kodak.COM:chemistry@ccl.net id AA04170; Tue, 24 Jan 95 13:48:38 -0500 Received: by xd88.kodak.com (AIX 3.2/UCB 5.64/4.03) id AA14659; Tue, 24 Jan 1995 13:35:26 -0500 Date: Tue, 24 Jan 1995 13:35:26 -0500 Message-Id: <9501241335.ZM16961@xd88.kodak.com> X-Mailer: Z-Mail (3.0.0 15dec93) To: chemistry@ccl.net Subject: Gaussian RW files Cc: mckelvey@Kodak.COM Content-Type: text/plain; charset=us-ascii Mime-Version: 1.0 Netters: Recently I posed the question brought up by Chris Ehrendorfer concerning very large RW files to Mike Frisch, unaware/oblivious to this posting. Mike's reply was to reduce the size of the DIIS history and by not computing quadrupole and higher moments. He commented that the following would reduce the RW file by 2/3: Iop(3/32=1,5/39=10) 3/32 concerns moments and 5/39 concerns DIIS cycles, a max of 10 in this example. Hope this helps... Maybe it should be default? Regards, John -- John M. McKelvey email: mckelvey@Kodak.COM Computational Science Laboratory phone: (716) 477-3335 2nd Floor, Bldg 83, RL Eastman Kodak Company Rochester, NY 14650-2216 -- From jxh@ibm12.biosym.com Tue Jan 24 17:46:27 1995 Received: from ibm12.biosym.com for jxh@ibm12.biosym.com by www.ccl.net (8.6.9/930601.1506) id QAA27372; Tue, 24 Jan 1995 16:32:05 -0500 Received: by ibm12.biosym.com (AIX 3.2/UCB 5.64/4.03) id AA17349; Tue, 24 Jan 1995 13:32:20 -0800 Date: Tue, 24 Jan 1995 13:32:20 -0800 From: jxh@ibm12.biosym.com (Joerg Hill) Message-Id: <9501242132.AA17349@ibm12.biosym.com> To: CHEMISTRY@ccl.net Subject: Re: CCL:van der Waals parameters from ab initio calc? Hi, sorry for wasting bandwidth, but a direct response did not work. Van-der-Waals parameters for repulsion can be obtained from ab initio calculations using a test particle ansatz. The most papers have been published by Ahlrichs: H.-J. Boehm, R. Ahlrichs: JCP 77 (1982) 2028 H.-J. Boehm, R. Ahlrichs, P. Scharf, H. Schiffer: JCP 81 (1984) 1389 are the both basic paper. Applications can be found in: H.-J. Boehm, C. Meissner, R. Ahlrichs: Mol. Phys. 53 (1984) 651 K. P. Sagarik, R. Ahlrichs, S. Brode: Mol. Phys. 57 (1986) 1247 K. P. Sagarik, R. Ahlrichs: Chem. Phys. Letters 131 (1986) 74 K. P. Sagarik, R. Ahlrichs: JCP 86 (1987) 5117 J.-R. Hill, J. Sauer: JPC 98 (1994) 1238 A new paper, which considers anisotropy is: A. J. Stone, C.-S. Tong: JCC 15 (1994) 1377 I don't know any papers concerning the derivation of dispersive parameters from ab initio calculations. But dispersion requires electron correlation and since these calculations are rather expensive, it could be that noone has triesd it so far. Density Functional calculations could change this. Tschuess Joerg P.S.: host name Physik.TU-Muenchen.DE NOT FOUND. -------------------------------------------------------------------------------- Dr. Joerg-Ruediger Hill | Every attempt to employ mathematical methods in the Biosym Technologies, Inc. | study of chemical questions must be considered pro- 9685 Scranton Road | foundly irrational and contrary to the spirit of San Diego, CA 92121-2777 | chemistry ... If mathematical analysis should ever USA | hold a prominent place in chemistry - an aberration | which is happily almost impossible - it would Phone (619) 546-5508 | occasion a rapid and widespread degeneration of Fax (619) 458-0136 | that science. E-mail jxh@biosym.com | A. Comte, 1830 -------------------------------------------------------------------------------- The opinions expressed in this message are my personal opinions and no offical statements of Biosym Technologies, Inc. For informations about Biosym products send mail to: rcenter@biosym.com. -------------------------------------------------------------------------------- From cletner@remcure.bmb.wright.edu Tue Jan 24 17:55:48 1995 Received: from remcure.bmb.wright.edu for cletner@remcure.bmb.wright.edu by www.ccl.net (8.6.9/930601.1506) id QAA27826; Tue, 24 Jan 1995 16:57:34 -0500 Received: by remcure.bmb.wright.edu (931110.SGI/921111.SGI.AUTO) for CHEMISTRY@ccl.net id AA12964; Tue, 24 Jan 95 16:49:08 -0800 Date: Tue, 24 Jan 1995 16:22:39 -0800 (PST) From: Charles Letner Subject: Crystal structures To: Computational Chemistry List Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello all, Let me start be stating that this post is ment only as a "conversation starter". It is not ment to be supportive of any one position. Instead it is an atempt to get a thread going on a topic that interest me and may interest others who subscribe to this list. Many times when reading papers on "optimizing" simulations or verifying force fields (I'm speaking to molecular mechanics calculations here) the authors compare the simulation results to the crystal structure. In many cases the authors chose the best simulation by the simulation that deviates the least from the crystal structure. This extends to analysis of simulations that include solvent. SO here is the basis for this post. Coincider crystal packing effects/forces. These effects could alter the crystal conformation from the actual conformation(s) in solution. So the question that comes to mind is: Are the simulation methods that are being developed really moving towards reproducing cystal conformations? If so, can the current force fields be used to get solution conformations? Lets see where this goes. My hope is that responses will go to the CCL to spur on other comments and provide an enlightening discussion. Best regards, Chuck Charles Letner Wright State University Department of Biochemistry Dayton, OH 45435 e-mail: cletner@remcure.bmb.wright.edu From separk@cs.usc.edu Tue Jan 24 19:39:24 1995 Received: from pollux.usc.edu for separk@cs.usc.edu by www.ccl.net (8.6.9/930601.1506) id TAA00325; Tue, 24 Jan 1995 19:35:21 -0500 Received: (separk@localhost) by pollux.usc.edu (8.6.8.1/8.6.4) id QAA26520 for CHEMISTRY@ccl.net; Tue, 24 Jan 1995 16:35:17 -0800 Date: Tue, 24 Jan 95 16:35:16 PST From: SEONGBIN PARK To: CHEMISTRY@ccl.net Subject: Help: QCPE access ? Message-ID: Hello, Could anyone tell me how to access QCPE (Quantum Chemistry Program Exchange) ? Thank you for your time ! Regards, Seongbin Park (separk@pollux.usc.edu) From RGROUP@aardvark.ucs.uoknor.edu Tue Jan 24 19:52:45 1995 Received: from aardvark.ucs.uoknor.edu for RGROUP@aardvark.ucs.uoknor.edu by www.ccl.net (8.6.9/930601.1506) id TAA00216; Tue, 24 Jan 1995 19:25:23 -0500 From: Received: from aardvark.ucs.uoknor.edu by aardvark.ucs.uoknor.edu (PMDF V4.3-13 #7521) id <01HM8FY5FAI80034GI@aardvark.ucs.uoknor.edu>; Tue, 24 Jan 1995 18:27:41 -0600 (CST) Date: Tue, 24 Jan 1995 18:27:41 -0600 (CST) Subject: Force field for ethers (help for a new guy). To: chemistry@ccl.net Message-id: <01HM8FY5H60Y0034GI@aardvark.ucs.uoknor.edu> X-Envelope-to: chemistry@ccl.net X-VMS-To: IN%"chemistry@ccl.net" MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Content-transfer-encoding: 7BIT I am just starting a Molec Dynamics project on PEO oligomers, and I have had difficulty finding a force field for simple ethers that do not use off-diagonal terms. I need a field with only terms on the diagonal for "AMBER". If you can help, please Email me. Thanks, Jeff Ciaccio, Dept of Chemistry Univ of OK From steve@chem.columbia.edu Tue Jan 24 20:05:04 1995 Received: from cucbs.chem.columbia.edu for steve@chem.columbia.edu by www.ccl.net (8.6.9/930601.1506) id TAA00167; Tue, 24 Jan 1995 19:20:15 -0500 Received: from amazon.chem.columbia.edu.columbia.edu (amazon.chem.columbia.edu) by cucbs.chem.columbia.edu with SMTP id AA21112 (5.65c/IDA-1.4.4 for ); Tue, 24 Jan 1995 19:21:29 -0500 Date: Tue, 24 Jan 1995 19:21:29 -0500 From: Steve Stuart Message-Id: <199501250021.AA21112@cucbs.chem.columbia.edu> Received: by amazon.chem.columbia.edu.columbia.edu (4.1/SMI-4.1) id AA24611; Tue, 24 Jan 95 19:21:28 EST To: chemistry@ccl.net Subject: (2nd) summary of expert systems for organic synthesis Here is a summary of the responses to my question last week on references to expert system approaches to organic synthesis. I am embarassed to say that I missed a similar question and summary a few weeks ago. For the benefit of anyone else who was a little hasty in plowing through their holiday messages, I have attached it, after the two new messages that I received. Thanks to everyone who answered! original request: >I would appreciate receiving any information on the current status of >AI or expert system approaches to synthetic organic chemistry. I know >nothing about this area, so I'm not sure what to expect - are there >programs as smart as an introductory course, for example? I am most >interested in references or reviews describing progress and/or >techniques, but pointers to specific programs would also be fine. I >will summarize any responses for the list, of course. ******************************************************************************* From elewars@alchemy.chem.utoronto.ca Thu Jan 19 08:45:23 1995 An inexpensive (ca. $160) program is sold by the ACS; phone them or see C&EN 1994 Sept 5, several pages of ACS advertisements. The program LHASA is probably the best org synth program; for details contact Dr Alan Long Director Dept of Chemistry Harvard University 12 Oxford St Cambridge, MA 02138 See also Angewandte Chemie, International Ed, 1993 32 201-227 Good Luck ******************************************************************************* From MARTIN@cmda.abbott.com Thu Jan 19 07:17:38 1995 Here is a really thorough review. It is worth hunting down the book. I don't know the year. Loftus, P. Computer-aided Synthesis Design. Chemical Structure Systems: Computational Techniques for Prepresentation, Searching, and Processing of Structural Information. New York, Ellis Horwood. J. E. Ash, W. A. Warr and P. Willett. 222-262. @@@@@@@@@@@ Yvonne Martin, Senior Project Leader @ Computer Assisted Molecular Design Project @@@@@@@@ @ D-47E, AP910 2fl @ @ Abbott Laboratories @ @ One Abbott Park Road @@@@@@@@@@ Abbott Park, IL 60064 Phone: 708 937-5362 FAX: 708 937-2625 ******************************************************************************* ORIGINAL SUMMARY: ------------------------------------------------------------------------------ From: "Robert K. Szilagyi" To: chemistry@ccl.net Subject: CCL:Synthesis desing and databases Dear Fellows, first of all, I would like to wish a happy and cheerful New Year to everyone on this list! As a matter of fact, I promised still in 1994 to give a summary about the synthesis planning expert systems. Here you are! Thanks again to everyone for helping me to get the taste of this topic. As it comes from the following messages, the LHASA, CAMEO and CHIRON are the most favourable softwares. Please, let me know if there is anything else! THE SUMMARY ******************************************************************************** >From dimitris@3dp.com Tue Nov 29 19:41:34 1994 There are a few around, but the most advanced is LHASA (Logic and Heuristics Applied to Synthetic Analysis) out of EJ Corey's group at Harvard. For more information, contact: Dr. Alan Long Director Department of Chemistry Harvard University 12 Oxford Street Cambridge, MA 02138 tel: (617) 495-4283 e-mail: long@chemistry.harvard.edu. or EJ himself at the same address. Please let me know if you need more information or can't get through to Alan. Dimitris K. Agrafiotis, PhD | e-mail: dimitris@3dp.com 3-Dimensional Pharmaceuticals, Inc. | tel: (215) 222-8950 3700 Market Street | fax: (215) 222-8960 Philadelphia, PA 19104 ******************************************************************************** >From BRIGGS@kitten.chem.uh.edu Tue Nov 29 19:49:14 1994 Rob, Check out CAMEO (Computer Assisted Mechanistic Evaluation of Organic Reactions) from the Jorgensen group at Yale. CAMEO predicts plausable results of an organic reaction based on the starting materials and conditions. The algorithms used in CAMEO are based on mechanistic rules/trends derived from the literature (i.e. NOT database driven). Prof. Jorgensen can be reached at: bill@doctor.chem.yale.edu Jim Briggs ******************************************************************************** >From MARTIN%cmda@randb.abbott.com Tue Nov 29 20:00:16 1994 You might be able to get Chiron from Stephen Hanessian at the University of Montreal. I think the price is nominal. Email hanessia@ere.umontreal.ca. Yvonne Martin Abbott Laboratories ******************************************************************************** >From eduffy@laplace.csb.yale.edu Tue Nov 29 21:56:37 1994 A portion of Bill Jorgensen's group at Yale develops CAMEO (Computer Assisted Mechanistic Evaluation of Organic Reactions). They may be reached through Bill: bill@adrik.chem.yale.edu. In addition, here is the lead reference: Jorgensen, W.L.; Laird, E.R.; Gushurst, A.J.; Fleisher, J.M.; Gothe, S.A.; Helson, H.E.; Paderes, G.D.; Sinclair, S. "CAMEO: a program for the logical prediction of the products of chemical reactions." Pure & Appl. Chem. (1990) v.62, 1921-1932. ******************************************************************************** >From Harold_Helson@camsci.com Wed Nov 30 16:15:47 1994 Another program is CAMEO, on which I worked as a graduate student. It operates in the forward (as opposed to retrosynthetic) direction, predicting the products of organic reactions given starting materials and conditions. For further information contact Professor William Jorgensen at bill@adrik.chem. yale.edu. Harold Helson ******************************************************************************** >From blurock@risc.uni-linz.ac.at Wed Nov 30 18:02:02 1994 In response to your inquiry about synthesis design programs, I could mention the system developed here. It is described in the paper: J. Chem. Inf. Comp. Sci. 30, pg 505 (1990) Computer-Aided Synthesis Design at RISC-Linz: Automatic Extraction and Use of Reaction Classes I plan to release it to public domain eventually. It runs in COMMON LISP under CLX (an X-window interface for LISP - public domain). At the moment it is a bare-bones system with no database. Part of the work toward releasing it to public domain will be building up (through its analysis techniques) a rudimentary database. It is still in its infancy in regards to 'real' organic reaction searches (This is mainly due to the database), but all the mechanisms are there (with room for improvement). I would be interested to know in more detail your intentions. This is partly for the pragmatic reason that I am only able to work on it in my sparse 'spare time' (thus progress towards public domain is still months away) and would be seriously interested in cooperations in reactivating the system (it has been dormant for a couple of years). Edward S. Blurock ******************************************************************************** >From larouche@ERE.UMontreal.CA Wed Nov 30 19:50:57 1994 Here are some information about computer programs out of S. Hanessian's group at Universite de Montreal. For more information, please send email to hanessia@ere.umontreal.ca The Chiron Program (version 4.22) --------------------------------- The Chiron Computer Program is an interactive program for the analysis and perception of stereochemical features in molecules and for the selection of chiral precursors in organic synthesis. It features Computer Assisted Stereochemical Analysis (CASA), and Computer Assisted Precursor Selection (CAPS). CASA is concerned with the recognition of stereochemical and symmetry elements in a molecule. CAPS probes the structure in question and suggest appropriate precursors from a data base of 4567 chiral and achiral molecules. The Chiron program also has 3-D graphics capability and interfaces with sybyl, macromodel, reaccs, x-ray data bases, etc. Applications in research (drug design and synthesis, chemical diversity, natural and unnatural product synthesis.) and in teaching. Available on Macintosh, SiliconGraphics and V.A.X. ChemProtect (version 1.0) ----------- ChemProtect is a new software designed to help chemists in the selection of protective groups in synthesis. ChemProtect works on the Apple Macintosh. It is available in two versions (English and French). A modified version of this software is also available on UNIX (Iris Series) and VAX/VMS. This software contains 346 protective groups and 161 reaction conditions for a total of 55706 possible reactivities. Finally, there are 1413 literature references built in the database. There are general references (reviews, etc.) and specific references to the primary literature. ChemProtect is innovative in many ways since the interface is interactive, intuitive and very easy to use. It has three search options: Compatibility, Deprotection and Incompatibility. - The Compatibility search allows you to find all protective groups for selected chemical functions that will be stable to 1 up to 10 reaction steps simultaneously. - The Incompatibility search allows you to look for conditions that modify selected protective groups (up to 10 also). - The Deprotection search allows you to look for conditions that selectively deprotect a set of protective groups up to 10 at the same time. Benoit Larouche Agent de Recherche | INTERNET : larouche@chimcn.umontreal.ca Departement de Chimie | larouche@ere.umontreal.ca Universite de Montreal | TELEPHONE: (514) 343-6111 x3969 ******************************************************************************** Rob, You recently requested via CCL information regarding "expert systems in synthesis design". I have pleasure in enclosing information about LHASA, which in my opinion is the most sophisticated retrosynthetic analysis program available. If you require further information you may contact me or probably more approriately Al Long. Regards, Craig A. Marby, Ph.D. __o _ \<,_ C.A. Marby marby@lhasa.harvard.edu (_)/ (_) +1 617 495 2654 (work) ~~~~~~~~~~ +1 617 482 3962 (home, not 24hrs) The LHASA Program The computer program LHASA (an acronym for Logic and Heuristics Applied to Synthetic Analysis), which has been under continuous development at Harvard and various collaborating universities for more than 20 years, is intended to assist organic chemists in designing multistep routes to complex molecules. The program accepts as input a target molecule drawn in the language of structural formulae that is common to all organic chemists. A perception of the target is conducted to identify molecular features that influence the development of retrosynthetic routes (e.g. functional groups, stereocenters, rings, etc.) The user is then prompted to specify a strategy and substrategy, or tactic, to guide the retrosynthetic analysis. Finally, the program selects retroreactions ("transforms") from its chemical knowledge base in accordance with the processing tactic and applies these transforms to generate retrosynthetic precursors which are structurally simpler than the target. The user selects one of the precursors for further processing, and the analysis proceeds in an interactive fashion until readily available hypothetical starting materials are obtained. Graphical Interface The concept of communicating chemical structural information graphically to a computer originated with the DEC PDP-1 version of LHASA (called OCSS) in the late 1960's. This early effort used graphical displays on three CRT's simultaneously, allowing coordinated viewing of a sketching window, a target and precursor display, and a retrosynthetic "tree". The current version of LHASA uses a single CRT, with control passed among several menus. Interaction with the program is entirely graphical, allowing chemists with little or no computer experience to use the program effectively. Considerable effort has been expended in the last few years to enhance the user-friendliness of the program. New features include on-line setup menus for modifying run-time parameters, graphical display of perception information, algorithms for automated selection of strategies and tactics, and on-line explanations of button functions. LHASA supports a variety of monochrome and color graphics devices, including X, the de-facto graphics standard for windowing systems under VMS and Unix. The LHASA program is now supported under VMS (both VAX and Alpha AXP), as well as a number of Unix platforms. Transform Selection and Evaluation The task of choosing the best transforms for retrosynthetic simplification of an arbitrary target structure drawn by the chemist is daunting. The variety of organic structures is enormous, and the number of chemical reactions which could be used to synthesize them is similarly overwhelming. LHASA uses a number of pattern-matching techniques to narrow the search for transforms to a subset of its knowledge base. Some of these techniques are relatively elemental, based only on atoms and the bonds between them, while others rely on convenient "synthetically-significant" structural features such as functional groups, rings, and stereochemical relationships. To further narrow the set of transforms that passes pattern-matching, LHASA evaluates each transform by reading and answering a list of scope-and-limitations questions, or qualifiers, which delineate precisely the molecular features required or prohibited by the transform. Knowledge base entries, including these qualifiers, are written in a special chemical English language, called CHMTRN, designed for LHASA and interpreted on-line by the program. Transforms passing all stages of this detailed evaluation are shown to the chemist, while failing transforms are killed and not shown. Strategy and Tactic Selection When planning a laboratory synthesis, the expert organic chemist does not simply apply every reaction that might be used to make the target structure and all intermediate structures. Rather, s/he identifies one or more strategies and tactics to guide the analysis in the direction of maximal retrosynthetic simplification of the target. In a similar fashion, LHASA uses strategies and tactics to emulate the chemists' reasoning and limit the scope of the search for transforms. There are five major strategies in LHASA: functional-group and pattern-based, topological or "strategic bond", key-transform, stereochemical, and starting-material-oriented. To assist the chemist in selecting strategies, a "LHASA Suggestions" mode has recently been implemented in which the program suggests tactics based on its perception of synthetically-significant structural features. Transform Knowledge Base The major focus of LHASA research at Harvard is in developing sophisticated algorithms for selecting and evaluating strategies, tactics, and transforms, rather than the writing of the transforms for the LHASA knowledge base. LHASA transforms are written to be very general, so that they can be applied to any target structure containing the correct retron, or keying substructure (ring, functional group arrangement, etc.). As such, they are difficult to write, since a multitude of structural possibilities must be considered, and also the necessary skills needed to write good CHMTRN take time to acquire. The LHASA knowledge base consists, at present, of some 2400 transforms and tactical combinations of transforms. A group of chemical and pharmaceutical companies in the United Kingdom has already dedicated considerable effort to knowledge- base expansion, with concentration in the area of heteroaromatic chemistry. A total of approximately 700 transforms in the LHASA knowledge base originate in the UK. Expansion of the knowledge base is continuing and recently an effort to update some of the older transforms has been undertaken. Other Related Software A small number of related programs have spun off from LHASA as well. While certain of these programs are of a proprietary nature, others are available for general use, among them DEREK (a substructure-based toxicology prediction program), APSO (a program for teaching principles of synthesis to organic chemistry students), and PROTECT (a graphically-oriented program for identification of protective groups in organic syntheses). Recently an interface to DEREK has been added to the LHASA program, allowing the chemist to directly use DEREK to process a precursor generated by LHASA and hence view the compounds predicted toxicology. International Distribution LHASA is used in approximately 20 industrial concerns and academic institutions world-wide. The LHASA group at Harvard maintains an ongoing collaboration with groups in several other universities, among them Leeds University (UK), the University of Helsinki, the University of Nijmegen (the Netherlands), and Chalmers Institute of Technology (Goteborg, Sweden). A non-profit corporation in the UK (LHASA UK, Ltd.) has also been formed to coordinate the expansion of knowledge bases for both LHASA and DEREK. Recent Literature Reviews E.J. Corey, A.K. Long, S.D. Rubenstein, Science 228 408 (1985). A.K. Long, S.D. Rubenstein, L.J. Joncas, Chemical and Engineering News, 22 (1983). For more information, contact: Dr. Alan K. Long Harvard Chemistry Dept. 12 Oxford Street Cambridge, MA 02138 UNITED STATES +1 617 495 4283 long@chemistry.harvard.edu ******************************************************************************** >From LHASA UK (jan@mi.leeds.ac.uk) Tue Dec 12 2:37:16 1994 Dear Sir, Just to let you know that there is an organisation called LHASA UK that distributes LHASA and CAMEO synthesis planning software to industrialists and academics in the UK and Europe. I will send (by post) information leaflets on this software to you. If you need to know any more, please get in touch. Yours sincerely, Dr. Jan J. Langowski LHASA UK Technical Manager -- ----------------------------------------------------------------------------- Robert K. Szilagyi University of Veszprem METMOD FF research fellow Dept. Org. Chem. L1 Email: szilagyi@miat0.vein.hu Veszprem, H-8201 L2 | R1 szilagyi@indy.mars.vein.hu Egyetem u. 10 >W=C< Phone: +36-(88)-422022/156 P.O.Box 158 L3 | R2 FAX: +36-(88)-426016 HUNGARY L4 http://indy.mars.vein.hu:8000/molmod.html ----------------------------------------------------------------------------- From states@ibc.wustl.edu Tue Jan 24 21:25:31 1995 Received: from wugate.wustl.edu for states@ibc.wustl.edu by www.ccl.net (8.6.9/930601.1506) id VAA01899; Tue, 24 Jan 1995 21:25:31 -0500 Received: by wugate.wustl.edu (5.67b/WUSTL-0.3) with SMTP id AA14168; Tue, 24 Jan 1995 20:24:53 -0600 Received: by ibc.WUStL.EDU (8.6.9/SMI-SVR4) id UAA07205; Tue, 24 Jan 1995 20:24:52 -0600 Date: Tue, 24 Jan 1995 20:24:52 -0600 From: states@ibc.wustl.edu (David J. States) Message-Id: <199501250224.UAA07205@ibc.WUStL.EDU> To: CHEMISTRY@ccl.net, Thomas.Huber@physik.tu-muenchen.de Subject: Re: CCL:van der Waals parameters from ab initio calc? X-Sun-Charset: US-ASCII |> Thomas Huber wrote: |> Could you please tell me how to derive van der Waals parameters from |> ab initio calculations! |> Any suggestions are wellcome (references, principles,...). For condensed matter, there is a fundamental problem with the derivation of non-bonded interactions from ab initio calculations on isolated molecules. High quality ab initio calculations include wavefunctions with quite large spatial extents, much larger than existence in a condensed matter environment would allow. So, if you are going to calculate non-bonded interactions, you need to start with realistic calculations including multiple molecules. The energy of interaction is straightforward. Deciding how much of it is "van der Waals" is another issue. David States From cbas25@vms.strath.ac.uk Tue Jan 24 21:39:27 1995 Received: from harris.cc.strath.ac.uk for cbas25@vms.strath.ac.uk by www.ccl.net (8.6.9/930601.1506) id UAA01535; Tue, 24 Jan 1995 20:43:00 -0500 Received: from vaxb.cc.strath.ac.uk (actually host vaxb.strath.ac.uk) by harris with SMTP (PP); Wed, 25 Jan 1995 01:42:46 +0000 Received: by vms.strath.ac.uk (MX V4.1 VAX) id 147; Wed, 25 Jan 1995 01:42:58 EST Date: Wed, 25 Jan 1995 01:38:38 EST From: "CBAS25 ::P_BLADON ::CBAS25" To: chemistry@ccl.net Message-ID: <0098AF7C.D775924C.147@vms.strath.ac.uk> Subject: pKa Values Dear Colleagues, I am writing to ask if anyone knows of software for calculation of pKa values of organic compounds. Ideally I would like to calculate the full range of organic structures, but if necessary it could be applicable to structures with conventional ionizable groups. Methods using addition of functional group parameters would be ideal. If there is any interest in this topic I will summarise for the group. Yours sincerely Peter Bladon Department of Pure and Applied Chemistry University of Strathclyde Glasgow G1 1XL Scotland UK cbas25@vms.strath.ac.uk Phone/Fax (+44)(0)141-776-1718