From owner-chemistry@ccl.net Thu Feb 2 07:27:00 2012 From: "ashok kumar dhaka ashok.ashokaraj.kumar8!=!gmail.com" To: CCL Subject: CCL: geetin error with configuration file Message-Id: <-46225-120202050308-10165-MpVT5GWsqZ1k0NgZCcSLdQ _ server.ccl.net> X-Original-From: "ashok kumar dhaka" Date: Thu, 2 Feb 2012 05:03:07 -0500 Sent to CCL by: "ashok kumar dhaka" [ashok.ashokaraj.kumar8.:.gmail.com] Hello you are heating the protein too fast!! Did you add the tcl libraries to your namd installation? What does your config file look like? Then I can tell you if there is something wrong with your config. I will bet that you have an unkown command error in your log file just above the errors you list below. Brian On Fri, 14 Nov 2003, xiongying99 wrote: > Dear sir, > I have another question. When I run a minimization, the program stopped > abnormally: > REINITIALIZING VELOCITIES AT STEP 100 TO 310 KELVIN. > TCL: Running for 100 steps > ERROR: Constraint failure in RATTLE algorithm for atom 1551! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 1193! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 2102! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 3254! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 3120! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 3575! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 4624! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 3069! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Exiting prematurely. > ========================================== > WallClock: 25.321195 CPUTime: 25.270000 Memory: 16074 kB > Program finished. > > From owner-chemistry@ccl.net Thu Feb 2 10:37:00 2012 From: "=?ISO-8859-1?Q?Miquel_Sol=E0?= miquel.sola^^udg.edu" To: CCL Subject: CCL: X Girona Seminar - Second Announcement - Registration Message-Id: <-46226-120202102439-26020-xLB7qpoNJYUQLtHvDls8pA::server.ccl.net> X-Original-From: =?ISO-8859-1?Q?Miquel_Sol=E0?= Content-Type: multipart/alternative; boundary="------------040802070308020200040405" Date: Thu, 02 Feb 2012 16:24:18 +0100 MIME-Version: 1.0 Sent to CCL by: =?ISO-8859-1?Q?Miquel_Sol=E0?= [miquel.sola^_^udg.edu] This is a multi-part message in MIME format. --------------040802070308020200040405 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 8bit *X Girona Seminar - Second Announcement* Dear colleagues, On behalf of the Local Organizing Committee and the International Advisory Board of the X Girona Seminar *http://stark.udg.edu/xgironaseminar)*, we are pleased to inform you that the web page of the Seminar is now open for registration. The Girona Seminars have taken place in the historic town of Girona every two years since back to 1993, with the aim of bringing together, in a beautiful environment and in an informal and friendly atmosphere, young and senior scientists. Close to Barcelona, located midway between the sea and the mountains, Girona boasts a privileged position. The Old Town is one of the most evocative historical centres in Catalonia, with certain elements that are unique in Europe: the Carolingian wall , an exceptionally well conserved Jewish quarter, and the grandeur of the Cathedral's Gothic nave, the widest in the world. Girona also has six museums which possess a patrimonial collection of great interest. The aim of the X Girona Seminar is to discuss the recent advances in the theoretical modeling of biochemical systems and biophysical processes, > from new methodological developments to applications. This will be the main subject, although, following the philosophy of the previous Girona Seminars, other aspects such as theoretical chemistry, photochemistry, reactivity of organic and organometallic molecules, catalysis, molecular properties or nature of the chemical bond will be also welcome. The X Girona Seminar will be held from June 2^nd till 5^th , 2012. It consists of a series of plenary lectures delivered by highly reputed scientists as well as short communications and poster sessions. Short communications will be selected among the abstracts sent by the participants requesting oral presentation. The official language of the congress is English, which will be used in all talks and other events. Social events have also been arranged. First, in the evening of Monday 2^nd July, after the poster session, there will be a guided tour to the Old Town of Girona (included in the registration fee for all participants). Second, in the afternoon of Tuesday 3^rd July we will arrange a visit to some nice spots located in the Costa Brava, in the Mediterranean coast, not far from Girona. Finally a Closing Banquet will take place on the evening of Wednesday 4^th July (included in the registration fee). The cost of the registration fee is 200 EUR for Ph. D. students, and 400 EUR for the rest of participants. All four lunches are included in the registration fee, together with all coffee breaks. We have pre-reserved a number of rooms in 4* and 3* hotels located in convenient places of the city that are offered to you during the registration process. We are looking forward to meeting you in Girona. Best wishes, Miquel Solà, Pedro Salvador and Jordi Poater Organizers of the X Girona Seminar ps.: We apologize for cross posting. -- Miquel Solà Institut de Química Computacional iDepartament de Química Universitat de Girona Phone +34.972.41.89.12, FAX +34.972.41.83.56 http://iqc.udg.es/~miquel/mike.html , e-mail:miquel.sola..udg.edu http://twitter.com/miquelsola Twitter http://www.researcherid.com/rid/A-6155-2009 ResearcherID http://es.linkedin.com/in/miquelsolapuig Linked*in* http://scholar.google.com/citations?user=wwh9fP4AAAAJ&hl=en Google Scholar Visita el blog dedicat a la Química:http://catquimica.cat --------------040802070308020200040405 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit

X Girona Seminar - Second Announcement

Dear colleagues,

On behalf of the Local Organizing Committee and the International Advisory Board of the X Girona Seminar http://stark.udg.edu/xgironaseminar), we are pleased to inform you that the web page of the Seminar is now open for registration.

The Girona Seminars have taken place in the historic town of Girona every two years since back to 1993, with the aim of bringing together, in a beautiful environment and in an informal and friendly atmosphere, young and senior scientists. Close to Barcelona, located midway between the sea and the mountains, Girona boasts a privileged position. The Old Town is one of the most evocative historical centres in Catalonia, with certain elements that are unique in Europe: the Carolingian wall, an exceptionally well conserved Jewish quarter, and the grandeur of the Cathedral’s Gothic nave, the widest in the world. Girona also has six museums which possess a patrimonial collection of great interest.

The aim of the X Girona Seminar is to discuss the recent advances in the theoretical modeling of biochemical systems and biophysical processes, from new methodological developments to applications. This will be the main subject, although, following the philosophy of the previous Girona Seminars, other aspects such as theoretical chemistry, photochemistry, reactivity of organic and organometallic molecules, catalysis, molecular properties or nature of the chemical bond will be also welcome.

The X Girona Seminar will be held from June 2nd till 5th, 2012. It consists of a series of plenary lectures delivered by highly reputed scientists as well as short communications and poster sessions. Short communications will be selected among the abstracts sent by the participants requesting oral presentation. The official language of the congress is English, which will be used in all talks and other events.

Social events have also been arranged. First, in the evening of Monday 2nd July, after the poster session, there will be a guided tour to the Old Town of Girona (included in the registration fee for all participants). Second, in the afternoon of Tuesday 3rd July we will arrange a visit to some nice spots located in the Costa Brava, in the Mediterranean coast, not far from Girona. Finally a Closing Banquet will take place on the evening of Wednesday 4th July (included in the registration fee).

The cost of the registration fee is 200 € for Ph. D. students, and 400 € for the rest of participants. All four lunches are included in the registration fee, together with all coffee breaks. We have pre-reserved a number of rooms in 4* and 3* hotels located in convenient places of the city that are offered to you during the registration process.

We are looking forward to meeting you in Girona.

Best wishes,

Miquel Solà, Pedro Salvador and Jordi Poater
Organizers of the X Girona Seminar

 

ps.: We apologize for cross posting.

-- 
Miquel Solà
Institut de Química Computacional i Departament de Química
Universitat de Girona
Phone +34.972.41.89.12, FAX   +34.972.41.83.56
http://iqc.udg.es/~miquel/mike.html, e-mail: miquel.sola..udg.edu
 
http://twitter.com/miquelsola Twitter
http://www.researcherid.com/rid/A-6155-2009 ResearcherID
http://es.linkedin.com/in/miquelsolapuig Linkedin
http://scholar.google.com/citations?user=wwh9fP4AAAAJ&hl=en Google Scholar
 
Visita el blog dedicat a la Química: http://catquimica.cat
 
 
 
--------------040802070308020200040405-- From owner-chemistry@ccl.net Thu Feb 2 16:04:01 2012 From: "David Danovich david.danovich*huji.ac.il" To: CCL Subject: CCL: Valence Bond workshop in Paris - July 2012 Message-Id: <-46227-120202104412-25626-Lh9yi+piO4Sj3vi0u1VM3w:+:server.ccl.net> X-Original-From: David Danovich Content-Type: multipart/alternative; boundary=047d7b2ed26ddd770004b7fd10d5 Date: Thu, 2 Feb 2012 17:43:44 +0200 MIME-Version: 1.0 Sent to CCL by: David Danovich [david.danovich---huji.ac.il] --047d7b2ed26ddd770004b7fd10d5 Content-Type: text/plain; charset=windows-1252 Content-Transfer-Encoding: quoted-printable Dear colleague, I am pleased to inform you that a workshop on ab initio Valence Bond theory will take place next 16-20 July 2012 in Paris (Universit=E9 Pierre e= t Marie Curie, campus de Jussieu). Registration if free, and it will be limited to the first 50 requests. Don=92t wait too much ! The purpose of the workshop is threefold : i) to guide newcomers to ab initio Valence Bond to learn the necessary basics of the theory and start using some of the available VB codes (especially the XMVB and BLW programs), ii) to be a meeting ground for chemists from diverse scientific communities, whose interest are related with aspects of ab initio VB theory ; iii) to stimulate further developments in VB methods and algorithms, new applications of VB theory to chemical problems, and new collaborations. Considering these purposes, this workshop will include plenary lectures on Valence Bond theory, methods, and related models; short talks given by participants on topics relevant to VB theory ; ample time dedicated to free discussions ; "hands-on" computational sessions: basic initiation to the XMVB and BLW software. Extension lectures will as well provide connections between VB and other related wave function methods as well as with related interpretative methods. This event will be sponsored by CECAM as part of 2012 series of =ABCECAM tutorials=BB, so no registration fees will be requested. We might be able t= o deliver some financial support to a few participants, but there is absolutely no garantee for the moment. We are trying to arrange affordable housing in Paris close to the campus, more information on that will follow. You will find more information on the workshop, including detailed schedule and lecturers names, on our web site : http://wiki.lct.jussieu.fr/workshop/index.php/Workshop_on_ab_initio_Valence= _Bond_theory_(VB ) and you can already register on the following page on the CECAM web site : http://www.cecam.org/workshop-6-778.html We hope to see you next July in Paris ! For the organizing committee, Beno=EEt BRAIDA, Philippe HIBERTY, Sason S. SHAIK, Yirong MO and Wei WU ___________________________________________________________________________= _ Dr. David Danovich, The Lise Meitner Minerva Center for Computational Quantum Chemistry, Institute of Chemistry, The Hebrew University, Edmond J. Safra Campus - Givat Ram, 91904 Jerusalem, Israel http://yfaat.ch.huji.ac.il/david.html, david.danovich a huji.ac.il FAX:(+972)-2-6584033, Phone:(+972)-2-6586934(w), Mobile:(+972)-544-768669 !!!!!! Workshop on Valence Bond theory - July 16-20 2012 in Paris !!!!!! !!!!!! All information : http://wiki.lct.jussieu.fr/workshop/ !!!!!! !!!!!! Register NOW at : http://www.cecam.org/workshop-0-778.html !!!!!! !!!!!! Free registration and limited to 50 participants !!!!!! --047d7b2ed26ddd770004b7fd10d5 Content-Type: text/html; charset=windows-1252 Content-Transfer-Encoding: quoted-printable

Dear colleague,

I am pleased to inform you that a= workshop on ab initio Valence Bond
theory will take place next 16-20 Ju= ly 2012 in Paris (Universit=E9 Pierre et
Marie Curie, campus de Jussieu)= .

Registration if free, and it will be limited to the first 50 requests.Don=92t wait too much !

The purpose of the workshop is threefold :<= /p>

i) to guide newcomers to ab initio Valence Bond to learn the necessar= y
basics of the theory and start using some of the available VB codes
(esp= ecially the XMVB and BLW programs),

ii) to be a meeting ground for ch= emists from diverse scientific
communities, whose interest are related w= ith aspects of ab initio VB
theory ;

iii) to stimulate further developments in VB methods and alg= orithms, new
applications of VB theory to chemical problems, and new col= laborations.

Considering these purposes, this workshop will include p= lenary lectures on
Valence Bond theory, methods, and related models; short talks given by
p= articipants on topics relevant to VB theory ; ample time dedicated to
fr= ee discussions ; "hands-on" computational sessions: basic initiat= ion to
the XMVB and BLW software. Extension lectures will as well provide
conne= ctions between VB and other related wave function methods as well as
wit= h related interpretative methods.

This event will be sponsored by CEC= AM as part of 2012 series of =ABCECAM
tutorials=BB, so no registration fees will be requested. We might be able t= o
deliver some financial support to a few participants, but there is
= absolutely no garantee for the moment. We are trying to arrange affordable<= br> housing in Paris close to the campus, more information on that will
foll= ow.

You will find more information on the workshop, including detaile= d
schedule and lecturers names, on our web site :

http://wiki.lct.jussieu.fr/workshop/index.php/Workshop_on_ab_i= nitio_Valence_Bond_theory_(VB)

and you can already register on the following page on the CECAM web site= :

http://www.ce= cam.org/workshop-6-778.html

We hope to see you next July in Paris= !

For the organizing committee,

Beno=EEt BRAIDA, Philippe HIBERTY, S= ason S. SHAIK, Yirong MO and Wei WU


=
_____________________________________________________= _______________________
Dr. David Danovich,=A0 The Lise Meitner Minerva Center for Computational Qu= antum Chemistry,
Institute of Chemistry, The Hebrew University, Edmond J. Safra Campus = - Givat Ram,
FAX:(+972)-2-6584033, Phone:(+972)-2-6586934(w),=A0 Mobile:(+972)-544-76866= 9

!!!!!! Workshop on Valence Bond theory - July 16-20 2012 in Paris = !!!!!!
!!!!!! =A0 =A0All information : http://wiki.lct.jussieu.fr/workshop/ =A0 =A0!!!= !!!
!!!!!! =A0Register NOW at : http://www.cecam.org/workshop-0-778.html !!!!!!=
!!!!!! =A0 =A0 =A0 Free registration and limited to 50 participants =A0 =A0= =A0!!!!!!

--047d7b2ed26ddd770004b7fd10d5-- From owner-chemistry@ccl.net Thu Feb 2 16:39:01 2012 From: "Ram Shankar S ramchemistry2011!=!gmail.com" To: CCL Subject: CCL:G: Semi empirical method available for Zr Complex? Message-Id: <-46228-120202123209-27304-Ci8DjKVIDYduKQerNn+ZkA[#]server.ccl.net> X-Original-From: "Ram Shankar S" Date: Thu, 2 Feb 2012 12:32:08 -0500 Sent to CCL by: "Ram Shankar S" [ramchemistry2011[a]gmail.com] Dear CCL members, My studies involve Zirconium complexes. I have studied in Cramer (Essentials of Computational Chemistry Book) that the semi empirical parameters are available for metal complexes, but if I run my calculation for Zr complex with PM3 or PM6 methods in Gaussian, it always end up with an following error. Could you please suggest any other semi empirical methods for running Zr complexes in Gaussian 03/09? Error in internal coordinate system. Error termination via Lnk1e in C:\G09W\l103.exe at Thu Feb 02 22:54:56 2012. Thanks in advance. Raam From owner-chemistry@ccl.net Thu Feb 2 17:14:00 2012 From: "David Sherrill sherrill.() .gatech.edu" To: CCL Subject: CCL: Georgia Tech Summer Theory Program Message-Id: <-46229-120202163200-11704-VbnlrxofR0lpINGtJSnhRg() server.ccl.net> X-Original-From: David Sherrill Content-Type: TEXT/PLAIN; format=flowed; charset=US-ASCII Date: Thu, 2 Feb 2012 16:31:48 -0500 (EST) MIME-Version: 1.0 Sent to CCL by: David Sherrill [sherrill!=!gatech.edu] Georgia Tech will host its annual Summer Theory Program as part of its NSF-sponsored Research Experiences for Undergraduates (REU) program in chemistry and biochemistry. The ten-week program runs from May 21 to July 27 and is open to students who will be in their junior or senior years during the next academic year. Theory students will work with Professors David Sherrill, Rigoberto Hernandez, Jean-Luc Bredas, or Angelo Bongiorno in the areas of electronic structure theory, nonequilibrium dynamics, electronic properties of materials, or condensed-matter simulations. The research experience is supplemented by an introductory lecture series in theoretical chemistry. Successful applicants will receive a stipend of $5000, a travel allowance, and housing. Further details are available at http://vergil.chemistry.gatech.edu/opp/summer.html and http://www.chemistry.gatech.edu/undergraduate/summer/index.php The deadline for applications is February 15, 2012. -- C. David Sherrill, Ph.D. Professor School of Chemistry & Biochemistry School of Computational Science and Engineering Georgia Institute of Technology www.chemistry.gatech.edu/faculty/Sherrill/ sherrill,,gatech.edu, tel: 404-894-4037, fax: 404-894-7452 From owner-chemistry@ccl.net Thu Feb 2 18:04:00 2012 From: "Bradley Welch bwelch5#%#slu.edu" To: CCL Subject: CCL:G: Semi empirical method available for Zr Complex? Message-Id: <-46230-120202175911-16208-crKhOjnm0r7EYABuAM2XJA*_*server.ccl.net> X-Original-From: Bradley Welch Content-Type: multipart/alternative; boundary=14dae934052b6b3e4f04b80324dd Date: Thu, 2 Feb 2012 16:59:02 -0600 MIME-Version: 1.0 Sent to CCL by: Bradley Welch [bwelch5|*|slu.edu] --14dae934052b6b3e4f04b80324dd Content-Type: text/plain; charset=ISO-8859-1 Try opt=Cartesian. How large is your system? Bradley Welch On Thu, Feb 2, 2012 at 11:32 AM, Ram Shankar S ramchemistry2011!=!gmail.com wrote: > > Sent to CCL by: "Ram Shankar S" [ramchemistry2011[a]gmail.com] > Dear CCL members, > > My studies involve Zirconium complexes. I have studied in Cramer > (Essentials of Computational Chemistry Book) that the semi empirical > parameters are available for metal complexes, but if I run my calculation > for Zr complex with PM3 or PM6 methods in Gaussian, it always end up with > an following error. Could you please suggest any other semi empirical > methods for running Zr complexes in Gaussian 03/09? > > Error in internal coordinate system. > Error termination via Lnk1e in C:\G09W\l103.exe at Thu Feb 02 22:54:56 > 2012. > > Thanks in advance. > Raam> > > --14dae934052b6b3e4f04b80324dd Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Try opt=3DCartesian. How large is your system?=A0


Bradley Welch

On Thu, Feb 2, 201= 2 at 11:32 AM, Ram Shankar S ramchemistry2011!=3D!gmail.com <owner-chemistry#%#ccl.net> wrote:

Sent to CCL by: "Ram Shankar S" [ramchemistry2011[a]gmail.com]
Dear CCL members,

=A0 =A0 =A0 =A0My studies involve Zirconium complexes. I have studied in C= ramer (Essentials of Computational Chemistry Book) that the semi empirical = parameters are available for metal complexes, but if I run my calculation f= or Zr complex with PM3 or PM6 methods in Gaussian, it always end up with an= following error. Could you please suggest any other semi empirical methods= for running Zr complexes in Gaussian 03/09?

Error in internal coordinate system.
=A0Error termination via Lnk1e in C:\G09W\l103.exe at Thu Feb 02 22:54:56 2= 012.

=A0Thanks in advance.
=A0Raam



-=3D This is automatically added to each message by the mailing script =3D-=
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--14dae934052b6b3e4f04b80324dd-- From owner-chemistry@ccl.net Thu Feb 2 21:50:00 2012 From: "David Gallagher gallagher.da_+_gmail.com" To: CCL Subject: CCL:G: Semi empirical method available for Zr Complex? Message-Id: <-46231-120202184107-9761-pGsd2pgpbaA3R05bgL1yXg#,#server.ccl.net> X-Original-From: David Gallagher Content-Type: multipart/alternative; boundary="------------090304090605010707020501" Date: Thu, 02 Feb 2012 15:40:53 -0800 MIME-Version: 1.0 Sent to CCL by: David Gallagher [gallagher.da ~~ gmail.com] This is a multi-part message in MIME format. --------------090304090605010707020501 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Why not try MOPAC2009 with PM3 and PM6? http://www.cacheresearch.com/mopac.html It is free for academics. David Gallagher On 2/2/2012 9:32 AM, Ram Shankar S ramchemistry2011!=!gmail.com wrote: > Sent to CCL by: "Ram Shankar S" [ramchemistry2011[a]gmail.com] > Dear CCL members, > > My studies involve Zirconium complexes. I have studied in Cramer (Essentials of Computational Chemistry Book) that the semi empirical parameters are available for metal complexes, but if I run my calculation for Zr complex with PM3 or PM6 methods in Gaussian, it always end up with an following error. Could you please suggest any other semi empirical methods for running Zr complexes in Gaussian 03/09? > > Error in internal coordinate system. > Error termination via Lnk1e in C:\G09W\l103.exe at Thu Feb 02 22:54:56 2012. > > Thanks in advance. > Raam> > > --------------090304090605010707020501 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Why not try MOPAC2009 with PM3 and PM6?
   http://www.cacheresearch.com/mopac.html
It is free for academics.

David Gallagher


On 2/2/2012 9:32 AM, Ram Shankar S ramchemistry2011!=!gmail.com wrote: 
Sent to CCL by: "Ram Shankar S" [ramchemistry2011[a]gmail.com]
Dear CCL members,

	My studies involve Zirconium complexes. I have studied in Cramer (Essentials of Computational Chemistry Book) that the semi empirical parameters are available for metal complexes, but if I run my calculation for Zr complex with PM3 or PM6 methods in Gaussian, it always end up with an following error. Could you please suggest any other semi empirical methods for running Zr complexes in Gaussian 03/09?

Error in internal coordinate system.
 Error termination via Lnk1e in C:\G09W\l103.exe at Thu Feb 02 22:54:56 2012.

 Thanks in advance.
 RaamE-mail to subscribers: CHEMISTRY__ccl.net or use:
      http://www.ccl.net/cgi-bin/ccl/send_ccl_message

E-mail to administrators: CHEMISTRY-REQUEST__ccl.net or use
      http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtml

Before posting, check wait time at: http://www.ccl.net

Job: http://www.ccl.net/jobs 
Conferences: http://server.ccl.net/chemistry/announcements/conferences/

Search Messages: http://www.ccl.net/chemistry/searchccl/index.shtmlhttp://www.ccl.net/spammers.txt

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--------------090304090605010707020501--