From owner-chemistry@ccl.net Fri Nov 17 02:26:00 2006 From: "Dr. Ponnadurai Ramasami ramchemi^-^intnet.mu" To: CCL Subject: CCL:G: transition state Message-Id: <-33050-061117015338-26689-IyYvZceRebjWImuKK6BqgQ(~)server.ccl.net> X-Original-From: "Dr. Ponnadurai Ramasami" Content-Type: multipart/alternative; boundary="----=_NextPart_000_0013_01C70A36.1EE36800" Date: Fri, 17 Nov 2006 10:49:56 +0400 MIME-Version: 1.0 Sent to CCL by: "Dr. Ponnadurai Ramasami" [ramchemi[*]intnet.mu] This is a multi-part message in MIME format. ------=_NextPart_000_0013_01C70A36.1EE36800 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Dear All I am trying to have the transition state for CH2F2 + OH using gaussian = 03W. My command line is #P hf/3-21G opt=3D(calcall,ts) freq=3D(noraman, readisotopes) = symm=3Dfollow My input file has a probable TS structure. It is running, it says "Finalising calculation" but I always get the = error " Error termination request processed by link 9999" Can anyone help? Thanks Ramasami ------=_NextPart_000_0013_01C70A36.1EE36800 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable

Dear All

I am trying to have the transition = state for CH2F2=20 + OH using gaussian 03W.

My command line is

#P hf/3-21G opt=3D(calcall,ts) = freq=3D(noraman,=20 readisotopes) symm=3Dfollow

My input file has a probable TS=20 structure.

It is running, it says "Finalising = calculation" but=20 I always get the error " Error termination request processed by link=20 9999"

Can anyone help?

Thanks

Ramasami

------=_NextPart_000_0013_01C70A36.1EE36800-- From owner-chemistry@ccl.net Fri Nov 17 03:01:01 2006 From: "Dr. Raphael Berger rberg_01{}uni-muenster.de" To: CCL Subject: CCL:G: Cartesian coordinates to Z-Matrix Message-Id: <-33051-061117003049-18978-IhCkAlT4jLoABb9QFowPwg=server.ccl.net> X-Original-From: "Dr. Raphael Berger" Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed Date: Fri, 17 Nov 2006 06:30:11 +0100 (MEZ) MIME-Version: 1.0 Sent to CCL by: "Dr. Raphael Berger" [rberg_01=-=uni-muenster.de] You can also use Molden (open it with *.xyz type files, then press ZMAT Editor and save the resulting file). Here You can check the results graphically. Cheers On Thu, 16 Nov 2006, Nuno A. G. Bandeira nuno.bandeira!^!ist.utl.pt wrote: > Date: Thu, 16 Nov 2006 21:54:05 -0500 > From: Nuno A. G. Bandeira nuno.bandeira!^!ist.utl.pt > Reply-To: CCL Subscribers > To: "Berger, Raphael " > Subject: CCL:G: Cartesian coordinates to Z-Matrix > > Sent to CCL by: "Nuno A. G. Bandeira" [nuno.bandeira\a/ist.utl.pt] > > Da Gao dagao06{=}gmail.com wrote: >> Sent to CCL by: "Da Gao" [dagao06,+,gmail.com] >> ------=_Part_125354_27878444.1163701336195 >> Content-Type: text/plain; charset=ISO-8859-1; format=flowed >> Content-Transfer-Encoding: 7bit >> Content-Disposition: inline >> >> Dear all, >> >> Is anyone here be aware of the software that can transfer Cartesian >> coordinates to Z-Matrix ? Thanks for sharing. >> > > Yes, you can use openbabel to convert from xyz coordinates to > Fenske-Hall (Gaussian) Z-Matrix. > > Regards, > > -- > Nuno A. G. Bandeira, AMRSC > Graduate researcher and molecular sculptor > Inorganic and Theoretical Chemistry Group, > Faculty of Science > University of Lisbon - C8 building, Campo Grande, > 1749-016 Lisbon,Portugal > http://cqb.fc.ul.pt/intheochem/nuno.html > Doctoral student _-_ IST,Lisbon > --> > > From owner-chemistry@ccl.net Fri Nov 17 04:26:01 2006 From: "Igor Avilov avilovi-*-averell.umh.ac.be" To: CCL Subject: CCL: couple AM1 and Molecular Dynamics Message-Id: <-33052-061117042403-10208-evH57RjwL1Dw8PcA9B/uWw a server.ccl.net> X-Original-From: "Igor Avilov" Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Fri, 17 Nov 2006 10:23:28 +0100 MIME-Version: 1.0 Sent to CCL by: "Igor Avilov" [avilovi . averell.umh.ac.be] Dear Tatsis, We recently used semi-empirical PM3 method to study conformational dynamics of sterically strained porphyrins in the triplet excited state (I. V. Avilov, E. I. Zenkevich, E. I. Sagun, and I. V. Filatov. J. Phys. Chem. A 2004, 108, 5684-5691) and AM1 to find different conformers of porphyrins' di-protonated forms (I.V. Avilov, A.Yu. Panarin, V.S. Chirvony. Chemical Physics Letters 389 (2004) 352-358). Best regards, Igor Avilov. -----Original Message----- > From: owner-chemistry|-|ccl.net [mailto:owner-chemistry|-|ccl.net] Sent: jeudi 16 novembre 2006 11:42 To: Igor Avilov Subject: CCL: couple AM1 and Molecular Dynamics Sent to CCL by: "Tatsis A Vasileios" [me01136]~[cc.uoi.gr] Hello to all CCLers!!! I, recently, managed to couple two well known packages in order to get quantum molecular dynamics trajectories. I am trying to find a way so i can validate my results(trajectories), (publications, other free software). Thanks in advancehttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Fri Nov 17 05:01:01 2006 From: "Jens Thomas j.m.h.thomas^^dl.ac.uk" To: CCL Subject: CCL: Cartesian coordinates to Z-Matrix Message-Id: <-33053-061117043236-20242-xapZ3yDRNfbhWXKW6Xwaog*o*server.ccl.net> X-Original-From: Jens Thomas Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Fri, 17 Nov 2006 09:32:07 +0000 MIME-Version: 1.0 Sent to CCL by: Jens Thomas [j.m.h.thomas#dl.ac.uk] Da Gao dagao06{=}gmail.com wrote: > Sent to CCL by: "Da Gao" [dagao06,+,gmail.com] > ------=_Part_125354_27878444.1163701336195 > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > Content-Transfer-Encoding: 7bit > Content-Disposition: inline > > Dear all, > > Is anyone here be aware of the software that can transfer Cartesian > coordinates to Z-Matrix ? Thanks for sharing. > > Hi, You can use the autoz feature of the CCP1GUI to do this. See: http://www.cse.clrc.ac.uk/qcg/ccp1gui/index.shtml Regards, Jens From owner-chemistry@ccl.net Fri Nov 17 05:36:01 2006 From: "Van Dam, HJJ $Huub$ h.j.j.vandam^dl.ac.uk" To: CCL Subject: CCL: Cartesian coordinates to Z-Matrix Message-Id: <-33054-061117044436-30627-9blRTthdKrhL5CmIgEtDLQ : server.ccl.net> X-Original-From: "Van Dam, HJJ $Huub$" Content-Class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Fri, 17 Nov 2006 09:01:05 -0000 MIME-Version: 1.0 Sent to CCL by: "Van Dam, HJJ $Huub$" [h.j.j.vandam::dl.ac.uk] Hi Da, The CCP1GUI will do that. It will also allow you to adjust the structure in cartesian or z-matrix coordinates if you want to. Have a look at http://sourceforge.net/projects/ccp1gui/ I hope this helps. Best wishes, Huub ========================================================== Huub van Dam (h.j.j.vandam|a|dl.ac.uk, +44-1925-603933) ========================================================== -----Original Message----- > From: owner-chemistry|a|ccl.net [mailto:owner-chemistry|a|ccl.net] Sent: 16 November 2006 20:36 To: Vandam, Huub Subject: CCL: Cartesian coordinates to Z-Matrix Sent to CCL by: "Da Gao" [dagao06,+,gmail.com] ------=_Part_125354_27878444.1163701336195 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Content-Disposition: inline Dear all, Is anyone here be aware of the software that can transfer Cartesian coordinates to Z-Matrix ? Thanks for sharing. -- Best Regards, Da ------=_Part_125354_27878444.1163701336195 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Dear all,

Is anyone here be aware of the software that can transfer Cartesian coordinates to Z-Matrix ? Thanks for sharing.

--
Best Regards,

Da ------=_Part_125354_27878444.1163701336195--http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Fri Nov 17 06:46:01 2006 From: "Tamas Gunda tgunda2005[*]puma.unideb.hu" To: CCL Subject: CCL: Cartesian coordinates to Z-Matrix CCL Message-Id: <-33055-061117063247-17380-bFQrZCGGMdMn51hbM5GiaQ[A]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: Fri, 17 Nov 2006 10:57:22 +0100 MIME-Version: 1.0 Sent to CCL by: "Tamas Gunda" [tgunda2005|*|puma.unideb.hu] Mol2Mol can interconvert between Cartesian <--> Z matrix <--> Polar coordinates in a large variety of formats, even user defined input/output formats are supported. http://web.interware.hu/frenzy/mol2mol/index.html Prof. Tamas E. Gunda University of Debrecen Department of Pharmaceutical Chemistry H-4010 Debrecen, POB 36, Hungary tgunda2005{at}puma.unideb.hu ----- Original Message ----- > From: "Da Gao dagao06{=}gmail.com" To: "Gunda, Tamas E " Sent: Thursday, November 16, 2006 21:46 PM Subject: CCL: Cartesian coordinates to Z-Matrix > Sent to CCL by: "Da Gao" [dagao06,+,gmail.com] > ------=_Part_125354_27878444.1163701336195 > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > Content-Transfer-Encoding: 7bit > Content-Disposition: inline > > Dear all, > > Is anyone here be aware of the software that can transfer Cartesian > coordinates to Z-Matrix ? Thanks for sharing. > > -- > Best Regards, > > Da > From owner-chemistry@ccl.net Fri Nov 17 08:45:01 2006 From: "Rino Ragno rino.ragno+/-uniroma1.it" To: CCL Subject: CCL: HBPLUS running problem under linux Message-Id: <-33056-061117045522-32523-p6VSVvLT90GC6USJeuFTGg _ server.ccl.net> X-Original-From: "Rino Ragno" Date: Fri, 17 Nov 2006 04:55:20 -0500 Sent to CCL by: "Rino Ragno" [rino.ragno[*]uniroma1.it] I nned to use the HBPLUS program. I successfully compiled it under linux and windows/cygwin. Unfortunately it works only under the windows/cygwin environment. In the LINUX system an out of memory message is given. Any of yoy CCLers can give me some suggestion in how to compile the hbplus source code to avoid the memory problem? Thanks From owner-chemistry@ccl.net Fri Nov 17 12:25:00 2006 From: "Alfredo Mayall Simas simas[-]ufpe.br" To: CCL Subject: CCL: Fw: couple AM1 and Molecular Dynamics Message-Id: <-33057-061117122339-29279-ntk3ZLaJCaLFDVX5zajMBA]~[server.ccl.net> X-Original-From: "Alfredo Mayall Simas" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="iso-8859-1" Date: Fri, 17 Nov 2006 14:23:26 -0300 MIME-Version: 1.0 Sent to CCL by: "Alfredo Mayall Simas" [simas-$-ufpe.br] Dear CCLers, When thinking about coupling AM1 or PM3 with molecular dynamics, perhaps RM1 could be considered as an option. RM1 is a free, newly developed and public domain semiempirical model, which is overall significantly more accurate than both AM1 and PM3. Further info on RM1 can be found at http://www.rm1.sparkle.pro.br Sincerely, Alfredo Mayall Simas ----- Original Message ----- > From: "Igor Avilov avilovi-*-averell.umh.ac.be" To: "Simas, Alfredo Mayall " Sent: Friday, November 17, 2006 6:31 AM Subject: CCL: couple AM1 and Molecular Dynamics Sent to CCL by: "Igor Avilov" [avilovi . averell.umh.ac.be] Dear Tatsis, We recently used semi-empirical PM3 method to study conformational dynamics of sterically strained porphyrins in the triplet excited state (I. V. Avilov, E. I. Zenkevich, E. I. Sagun, and I. V. Filatov. J. Phys. Chem. A 2004, 108, 5684-5691) and AM1 to find different conformers of porphyrins' di-protonated forms (I.V. Avilov, A.Yu. Panarin, V.S. Chirvony. Chemical Physics Letters 389 (2004) 352-358). Best regards, Igor Avilov. -----Original Message----- > From: owner-chemistry()ccl.net [mailto:owner-chemistry()ccl.net] Sent: jeudi 16 novembre 2006 11:42 To: Igor Avilov Subject: CCL: couple AM1 and Molecular Dynamics Sent to CCL by: "Tatsis A Vasileios" [me01136]~[cc.uoi.gr] Hello to all CCLers!!! I, recently, managed to couple two well known packages in order to get quantum molecular dynamics trajectories. I am trying to find a way so i can validate my results(trajectories), (publications, other free software). Thanks in advancehttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Fri Nov 17 15:55:01 2006 From: "Shobe, David David.Shobe..sud-chemie.com" To: CCL Subject: CCL:G: transition state Message-Id: <-33058-061117153547-20020-DDGKrZwksgNOQaCjLQ6O6w],[server.ccl.net> X-Original-From: "Shobe, David" Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Fri, 17 Nov 2006 21:35:30 +0100 MIME-Version: 1.0 Sent to CCL by: "Shobe, David" [David.Shobe+*+sud-chemie.com] Ramasami, If you have a visualization program (highly recommended), make sure that the geometry is still that of the transition state. If the geometry looks OK and you are making progress (the forces and displacements given at the end of each step are getting smaller), you can probably just continue the calculation with: #p hf/3-21G opt=ts freq=(noraman, readisotopes) symm=follow geom=check guess=read Erase the Z-matrix/coordinates from the input file. If things are goinw wrong, you may want to start over with a different starting geometry. --David Shobe -----Original Message----- > From: owner-chemistry(!)ccl.net [mailto:owner-chemistry(!)ccl.net] Sent: Friday, November 17, 2006 2:30 AM To: Shobe, David Subject: CCL:G: transition state Sent to CCL by: "Dr. Ponnadurai Ramasami" [ramchemi[*]intnet.mu] This is a multi-part message in MIME format. ------=_NextPart_000_0013_01C70A36.1EE36800 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Dear All I am trying to have the transition state for CH2F2 + OH using gaussian = 03W. My command line is #P hf/3-21G opt=3D(calcall,ts) freq=3D(noraman, readisotopes) = symm=3Dfollow My input file has a probable TS structure. It is running, it says "Finalising calculation" but I always get the = error " Error termination request processed by link 9999" Can anyone help? Thanks Ramasami ------=_NextPart_000_0013_01C70A36.1EE36800 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable

Dear All

I am trying to have the transition = state for CH2F2=20 + OH using gaussian 03W.

My command line is

#P hf/3-21G opt=3D(calcall,ts) = freq=3D(noraman,=20 readisotopes) symm=3Dfollow

My input file has a probable TS=20 structure.

It is running, it says "Finalising = calculation" but=20 I always get the error " Error termination request processed by link=20 9999"

Can anyone help?

Thanks

Ramasami

------=_NextPart_000_0013_01C70A36.1EE36800--http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txtThis e-mail message may contain confidential and / or privileged information. If you are not an addressee or otherwise authorized to receive this message, you should not use, copy, disclose or take any action based on this e-mail or any information contained in the message. If you have received this material in error, please advise the sender immediately by reply e-mail and delete this message. Thank you. From owner-chemistry@ccl.net Fri Nov 17 18:10:00 2006 From: "Osman Guner oguner(_)turquoisecons.com" To: CCL Subject: CCL: Last call for papers, ACS Chicago Message-Id: <-33059-061117180444-9067-d+AWwi+JC4K7+KPGADzFbQ|-|server.ccl.net> X-Original-From: "Osman Guner" Content-Type: multipart/alternative; boundary="----=_NextPart_000_0040_01C70A59.B3858E70" Date: Fri, 17 Nov 2006 15:04:37 -0800 MIME-Version: 1.0 Sent to CCL by: "Osman Guner" [oguner]*[turquoisecons.com] This is a multi-part message in MIME format. ------=_NextPart_000_0040_01C70A59.B3858E70 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable I have room for three more papers. The deadline for abstract submission = was November 17. If you are interested, please email your abstract to me = ASAP, and if accepted, I will enter it to the system manually. The first = three submissions go in. =20 =20 Advances in Pharmacophores and 3D Screening =20 Organized by Chemical Information Division (CINF) Co-sponsored by Computers in Chemistry (COMP), and Medicinal Chemistry (MEDI) Divisions =20 At 233rd ACS National Meeting, Chicago, IL, March 25-29, 2007 =20 Recent developments in three-dimensional screening and data-mining techniques will be covered with specific focus in pharmacophores and 3D-searching. =20 Feel free to contact me with any questions. =20 =20 --- Osman F, G=FCner, PhD Principal, Turquoise Consulting oguner:turquoisecons.com=20 http://www.turquoisecons.com=20 Skype: turquoisecons =20 =20 ------=_NextPart_000_0040_01C70A59.B3858E70 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable

I have room for = three more papers.=A0 The deadline for abstract submission was November 17.=A0 If = you are interested, please email your abstract to me ASAP, and if accepted, I = will enter it to the system manually.=A0 The first three submissions go = in.

Advances in = Pharmacophores and 3D Screening

Organized by = Chemical Information Division (CINF)

Co-sponsored by = Computers in Chemistry (COMP), and Medicinal Chemistry (MEDI) = Divisions

At 233rd ACS = National Meeting, Chicago, IL, March 25-29, = 2007

Recent developments = in three-dimensional screening and data-mining techniques will be covered = with specific focus in pharmacophores and = 3D-searching.

=A0

Feel free to = contact me with any questions.

---

Osman F, G=FCner, PhD

Principal, Turquoise = Consulting

oguner:turquoisecons.com&nbs= p;

http://www.turquoisecons.com&nb= sp;

Skype: turquoisecons

------=_NextPart_000_0040_01C70A59.B3858E70--