From owner-chemistry@ccl.net Tue Oct 18 10:19:00 2005 From: "yang zhen na yangzn553/a\nenu.edu.cn" To: CCL Subject: CCL: W:Bond order Message-Id: <-29634-051018091014-29973-UdeME4FFagwTagvkHB4xAw---server.ccl.net> X-Original-From: "yang zhen na" Sent to CCL by: "yang zhen na" [yangzn553**nenu.edu.cn] How to calculate the bond order of large molecule? From owner-chemistry@ccl.net Tue Oct 18 10:54:00 2005 From: "David Cornil cornildavid,;,yahoo.fr" To: CCL Subject: CCL: W:Program MAKPOL Message-Id: <-29635-051018093503-32367-GYEzD94zrQ6QUxQqPA3vZg+*+server.ccl.net> X-Original-From: "David Cornil" Sent to CCL by: "David Cornil" [cornildavid#yahoo.fr] I want to know use program MAKPOL to build an infinite package of molecule and calculate the dipole of the strucutre. If anybody could send to me an input as exemple or have information about that it will be great Cornil David cornildavid:-:yahoo.fr From owner-chemistry@ccl.net Tue Oct 18 11:48:00 2005 From: "Takumi Hori thori3jp{=}mac.com" To: CCL Subject: CCL: References for Ionic Liguids Message-Id: <-29636-051018113008-11023-+gEolFXpKDC4Q7iroNOiTg#server.ccl.net> X-Original-From: Takumi Hori Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Date: Tue, 18 Oct 2005 10:48:11 -0400 Mime-Version: 1.0 (Apple Message framework v734) Sent to CCL by: Takumi Hori [thori3jp()mac.com] Dear CCL members, Can anyone tell me good references for ionic liquids including experiments and simulations? Any informations you know will be greatly appreciated. Best regard, Takumi -- Dr. Takumi Hori Postdoctoral Research Associate Department of Chemistry Duke University Durham, NC 27708-0349 USA Tel : 1-919-660-1658 E-mail : thori=-=duke.edu thori3jp=-=mac.com URL : http://www.chem.duke.edu/~yang/ From owner-chemistry@ccl.net Tue Oct 18 12:23:00 2005 From: "David Cornil cornildavid---yahoo.fr" To: CCL Subject: CCL: W:Prog_MAKPOL Message-Id: <-29637-051018114217-17063-A7wHFaordDHCRlLekyGt0A++server.ccl.net> X-Original-From: "David Cornil" Sent to CCL by: "David Cornil" [cornildavid ~ yahoo.fr] How to use the programme MAKPOL to build and calculate properties of a stack ? From owner-chemistry@ccl.net Tue Oct 18 12:58:00 2005 From: "Grant Hill jgh105 _ york.ac.uk" To: CCL Subject: CCL: Compiling Gaussian on EM64T machines Message-Id: <-29638-051018105548-23242-NYAd8w2awG3ZSdlhihae2g++server.ccl.net> X-Original-From: Grant Hill Content-Type: text/plain; format=flowed; charset=ISO-8859-1 Date: 18 Oct 2005 14:54:11 +0100 Mime-Version: 1.0 Sent to CCL by: Grant Hill [jgh105_._york.ac.uk] Hi all, I'm trying to compile Gaussian 03 (Rev C01) on a machine with dual EM64T intel Xeon cpus, running SuSE linux 9.3 (64-bit version, with all current updates applied). When I source the the g03.login script I get errors of the type: ]![: Badly formed number. When I launch the build process I get similar errors throughout the log file suggesting to me that the shell (or perhaps automake / something similar) is having trouble. The errors are of the type: ../bsd/updatelink1 ../bsd/g03.make JUNK1=JUNK DO-LIB abt1dt.F ]![: Badly formed number. -f: Command not found. ar: No match. rm: No match. set noglob end Is this something particular to the building of g03 on EM64T systems, or is it perhaps something more sinister going on with my distro? FWIW, I've tried with both the pgf compiler and intels compiler. Any tips or ideas will be much appreciated (I'll summarise anything useful that comes off list). Thanks in advance, Grant Hill From owner-chemistry@ccl.net Tue Oct 18 13:33:00 2005 From: "Baber, Christian cbaber ~ neurocrine.com" To: CCL Subject: CCL: W:Bond order Message-Id: <-29639-051018115216-21949-xbItW1+VDHdwJx0tg2R2Lg.@.server.ccl.net> X-Original-From: "Baber, Christian" Content-Class: urn:content-classes:message Content-Type: multipart/mixed; boundary="_-==6F4BC5A829469331==-_" Date: Tue, 18 Oct 2005 08:51:49 -0700 MIME-Version: 1.0 Sent to CCL by: "Baber, Christian" [cbaber_+_neurocrine.com] --_-==6F4BC5A829469331==-_ Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Yang, If you are talking about the assignment of bond orders to compounds on = the basis of 3D coordinates then a number of methods have been published = - and are used in various pieces of software. A new method was published recently by Paul Labute from CCG (Labut, = Paul, On the Perception of Molecules from 3D Atomic Coordinates, = J.Chem.Inf.Model, 2005, 46, 215-221). As well as describing his new = algorithm he provides pointers to a number of others currently in use. Cheers, Christian J. Christian Baber Principal Scientist, Computational Chemistry Neurocrine Biosciences Inc. > -----Original Message----- > From: yang zhen na yangzn553/anenu.edu.cn > [mailto:owner-chemistry*|*ccl.net] > Sent: Tuesday, 18 October, 2005 7:27 AM > To: Baber, Christian > Subject: CCL: W:Bond order >=20 >=20 >=20 > Sent to CCL by: "yang zhen na" [yangzn553**nenu.edu.cn] > How to calculate the bond order of large molecule? >=20 >=20 >=20 > -=3D This is automatically added to each message by the mailing=20 > script =3D- > To recover the email address of the author of the message,=20 > please change>=20>=20>=20 > Subscribe/Unsubscribe:=20>=20>=20 > Job advertisements: http://www.ccl.net/jobs=20 >=20>=20 > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > -+-+-+-+-+ >=20 >=20 >=20 >=20 --_-==6F4BC5A829469331==-_ Content-Type: text/plain; charset=iso-8859-1; name=mmsinfo.txt Content-Transfer-Encoding: 7bit Content-Disposition: attachment; filename=mmsinfo.txt "MMS " made the following annotations on 10/18/2005 08:52:02 AM ------------------------------------------------------------------------------ This email may contain confidential and privileged material for the sole use of the intended recipient. Any review or distribution by others is strictly prohibited. If you are not the intended recipient, please contact the sender and delete all copies. ============================================================================== --_-==6F4BC5A829469331==-_-- From owner-chemistry@ccl.net Tue Oct 18 14:08:01 2005 From: "S. I. Gorelsky gorelsky::stanford.edu" To: CCL Subject: CCL: W:Bond order Message-Id: <-29640-051018122758-6035-ntvk4sX+U8Gi8D2ZbVlWYw|-|server.ccl.net> X-Original-From: "S. I. Gorelsky" Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Tue, 18 Oct 2005 09:27:45 -0700 MIME-Version: 1.0 Sent to CCL by: "S. I. Gorelsky" [gorelsky##stanford.edu] Hello, calculations of various bond orders (2-center Wiberg, Mayer, and Lowdin, abd 3-center indices) for large molecules can be done using the AOMix package (http://www.sg-chem.net/aomix/). For the calculation details and references, please check the AOMix Manual. Best regards, S. Gorelsky Quoting "yang zhen na yangzn553/anenu.edu.cn" : > > Sent to CCL by: "yang zhen na" [yangzn553**nenu.edu.cn] > How to calculate the bond order of large molecule?> > > > From owner-chemistry@ccl.net Tue Oct 18 14:43:00 2005 From: "Jayasree Eambalassery jayaeg]_[berkeley.edu" To: CCL Subject: CCL: W:frequency error Message-Id: <-29641-051018123353-8345-z0lVAhkLMUy769J+MWtl3g||server.ccl.net> X-Original-From: "Jayasree Eambalassery" Sent to CCL by: "Jayasree Eambalassery" [jayaeg{}berkeley.edu] Dear CCL subscribers, Did anybody come across the error message on a frequency calculation after the optimization? Do you know how to get around the problem? *************** 1 vectors were produced by pass998. PrismC: NFx= 2048 NFxT= 5 NFxU= 5. 1 vectors were produced by pass999. PrismC: NFx= 2048 NFxT= 5 NFxU= 5. 1 vectors were produced by pass***. CPHF failed to converge in LinEq2. Error termination via Lnk1e in /usr/software/gaussian/g03/l1002.exe at Sun *************************** Any helpful replies will be highly appreciated ...thanks...Jay From owner-chemistry@ccl.net Tue Oct 18 15:18:00 2005 From: "Cory Pye cpye^-^crux.smu.ca" To: CCL Subject: CCL: References for Ionic Liguids Message-Id: <-29642-051018131411-3681-61ExEcgEI6Yy2M6+alOZKA^server.ccl.net> X-Original-From: Cory Pye Content-Type: TEXT/PLAIN; charset=US-ASCII Date: Tue, 18 Oct 2005 14:13:55 -0300 (ADT) MIME-Version: 1.0 Sent to CCL by: Cory Pye [cpye.__.crux.smu.ca] On Tue, 18 Oct 2005, Takumi Hori thori3jp{=}mac.com wrote: > > Sent to CCL by: Takumi Hori [thori3jp()mac.com] > Dear CCL members, > > Can anyone tell me good references for ionic liquids including > experiments and simulations? > Any informations you know will be greatly appreciated. > > Best regard, > Takumi > Hi Takumi, A (somewhat biased) start is C. C. Pye, E. A. Turner, R. D. Singer, J. Phys. Chem. A, 107, 2277 (2003). - ab initio There are also numerous simulation studies by the groups of Chris Hardacre and Georges Wipff. A very recent vib. study also appeared in J Phys Chem B by Berg, Seddon and others, although they don't appear to be aware of (or choose to ignore) previous computational work, along with a few DFT studies scattered through the literature. -Cory ************* ! Dr. Cory C. Pye ***************** ! Associate Professor *** ** ** ** ! Theoretical and Computational Chemistry ** * **** ! Department of Chemistry, Saint Mary's University ** * * ! 923 Robie Street, Halifax, NS B3H 3C3 ** * * ! cpye__crux.stmarys.ca http://apwww.stmarys.ca/~cpye *** * * ** ! Ph: (902)-420-5654 FAX:(902)-496-8104 ***************** ! ************* ! Les Hartree-Focks (Apologies to Montreal Canadien Fans) From owner-chemistry@ccl.net Tue Oct 18 15:53:01 2005 From: "Ary Junior junior|a|aryjr.com" To: CCL Subject: CCL: W:Queue of processes and more than one processor Message-Id: <-29643-051018141226-23650-UY7ZZXgMqAhxdQnCdcbmGg]_[server.ccl.net> X-Original-From: "Ary Junior" Sent to CCL by: "Ary Junior" [junior- -aryjr.com] Hello, I have one machine with two Intel HT Xeon processors. I need a software that create and manage a queue of , for example, abinit processes. Any suggestion? Thanks very much!!! Ary Junior From owner-chemistry@ccl.net Tue Oct 18 16:28:00 2005 From: "Elaine Ching-su Meng meng!^!cgl.ucsf.edu" To: CCL Subject: CCL: W:UCSF Chimera Workshop Nov. 17-18, 2005 Message-Id: <-29644-051018141706-25979-VBVu2qo9k81j5OWJ+jl0vw[a]server.ccl.net> X-Original-From: "Elaine Ching-su Meng" Sent to CCL by: "Elaine Ching-su Meng" [meng-,-cgl.ucsf.edu] A workshop on the molecular graphics program UCSF Chimera will be held November 17 and 18, 2005 at the Mission Bay Campus, University of California San Francisco (UCSF). The workshop is free of charge, but space is limited. Additional information and registration: http://www.cgl.ucsf.edu/Outreach/Workshops/ Topics will be covered in short presentations followed by hands-on experience, and time will be allotted for getting help with your own data and systems of interest. Outline: ------------ Day 1 ------------ Introduction to Chimera Exploring sequence-structure relationships Viewing docked ligands MD trajectory playback and analysis Defining and calculating attributes ------------ Day 2 ------------ Virus capsid and multiscale visualization Viewing X-ray and EM density maps Publication/presentation images and animations Writing Chimera scripts and demos Panel discussion - Chimera future plans ------------ UCSF Chimera is free to academic and non-profit users and is available for Windows, Linux, Mac OS X, IRIX, and Tru64 Unix. http://www.cgl.ucsf.edu/chimera/ On behalf of the Chimera development team, Elaine Meng meng:_:cgl.ucsf.edu Computer Graphics Laboratory Resource for Biocomputing, Visualization, and Informatics University of California, San Francisco From owner-chemistry@ccl.net Tue Oct 18 17:02:00 2005 From: "Igor Filippov Contr igorf.,.helix.nih.gov" To: CCL Subject: CCL: Compiling Gaussian on EM64T machines Message-Id: <-29645-051018141430-24764-9y8lZ6cOS35/0Ivd9sMR8A,server.ccl.net> X-Original-From: "Igor Filippov [Contr]" Content-Transfer-Encoding: 7bit Content-Type: text/plain Date: Tue, 18 Oct 2005 14:14:21 -0400 Mime-Version: 1.0 Sent to CCL by: "Igor Filippov [Contr]" [igorf**helix.nih.gov] Something tells me when you get an error like "-f: Command not found" it's not a problem with the compiler or 64-bit architecture... Igor On Tue, 2005-10-18 at 14:54 +0100, Grant Hill jgh105 _ york.ac.uk wrote: > Sent to CCL by: Grant Hill [jgh105_._york.ac.uk] > Hi all, > > I'm trying to compile Gaussian 03 (Rev C01) on a machine with dual EM64T > intel Xeon cpus, running SuSE linux 9.3 (64-bit version, with all current > updates applied). When I source the the g03.login script I get errors of > the type: > > -#-: Badly formed number. > > When I launch the build process I get similar errors throughout the log > file suggesting to me that the shell (or perhaps automake / something > similar) is having trouble. The errors are of the type: > > ./bsd/updatelink1 ../bsd/g03.make JUNK1=JUNK DO-LIB abt1dt.F > -#-: Badly formed number. > -f: Command not found. > ar: No match. > rm: No match. > set noglob > end > > Is this something particular to the building of g03 on EM64T systems, or is > it perhaps something more sinister going on with my distro? FWIW, I've > tried with both the pgf compiler and intels compiler. > > Any tips or ideas will be much appreciated (I'll summarise anything useful > that comes off list). > > Thanks in advance, > > Grant Hill> From owner-chemistry@ccl.net Tue Oct 18 17:38:00 2005 From: "Perry E. Metzger perry{=}piermont.com" To: CCL Subject: CCL: Compiling Gaussian on EM64T machines Message-Id: <-29646-051018143823-4052-nAxgjRwRFgqwAVWT8rYd0Q*|*server.ccl.net> X-Original-From: "Perry E. Metzger" Content-Type: text/plain; charset=us-ascii Date: Tue, 18 Oct 2005 14:38:15 -0400 MIME-Version: 1.0 Sent to CCL by: "Perry E. Metzger" [perry(~)piermont.com] "Grant Hill jgh105 _ york.ac.uk" writes: > Sent to CCL by: Grant Hill [jgh105_._york.ac.uk] > Hi all, > > I'm trying to compile Gaussian 03 (Rev C01) on a machine with dual > EM64T intel Xeon cpus, running SuSE linux 9.3 (64-bit version, with > all current updates applied). When I source the the g03.login script I > get errors of the type: > > -#-: Badly formed number. Okay, the first thing you need to do in debugging this is to get the script to tell you what exactly is failing. I don't know offhand if this is a csh or sh script you're having trouble with, but either way, you should turn on debugging. For both csh and sh, adding "-x" to the shell invocation will print every command as it is executed, so you can determine which command exactly it is. (I suspect that this is a csh script, but it either way...) You may have to edit the script to cause the #! line to include the -x. > When I launch the build process I get similar errors throughout the > log file suggesting to me that the shell (or perhaps automake / > something similar) is having trouble. The errors are of the type: > > ./bsd/updatelink1 ../bsd/g03.make JUNK1=JUNK DO-LIB abt1dt.F > -#-: Badly formed number. > -f: Command not found. > ar: No match. > rm: No match. > set noglob > end That looks like a shell getting very badly confused -- it is treating switches as command names, and command names as globs. Again, doing the "-x" trick will help in figuring out what command is going wrong and thus causing everything to go out of wack. Perry From owner-chemistry@ccl.net Tue Oct 18 18:34:00 2005 From: "Perry E. Metzger perry[#]piermont.com" To: CCL Subject: CCL: W:Queue of processes and more than one processor Message-Id: <-29647-051018182502-25865-TJjCMeq95SrxTDE3rSAUpg]_[server.ccl.net> X-Original-From: "Perry E. Metzger" Content-Type: text/plain; charset=us-ascii Date: Tue, 18 Oct 2005 18:24:51 -0400 MIME-Version: 1.0 Sent to CCL by: "Perry E. Metzger" [perry^^piermont.com] "Ary Junior junior|a|aryjr.com" writes: > Hello, I have one machine with two Intel HT Xeon processors. I need > a software that create and manage a queue of , for example, abinit > processes. Any suggestion? Unfortunately, you haven't mentioned the operating system you are running, which is kind of key here, as well as the goal that you have. It isn't clear precisely what you mean, but I'll assume that your goal is to maintain a queue of jobs to be worked on in a strict sequence. I'm going to assume that you're running a Unix variant of some sort -- if you're using Windows my advice doesn't per se apply. If what you are trying to do is just run a sequence of commands informally over a long period but you personally are the only user, a complicated piece of scheduling software is probably overkill. Listing a series of commands in a shell script, or doing something slightly more sophisticated like having a shell script that iterates over the commands that it finds in a particular directory (re-parsing the directory after each command completes), may be more than enough. You can rig up either in just a couple of minutes. If you really need something more sophisticated, what you are looking for is a "job scheduler". There are a number of open source ones out there -- if you go over to freshmeat.net and query for "job scheduler" or "job manager" you will find several that might meet your needs. However, I'm not entirely sure this is the question you were asking -- your question was somewhat underspecified. If this doesn't cover what you are looking for please do ask again. Perry From owner-chemistry@ccl.net Tue Oct 18 20:01:00 2005 From: "Alexander Martins Silva alex.msilva,;,uol.com.br" To: CCL Subject: CCL: Gamess in parallel Message-Id: <-29648-051018195305-1633-qW3gB2xiEjHPIMjQ8YLRRg!A!server.ccl.net> X-Original-From: Alexander Martins Silva Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 18 Oct 2005 21:52:54 +0000 MIME-Version: 1.0 Sent to CCL by: Alexander Martins Silva [alex.msilva:-:uol.com.br] Hi, I'm trying to run the latest release of GAMESS on a linux cluster under Mandrake 10.0. The compilation went fine and all tests were passed. The rsh and ssh (without password) are working fine. The non-root user can acesses any node of the cluster from the server. However, I can't execute a parallel job, and the generic error message is obtained: > /usr/local/gamess/ddikick.x /usr/local/gamess/gamess.01.x exam01.inp -ddi 2 2 node01 node02 -scr Distributed Data Interface kickoff program. Initiating 2 compute processes on 2 nodes to run the following command: /usr/local/gamess/gamess.01.x exam01.inp TCP connect error: ECONNREFUSED. TCP connect error: ECONNREFUSED. TCP: Connect failed. at1 -> at1101.ime.eb.br:35389. A fatal error occurred on DDI Process 0. TCP: Connect failed. at1 -> at1101.ime.eb.br:35389. A fatal error occurred on DDI Process 2. TCP connect error: ECONNREFUSED. TCP: Connect failed. at1102 -> at1101.ime.eb.br:35389. A fatal error occurred on DDI Process 1. TCP connect error: ECONNREFUSED. TCP: Connect failed. at1102 -> at1101.ime.eb.br:35389. A fatal error occurred on DDI Process 3. ddikick.x: Timed out while waiting for DDI processes to check in. ddikick.x: Fatal error detected. The error is most likely to be in the application, so check for input errors, disk space, memory needs, application bugs, etc. ddikick.x will now clean up all processes, and exit... ddikick.x: Sending kill signal to DDI processes. ddikick.x: Execution terminated due to error(s). What's the problem? How can I fix it? Thanks in advance, Alexander. From owner-chemistry@ccl.net Tue Oct 18 20:35:00 2005 From: "Eduard Matito eduard()stark.udg.es" To: CCL Subject: CCL: W:Bond order Message-Id: <-29649-051018152046-15633-f1a0flcrieUDEF5TEr9Gjw : server.ccl.net> X-Original-From: Eduard Matito Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 18 Oct 2005 20:20:31 +0200 MIME-Version: 1.0 Sent to CCL by: Eduard Matito [eduard{=}stark.udg.es] It depends on what you mean by "large", but maybe you can try using fuzzy-atom bond orders. Check for instance: Mayer, Salvador CPL 383 (2004) 368. They give their program for free. It has applied to C60, and maybe you can go further ... yang zhen na yangzn553/anenu.edu.cn wrote: >Sent to CCL by: "yang zhen na" [yangzn553**nenu.edu.cn] >How to calculate the bond order of large molecule?> > > > > > From owner-chemistry@ccl.net Tue Oct 18 22:03:00 2005 From: "Brian Salter-Duke b_duke%x%octa4.net.au" To: CCL Subject: CCL: W:Queue of processes and more than one processor Message-Id: <-29650-051018205835-6842-+Lrp0oyYXtwpPJYt7zBNTA ~ server.ccl.net> X-Original-From: Brian Salter-Duke Content-Disposition: inline Content-Type: text/plain; charset=us-ascii Date: Wed, 19 Oct 2005 08:48:06 +1000 Mime-Version: 1.0 Sent to CCL by: Brian Salter-Duke [b_duke_+_octa4.net.au] On Tue, Oct 18, 2005 at 04:42:17PM -0400, Ary Junior junior|a|aryjr.com wrote: > > Sent to CCL by: "Ary Junior" [junior- -aryjr.com] > Hello, I have one machine with two Intel HT Xeon processors. > I need a software that create and manage a queue of , for example, > abinit processes. Any suggestion? Try my simple queueing system - http://sqs.sourceforge.net/ Brian. > Thanks very much!!! > > Ary Junior> -- Brian Salter-Duke (Brian Duke) b_duke#octa4.net.au Post: 626 Melbourne Rd, Spotswood, VIC, 3015, Australia Phone 03-93992847. http://members.iinet.net.au/~linden1/brian/ Honorary Researcher, Chem., Melbourne Univ. & Med. Chem., Monash Univ.