From owner-chemistry@ccl.net Sat Jan 13 05:31:00 2007 From: "soumya s soumya_samineni%x%rediffmail.com" To: CCL Subject: CCL: G98: Script Message-Id: <-33361-070113052912-11809-7jq+J5JjBhj9qQY+IcucEw-$-server.ccl.net> X-Original-From: "soumya s" Date: Sat, 13 Jan 2007 05:29:08 -0500 Sent to CCL by: "soumya s" [soumya_samineni..:..rediffmail.com] Dear all.. Does some one have a small program or script to pull out the final geometry from the .log file (output of optimisation file). thanx in advance soumya From owner-chemistry@ccl.net Sat Jan 13 06:57:00 2007 From: "Anselm.Horn%a%chemie.uni-erlangen.de" To: CCL Subject: CCL:G: G98: Script Message-Id: <-33362-070113064510-8457-EbehKq4ZMINKcP/qQbFjeA~~server.ccl.net> X-Original-From: Anselm.Horn**chemie.uni-erlangen.de Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Sat, 13 Jan 2007 12:44:55 +0100 (CET) MIME-Version: 1.0 Sent to CCL by: Anselm.Horn*chemie.uni-erlangen.de > Does some one have a small program or script to pull out the final > geometry from the .log file (output of optimisation file). > thanx in advance > soumya we used a small F77 program for that purpose. The program 'makexyz' extracts the last geometry out of a Gaussian output file (so it can also be used to monitor the progress of geometry opitmizations in terms of structural changes) and writes the coordinates in xmol format. See http://www.chemie.uni-erlangen.de/hommes/molecule/index.html for more information. The program, written by Nico van Eikema Hommes, is freely available from http://www.chemie.uni-erlangen.de/hommes/molecule/makexyz.f . Regards, Anselm From owner-chemistry@ccl.net Sat Jan 13 11:24:00 2007 From: "Martin Mueller martin.mueller++ime.fraunhofer.de" To: CCL Subject: CCL: chemical database software Message-Id: <-33363-070112133926-25323-o+NvvOKiLTeair8dvFt/Jg:+:server.ccl.net> X-Original-From: Martin Mueller Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Fri, 12 Jan 2007 18:59:08 +0100 MIME-Version: 1.0 Sent to CCL by: Martin Mueller [martin.mueller===ime.fraunhofer.de] Hi, I'm looking for database software (commercial or free) for storage of chemical structures and related data (something like MDL Direct) Thanks in advance Martin From owner-chemistry@ccl.net Sat Jan 13 11:59:00 2007 From: "Emad Tajkhorshid emad(_)ks.uiuc.edu" To: CCL Subject: CCL: force field paramters for B12/cobalamin Message-Id: <-33364-070112133755-24676-kJVO9zUeUe9dZ4LjJlrJTQ]![server.ccl.net> X-Original-From: Emad Tajkhorshid Content-Type: multipart/alternative; boundary=Apple-Mail-114--808136815 Date: Fri, 12 Jan 2007 12:05:07 -0600 Mime-Version: 1.0 (Apple Message framework v752.2) Sent to CCL by: Emad Tajkhorshid [emad/./ks.uiuc.edu] --Apple-Mail-114--808136815 Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Thanks a lot! - Emad On Jan 12, 2007, at 9:37 AM, Marcin Krol mykrol() cyf-kr.edu.pl wrote: > > Sent to CCL by: Marcin Krol [mykrol,,cyf-kr.edu.pl] > Hi Emad > Look at Silvano Geremia, Mario Calligaris, Lucio Randaccio A Molecular > Mechanics Force Field for Alkylcobaloximes, a Model of Vitamin B12 > Coenzyme - Implications of Steric and Electronic Factors in the Co- > C Bond > Cleavage, European Journal of Inorganic Chemistry Volume 1999, > Issue 6 , > Pages 981 - 992 > > Also search discussion lists at www.charmm.org and > amber.scripps.edu I'm > sure someone has already done it. > > Hope this helps > marcin > >> >> Sent to CCL by: "Emad Tajkhorshid" [emad###life.uiuc.edu] >> Hi, >> >> Does anybody know of any set of parameters for vit. B12 >> (cobalamin) developed for any classical force >> field (CHARMM, AMBER, GROMACS, ...)? Any input would be helpful. >> >> Thanks, >> ET> >> >> > > > > -= This is automatically added to each message by the mailing > script =- > To recover the email address of the author of the message, please > change> Conferences: http://server.ccl.net/chemistry/announcements/ > conferences/ > > Search Messages: http://www.ccl.net/htdig (login: ccl, Password: > search)> > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+- > +-+-+ > > --Apple-Mail-114--808136815 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=ISO-8859-1 Thanks a lot!=A0
- = Emad

On Jan = 12, 2007, at 9:37 AM, Marcin Krol mykrol() cyf-kr.edu.pl wrote:


Sent to = CCL by: Marcin Krol [mykrol,,cyf-kr.edu.pl]
Hi = Emad
Look at Silvano Geremia, Mario = Calligaris, Lucio Randaccio A Molecular
Coenzyme - Implications of = Steric and Electronic Factors in the Co-C Bond
Cleavage, European Journal of Inorganic Chemistry = Volume 1999, Issue 6 ,
Pages 981 - 992

Also = search discussion lists at www.charmm.org and amber.scripps.edu = I'm
sure someone has already done = it.

Hope this helps

=
Sent to CCL by: "Emad=A0 Tajkhorshid" = [emad###life.uiuc.edu]
Hi,

Does = anybody know of any set of parameters for vit. B12 (cobalamin) developed = for any classical force
field = (CHARMM, AMBER, GROMACS, ...)?=A0 = Any input would be helpful.

Thanks,
ET>


=



-=3D This is = automatically added to each message by the mailing script =3D-
To recover the email address of the author of the = message, please change
the strange characters on = the top line to the ^-^ sign. You can also
look up = the X-Original-From: line in the mail header.

E-mail = to subscribers: CHEMISTRY^-^ccl.net= or use:

E-mail to administrators: CHEMISTRY-REQUEST^-^ccl.net = or use

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If your mail bounces from CCL with 5.7.1 error, = check:




=

= --Apple-Mail-114--808136815-- From owner-chemistry@ccl.net Sat Jan 13 13:13:00 2007 From: "Karol Langner karol.langner() kn.pl" To: CCL Subject: CCL:G: G98: Script Message-Id: <-33365-070113121406-29998-TFPeJ0+EdcouhC4YMZkPHg[-]server.ccl.net> X-Original-From: Karol Langner Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="iso-8859-2" Date: Sat, 13 Jan 2007 17:13:35 +0100 MIME-Version: 1.0 Sent to CCL by: Karol Langner [karol.langner---kn.pl] On Saturday 13 of January 2007 11:29, soumya s soumya_samineni%x%rediffmail.com wrote: > Sent to CCL by: "soumya s" [soumya_samineni.|a|.rediffmail.com] > Dear all.. > Does some one have a small program or script to pull out the final geometry > from the .log file (output of optimisation file). thanx in advance > soumya > You might like to look cclib: http://cclib.sourceforge.net It can extract coordiantes from your g98 files, and many more things. Note that this is only a Python interface. If you want a graphical program, you might want to try out GaussSum or PyMOlyze (both based on cclib): http://gausssum.sourceforge.net/ http://pymolyze.sourceforge.net/ Cheers, Karol -- written by Karol Langner Sat Jan 13 17:10:50 CET 2007 From owner-chemistry@ccl.net Sat Jan 13 13:48:00 2007 From: "Tamas Gunda tgunda2###puma.unideb.hu" To: CCL Subject: CCL:G: G98: Script Message-Id: <-33366-070113084824-11744-3l1JlJ217FNlEJ3LHoXQ6w**server.ccl.net> X-Original-From: "Tamas Gunda" Content-Transfer-Encoding: 7bit Content-Type: text/plain; format=flowed; charset="iso-8859-1"; reply-type=original Date: Sat, 13 Jan 2007 14:09:33 +0100 MIME-Version: 1.0 Sent to CCL by: "Tamas Gunda" [tgunda2^^puma.unideb.hu] Try Mol2mol, it can extract the coordinates from the output file. http://web.interware.hu/frenzy/mol2mol Tamas Gunda ----- Original Message ----- > From: "soumya s soumya_samineni%x%rediffmail.com" To: "Gunda, Tamas " Sent: Saturday, January 13, 2007 11:29 Subject: CCL: G98: Script > > Sent to CCL by: "soumya s" [soumya_samineni.-.-.rediffmail.com] > Dear all.. > Does some one have a small program or script to pull out the final geometry from the .log file (output of optimisation > file). > thanx in advance > soumya> > > From owner-chemistry@ccl.net Sat Jan 13 14:24:01 2007 From: "Michel Petitjean ptitjean:-:itodys.jussieu.fr" To: CCL Subject: CCL: portable f77 random number generator Message-Id: <-33367-070113135756-22469-kUVK9JsSt7gUrbvj1Qs8pg]-[server.ccl.net> X-Original-From: Michel Petitjean Date: Sat, 13 Jan 2007 19:57:41 +0100 (MET) Sent to CCL by: Michel Petitjean [ptitjean^_^itodys.jussieu.fr] To: chemistry#ccl.net Subj: portable f77 random number generator For convenience, my free portable random number generator is now available from my web site at: http://petitjeanmichel.free.fr/itoweb.download.loiuab.f77 (returns a real*8 following the uniform law over an interval) Method: congruential multiplicative additive (parametrized: you can change the data and have your own congruential multiplicative additive r.g., up to 64 bits). The comments are in french, but the meaning and the use of the routine are obvious. Michel Petitjean, Email: petitjean#itodys.jussieu.fr ITODYS (CNRS, UMR 7086) ptitjean#ccr.jussieu.fr 1 rue Guy de la Brosse Phone: +33 (0)1 44 27 48 57 75005 Paris, France. FAX : +33 (0)1 44 27 68 14 http://petitjeanmichel.free.fr/itoweb.petitjean.html From owner-chemistry@ccl.net Sat Jan 13 15:31:01 2007 From: "spitaleri.andrea:-:hsr.it" To: CCL Subject: CCL:G: A free supercomputer center Message-Id: <-33368-070112183333-26159-HOv3Yg/jXLa7hfxjH5TCJQ**server.ccl.net> X-Original-From: Content-Language: en Content-Type: multipart/mixed; boundary="--6cd677944f4316fd" Date: Fri, 12 Jan 2007 23:23:59 +0100 MIME-Version: 1.0 Sent to CCL by: [spitaleri.andrea|,|hsr.it] This is a multi-part message in MIME format. ----6cd677944f4316fd Content-Type: text/plain; charset=us-ascii Content-Disposition: inline Content-Transfer-Encoding: 7bit Hi, think about to apply to hpc program. for more information: http://www.hpc-europa.org/ you can have 4-8 weeks usage for a supercomputer in Europe (Spain, Italy, UK, Germany, France, NL). You have to write down your own project and then find a host where to stay. I hope this help and Andrea Spitaleri PhD Dulbecco Telethon Institute c/o DIBIT Scientific Institute Biomolecular NMR, 1B4 Via Olgettina 58 20132 Milano (Italy) ----- Original Message ----- > From: "Elda Rossi e.rossi * cineca.it" Date: Friday, January 12, 2007 9:44 am Subject: CCL:G: A free supercomputer center > > Sent to CCL by: Elda Rossi [e.rossi|a|cineca.it] > > > Dear Masao, > > In my computing Center (CINECA - Bologna, Italy), you can use G03 free > of charge. > We have got a "site" licence and users here are allowed to freely > accessall the software, including G03. > Of course you have to pay the cpu time, so perhaps this doesn't solve > your problem. > > Regards, > Elda Rossi > > > Masao Fiegl at5gomi() rose.plala.or.jp ha scritto: > > Sent to CCL by: Masao Fiegl [at5gomi() rose.plala.or.jp] > > Dear CCL members, > > > > I am looking for a supercomputer center at North America and > Europe where anyone can use Gaussian 03 free of charge. I am very > grateful for any suggestions. > > > > Thanks for your help. > > Masao> > > > > > > > > > > > > -= This is automatically added to each message by the mailing > script =- > To recover the email address of the author of the message, please > changethe strange characters on the top line to the ,+, sign. You > can also> Conferences: http://server.ccl.net/chemistr > > Search Messages: http://www.ccl.net/htdig (login: ccl, Password: > search)> > RTFI: http://www.ccl.net/chemistr > > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+- > +-+-+ > > > > ----6cd677944f4316fd Content-Type: text/x-vcard; name="spitaleri.andrea.vcf"; charset="iso-8859-1" Content-Disposition: attachment; filename="spitaleri.andrea.vcf" Content-Description: Card for Content-Transfer-Encoding: quoted-printable begin=3Avcard n=3ASpitaleri=3BAndrea fn=3AAndrea Spitaleri tel=3Bfax=3A+390226434153 org=3ADibit Scientific Insititute=3BBioMolecular Structure adr=3A=3B=3Bvia Olgettina 58=3BMilan=3B=3B24132=3BItaly version=3A2=2E1 email=3Binternet=3Aspitaleri=2Eandrea=40hsr=2Eit title=3ADr end=3Avcard ----6cd677944f4316fd--