From owner-chemistry@ccl.net Thu Apr 6 01:36:00 2006 From: "Mathias Weigt m.weigt(_)uni-bonn.de" To: CCL Subject: CCL: XYZ to PDB translation Message-Id: <-31433-060405152940-28648-7hYizIp4k7TYEey62ssR/A[a]server.ccl.net> X-Original-From: Mathias Weigt Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 05 Apr 2006 20:29:10 +0200 MIME-Version: 1.0 Sent to CCL by: Mathias Weigt [m.weigt_._uni-bonn.de] Mikhail Ladanov mladanov:mail.usf.edu wrote: >Sent to CCL by: "Mikhail Ladanov" [mladanov/./mail.usf.edu] >I work with MD simulations of system with very big number of atoms. >Im trying to translate my XYZ file into PDB using OpenBabel 2.0 >As soon as I have a file of size about 15-20 Mb, Babel results with segmentation fault. >I have therefore 2 questions: >1. Is there any way to make OpenBabel work with big files without any errors? >2. Is there any other utility I could translate XYZ to PDB with? > > This might not be a fault of Openbabel. How many atoms does your XYZ-File have? PDB is only defined up to 99999 atoms. With 15-20Mb you could have more... Mathias From owner-chemistry@ccl.net Thu Apr 6 03:49:00 2006 From: "Satyan Sharma satyan|sun3.oulu.fi" To: CCL Subject: CCL: ONIOM and TS Message-Id: <-31434-060406033537-5545-ttOefHZc2ksTmgkYlb+H5w**server.ccl.net> X-Original-From: Satyan Sharma Content-Type: TEXT/PLAIN; charset=US-ASCII Date: Thu, 6 Apr 2006 10:35:19 +0300 (EEST) MIME-Version: 1.0 Sent to CCL by: Satyan Sharma [satyan_._sun3.oulu.fi] Hi everyone, I am trying to search for TS using ONIOM and I had to restart my TS job. I started with OPT=(TS,CalcFc,noeigen,Addredundant). After a couple of steps, I had All quantities printed in internal units (Hartrees-Bohrs-Radians) Swaping is turned off. Update second derivatives using D2CorX and points 49 50 Eigenvalues --- -0.00019 -0.00011 0.00070 0.00102 0.00128 Eigenvalues --- 0.00149 0.00175 0.00211 0.00243 0.00264 Eigenvalues --- 0.00294 0.00331 0.00394 0.00409 0.00499 And the convergence was Maximum Force 0.000909 0.000450 NO RMS Force 0.000099 0.000300 YES Maximum Displacement 0.109350 0.001800 NO RMS Displacement 0.010304 0.001200 NO Predicted change in Energy= 8.959984D-05 After this step I restarted th TS job using OPT=(TS,restart,rcfc,noeigen,Addredundant) Now in the very next step ..I have All quantities printed in internal units (Hartrees-Bohrs-Radians) Swaping is turned off. Update second derivatives using D2CorX and points 49 50 Eigenvalues --- -14.42545 0.00010 0.00079 0.00105 0.00141 Eigenvalues --- 0.00174 0.00191 0.00222 0.00243 0.00276 And convergence part Item Value Threshold Converged? Maximum Force 4.928076 0.000450 NO RMS Force 0.228676 0.000300 NO Maximum Displacement 0.208783 0.001800 NO RMS Displacement 0.016753 0.001200 NO Predicted change in Energy= 3.429304D-02 Is this OK or I should have done something else.. Cheers, Satyan From owner-chemistry@ccl.net Thu Apr 6 04:23:00 2006 From: "Luca Bertini luca.bertini .. istm.cnr.it" To: CCL Subject: CCL: TDDFT for Large Unsaturated pi-Systems Message-Id: <-31435-060406041426-25787-0AQh6FE/YKWOvV8XugobHA!^!server.ccl.net> X-Original-From: "Luca Bertini" Content-Type: text/plain; charset=iso-8859-1 Date: Thu, 6 Apr 2006 09:38:57 +0200 MIME-Version: 1.0 Sent to CCL by: "Luca Bertini" [luca.bertini{=}istm.cnr.it] I'm not saying that TDDFT is wrong at all, but I was simply reporting a known problem of TDDFT in treating the excited states with double-excitation character. Indeed, the exchange-correlation kernel (the second functional derivative with respect to the density) within RPA-TDDFT approach is approximated as frequency independent (the so called static limit in the adiabatic approximation). It can be proof that this approximation fails when one consider such double-excitation excited states. This makes sense to me since also because we're dealing with an independent-particle picture method, after all! ---------- Original Message ----------- > From: "makowskm##chemia.uj.edu.pl" To: "Bertini, Luca " Sent: Tue, 4 Apr 2006 13:31:07 -0400 Subject: CCL: TDDFT for Large Unsaturated pi-Systems > Sent to CCL by: makowskm_+_chemia.uj.edu.pl > For polyenes it's a little bit counterintuitive. The excitation > energy for doubly excited A_g state is usually not so bad (but > optimal geometry is not so good), but strong B_u is severely too > low. Definitely, it's still the problem with functionals, but saying > that TDDFT is just wrong for states dominated by double excitations > is not absolutely true. > > > Sent to CCL by: "Luca Bertini" [luca.bertini ~ istm.cnr.it] > > > > Furthemore is known that the adiabatic exchange-correlation kernel is > > wrong > > for excited states with non-negligible double-excitation character, as it > > is > > the case of polyenes. therefore is not only a problem of DFT functional > > but > > also a problem of the TDDFT method. > > > > Luca > > > > ---------- Original Message ----------- > >> From: "makowskm(!)chemia.uj.edu.pl" > > To: "Bertini, Luca " > > Sent: Tue, 4 Apr 2006 08:24:11 -0400 > > Subject: CCL: TDDFT for Large Unsaturated pi-Systems > > > >> Sent to CCL by: makowskm**chemia.uj.edu.pl > >> If you mean polyenes for example - the answer is none. There were > >> some papers claiming that Tamm-Dancoff approximation to TDDFT > >> combined with non-hybrid functionals gave decent excitation energies. > >> > Sent to CCL by: "Sue L" [chsue2004|-|yahoo.com] > >> > Does anyone know which DFT functional in TDDFT is suitable to > >> calculate > >> > the singlet-singlet excitations for large unsaturated pi-systems? > >> B3LYP > >> > usually underestimate the excitation energies for these systems > >> > > >> > Thank you very much > >> > > >> > Sue> > >> > > >> > > >> > > >> > >> -- > >> Dr Marcin Makowski > >> Jagiellonian University > >> Department of Theoretical Chemistry > >> email:makowskm]![chemia.uj.edu.pl > >> or > >> Kyushu University > >> email:marcin]![cube.kyushu-u.ac.jp > >> > >> -= This is automatically added to each message by the mailing script > >> =- 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> > >> Search Messages: http://www.ccl.net/htdig (login: ccl, Password: > >> search)> > >> -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+- > >> +-+ > > ------- End of Original Message -------> > > > > > > > > -- > Dr Marcin Makowski > Jagiellonian University > Department of Theoretical Chemistry > email:makowskm%a%chemia.uj.edu.pl > or > Kyushu University > email:marcin%a%cube.kyushu-u.ac.jp > > -= This is automatically added to each message by the mailing script > =- 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> > Search Messages: http://www.ccl.net/htdig (login: ccl, Password: > search)> > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+- > +-+ ------- End of Original Message ------- From owner-chemistry@ccl.net Thu Apr 6 05:31:01 2006 From: "Luca Bertini luca.bertini{=}istm.cnr.it" To: CCL Subject: CCL: jacs.sty Message-Id: <-31436-060406052327-26055-3G6L2CnMl2KjM0DLj2Qb8A{=}server.ccl.net> X-Original-From: "Luca Bertini" Content-Type: text/plain; charset=iso-8859-1 Date: Thu, 6 Apr 2006 11:23:22 +0200 MIME-Version: 1.0 Sent to CCL by: "Luca Bertini" [luca.bertini * istm.cnr.it] Hi folks, does anyone knows where I can find the JACS latex style jacs.sty? reading the notes of jacs to prepare a manuscript using latex, I found that exist somewhere this jacs.sty style, but I can't find it on internet. I also have the feeling that jacs tends to discourage to use latex. Luca B. From owner-chemistry@ccl.net Thu Apr 6 07:38:00 2006 From: "Noel O Boyle no228**cam.ac.uk" To: CCL Subject: CCL: jacs.sty Message-Id: <-31437-060406064628-26736-eSc6C2yCCSce8pLLLmWjCA-,-server.ccl.net> X-Original-From: "Noel O'Boyle" Content-Transfer-Encoding: 7bit Content-Type: text/plain Date: Thu, 06 Apr 2006 11:09:04 +0100 Mime-Version: 1.0 Sent to CCL by: "Noel O'Boyle" [no228*_*cam.ac.uk] A number of useful LaTeX style files for chemistry can be found at: http://texcatalogue.sarovar.org/bytopic.html#chem (I think you're looking for achemso.sty) I understand your difficulties - I am a user of Linux, and need to use LaTeX or I cannot submit to ACS journals. I am not looking forward to sending my supervisor (who uses Windows) a lovely LaTeX document for review. Regards, Noel On Thu, 2006-04-06 at 05:37 -0400, Luca Bertini luca.bertini{=}istm.cnr.it wrote: > Sent to CCL by: "Luca Bertini" [luca.bertini * istm.cnr.it] > Hi folks, does anyone knows where I can find the JACS latex style jacs.sty? > reading the notes of jacs to prepare a manuscript using latex, I found that > exist somewhere this jacs.sty style, but I can't find it on internet. I also > have the feeling that jacs tends to discourage to use latex. > > Luca B.> > > From owner-chemistry@ccl.net Thu Apr 6 08:29:00 2006 From: "makowskm++chemia.uj.edu.pl" To: CCL Subject: CCL: TDDFT for Large Unsaturated pi-Systems Message-Id: <-31438-060406082736-24116-NqlbW7MN85srHBY35BpeTg(0)server.ccl.net> X-Original-From: makowskm ~~ chemia.uj.edu.pl Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-2 Date: Thu, 6 Apr 2006 14:27:32 +0200 (CEST) MIME-Version: 1.0 Sent to CCL by: makowskm.[*].chemia.uj.edu.pl And what I was saying was not that you claim that TDDFT is wrong, but that TDDFT for doubly excited states is wrong ;) This is too general opinion in my view. Some implementations of TDDFT are wrong for sure, but methodology in its general formulation does not include anything that would fail for such states by definition. Can you point to the publication containing the proof you mentioned. I would be really interested to read it. Regards, Marcin > Sent to CCL by: "Luca Bertini" [luca.bertini{=}istm.cnr.it] > > I'm not saying that TDDFT is wrong at all, but I was simply reporting a > known > problem of TDDFT in treating the excited states with double-excitation > character. Indeed, the exchange-correlation kernel (the second functional > derivative with respect to the density) within RPA-TDDFT approach is > approximated as frequency independent (the so called static limit in the > adiabatic approximation). It can be proof that this approximation fails > when > one consider such double-excitation excited states. This makes sense to me > since also because we're dealing with an independent-particle picture > method, > after all! > > > > ---------- Original Message ----------- >> From: "makowskm##chemia.uj.edu.pl" > To: "Bertini, Luca " > Sent: Tue, 4 Apr 2006 13:31:07 -0400 > Subject: CCL: TDDFT for Large Unsaturated pi-Systems > >> Sent to CCL by: makowskm_+_chemia.uj.edu.pl >> For polyenes it's a little bit counterintuitive. The excitation >> energy for doubly excited A_g state is usually not so bad (but >> optimal geometry is not so good), but strong B_u is severely too >> low. Definitely, it's still the problem with functionals, but saying >> that TDDFT is just wrong for states dominated by double excitations >> is not absolutely true. >> >> > Sent to CCL by: "Luca Bertini" [luca.bertini ~ istm.cnr.it] >> > >> > Furthemore is known that the adiabatic exchange-correlation kernel is >> > wrong >> > for excited states with non-negligible double-excitation character, as >> it >> > is >> > the case of polyenes. therefore is not only a problem of DFT >> functional >> > but >> > also a problem of the TDDFT method. >> > >> > Luca >> > >> > ---------- Original Message ----------- >> >> From: "makowskm(!)chemia.uj.edu.pl" >> > To: "Bertini, Luca " >> > Sent: Tue, 4 Apr 2006 08:24:11 -0400 >> > Subject: CCL: TDDFT for Large Unsaturated pi-Systems >> > >> >> Sent to CCL by: makowskm**chemia.uj.edu.pl >> >> If you mean polyenes for example - the answer is none. There were >> >> some papers claiming that Tamm-Dancoff approximation to TDDFT >> >> combined with non-hybrid functionals gave decent excitation energies. >> >> > Sent to CCL by: "Sue L" [chsue2004|-|yahoo.com] >> >> > Does anyone know which DFT functional in TDDFT is suitable to >> >> calculate >> >> > the singlet-singlet excitations for large unsaturated pi-systems? >> >> B3LYP >> >> > usually underestimate the excitation energies for these systems >> >> > >> >> > Thank you very much >> >> > >> >> > Sue> >> >> > >> >> > >> >> > >> >> >> >> -- >> >> Dr Marcin Makowski >> >> Jagiellonian University >> >> Department of Theoretical Chemistry >> >> email:makowskm]![chemia.uj.edu.pl >> >> or >> >> Kyushu University >> >> email:marcin]![cube.kyushu-u.ac.jp >> >> >> >> -= This is automatically added to each message by the mailing script >> >> =- 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> >> >> Search Messages: http://www.ccl.net/htdig (login: ccl, Password: >> >> search)> >> >> -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+- >> >> +-+ >> > ------- End of Original Message -------> >> > >> > >> > >> >> -- >> Dr Marcin Makowski >> Jagiellonian University >> Department of Theoretical Chemistry >> email:makowskm%a%chemia.uj.edu.pl >> or >> Kyushu University >> email:marcin%a%cube.kyushu-u.ac.jp >> >> -= This is automatically added to each message by the mailing script >> =- 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> >> Search Messages: http://www.ccl.net/htdig (login: ccl, Password: >> search)> >> -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+- >> +-+ > ------- End of Original Message -------> > > > -- Dr Marcin Makowski Jagiellonian University Department of Theoretical Chemistry email:makowskm[*]chemia.uj.edu.pl or Kyushu University email:marcin[*]cube.kyushu-u.ac.jp From owner-chemistry@ccl.net Thu Apr 6 09:12:01 2006 From: "Luca Bertini luca.bertini- -istm.cnr.it" To: CCL Subject: CCL: TDDFT for Large Unsaturated pi-Systems Message-Id: <-31439-060406091042-15459-kv3W9qeHB1aDOlGaKk9M+w||server.ccl.net> X-Original-From: "Luca Bertini" Content-Type: text/plain; charset=iso-8859-1 Date: Thu, 6 Apr 2006 15:10:39 +0200 MIME-Version: 1.0 Sent to CCL by: "Luca Bertini" [luca.bertini*o*istm.cnr.it] I'm refering to the paper by Maitra et al, JCP, 5932, 120, (2004). I'm not understant what you mean with implementation of TDDFT. I'm thinking to the standard RPA-TDDFT theory. ---------- Original Message ----------- > From: "makowskm++chemia.uj.edu.pl" To: "Bertini, Luca " Sent: Thu, 6 Apr 2006 08:37:34 -0400 Subject: CCL: TDDFT for Large Unsaturated pi-Systems > Sent to CCL by: makowskm.%.chemia.uj.edu.pl > And what I was saying was not that you claim that TDDFT is wrong, > but that TDDFT for doubly excited states is wrong ;) This is too > general opinion in my view. Some implementations of TDDFT are wrong > for sure, but methodology in its general formulation does not > include anything that would fail for such states by definition. > > Can you point to the publication containing the proof you mentioned. > I would be really interested to read it. > > Regards, > Marcin > > > Sent to CCL by: "Luca Bertini" [luca.bertini{=}istm.cnr.it] > > > > I'm not saying that TDDFT is wrong at all, but I was simply reporting a > > known > > problem of TDDFT in treating the excited states with double-excitation > > character. Indeed, the exchange-correlation kernel (the second functional > > derivative with respect to the density) within RPA-TDDFT approach is > > approximated as frequency independent (the so called static limit in the > > adiabatic approximation). It can be proof that this approximation fails > > when > > one consider such double-excitation excited states. This makes sense to me > > since also because we're dealing with an independent-particle picture > > method, > > after all! > > > > > > > > ---------- Original Message ----------- > >> From: "makowskm##chemia.uj.edu.pl" > > To: "Bertini, Luca " > > Sent: Tue, 4 Apr 2006 13:31:07 -0400 > > Subject: CCL: TDDFT for Large Unsaturated pi-Systems > > > >> Sent to CCL by: makowskm_+_chemia.uj.edu.pl > >> For polyenes it's a little bit counterintuitive. The excitation > >> energy for doubly excited A_g state is usually not so bad (but > >> optimal geometry is not so good), but strong B_u is severely too > >> low. Definitely, it's still the problem with functionals, but saying > >> that TDDFT is just wrong for states dominated by double excitations > >> is not absolutely true. > >> > >> > Sent to CCL by: "Luca Bertini" [luca.bertini ~ istm.cnr.it] > >> > > >> > Furthemore is known that the adiabatic exchange-correlation kernel is > >> > wrong > >> > for excited states with non-negligible double-excitation character, as > >> it > >> > is > >> > the case of polyenes. therefore is not only a problem of DFT > >> functional > >> > but > >> > also a problem of the TDDFT method. > >> > > >> > Luca > >> > > >> > ---------- Original Message ----------- > >> >> From: "makowskm(!)chemia.uj.edu.pl" > >> > To: "Bertini, Luca " > >> > Sent: Tue, 4 Apr 2006 08:24:11 -0400 > >> > Subject: CCL: TDDFT for Large Unsaturated pi-Systems > >> > > >> >> Sent to CCL by: makowskm**chemia.uj.edu.pl > >> >> If you mean polyenes for example - the answer is none. There were > >> >> some papers claiming that Tamm-Dancoff approximation to TDDFT > >> >> combined with non-hybrid functionals gave decent excitation energies. > >> >> > Sent to CCL by: "Sue L" [chsue2004|-|yahoo.com] > >> >> > Does anyone know which DFT functional in TDDFT is suitable to > >> >> calculate > >> >> > the singlet-singlet excitations for large unsaturated pi-systems? > >> >> B3LYP > >> >> > usually underestimate the excitation energies for these systems > >> >> > > >> >> > Thank you very much > >> >> > > >> >> > Sue> > >> >> > > >> >> > > >> >> > > >> >> > >> >> -- > >> >> Dr Marcin Makowski > >> >> Jagiellonian University > >> >> Department of Theoretical Chemistry > >> >> email:makowskm]![chemia.uj.edu.pl > >> >> or > >> >> Kyushu University > >> >> email:marcin]![cube.kyushu-u.ac.jp > >> >> > >> >> -= This is automatically added to each message by the mailing script > >> >> =- 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> > >> >> Search Messages: http://www.ccl.net/htdig (login: ccl, Password: > >> >> search)> > >> >> -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+- > >> >> +-+ > >> > ------- End of Original Message -------> > >> > > >> > > >> > > >> > >> -- > >> Dr Marcin Makowski > >> Jagiellonian University > >> Department of Theoretical Chemistry > >> email:makowskm%a%chemia.uj.edu.pl > >> or > >> Kyushu University > >> email:marcin%a%cube.kyushu-u.ac.jp > >> > >> -= This is automatically added to each message by the mailing script > >> =- 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> > >> Search Messages: http://www.ccl.net/htdig (login: ccl, Password: > >> search)> > >> -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+- > >> +-+ > > ------- End of Original Message -------> > > > > > > > > -- > Dr Marcin Makowski > Jagiellonian University > Department of Theoretical Chemistry > email:makowskm|-|chemia.uj.edu.pl > or > Kyushu University > email:marcin|-|cube.kyushu-u.ac.jp > > -= This is automatically added to each message by the mailing script > =- 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> > Search Messages: http://www.ccl.net/htdig (login: ccl, Password: > search)> > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+- > +-+ ------- End of Original Message ------- From owner-chemistry@ccl.net Thu Apr 6 09:49:01 2006 From: "Mikael Johansson mikael.johansson.:.helsinki.fi" To: CCL Subject: CCL: jacs.sty Message-Id: <-31440-060406091145-16082-VRt7CYWKD936Sa29ycPsjA^-^server.ccl.net> X-Original-From: Mikael Johansson Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed Date: Thu, 6 Apr 2006 15:09:40 +0300 (EEST) MIME-Version: 1.0 Sent to CCL by: Mikael Johansson [mikael.johansson+/-helsinki.fi] Hello! On Thu, 6 Apr 2006, Noel O Boyle no228**cam.ac.uk wrote: > I understand your difficulties - I am a user of Linux, and need to use > LaTeX or I cannot submit to ACS journals. I am not looking forward to > sending my supervisor (who uses Windows) a lovely LaTeX document for > review. I've found the LaTeX2rtf package to do a reasonable job in converting LaTeX into MS-readable format. Sure, you need to open up the RTF and edit a few things, but the major formatting and references work quite well, in my opinion. And RTF is of course quite editable under Linux also. And if the receiver doesn't need to edit the document, one can naturally always produce a PDF. http://latex2rtf.sourceforge.net/ Have a nice day, Mikael J. http://www.iki.fi/~mpjohans/ From owner-chemistry@ccl.net Thu Apr 6 10:36:01 2006 From: "Fco. Javier Modrego modrego~~unizar.es" To: CCL Subject: CCL: jacs.sty Message-Id: <-31441-060406082421-23782-yOZkG3mV2ruB3cwK00uDJA*_*server.ccl.net> X-Original-From: "Fco. Javier Modrego" Content-Type: multipart/alternative; boundary="============_-1067799387==_ma============" Date: Thu, 6 Apr 2006 13:31:46 +0200 Mime-Version: 1.0 Sent to CCL by: "Fco. Javier Modrego" [modrego#%#unizar.es] --============_-1067799387==_ma============ Content-Type: text/plain; charset="us-ascii" ; format="flowed" Perhaps you could try achemso.sty Look at http://www.ctan.org/ or (better) at http://texcatalogue.sarovar.org/bytopic.html Good luck F.J. Modrego >Sent to CCL by: "Luca Bertini" [luca.bertini * istm.cnr.it] >Hi folks, does anyone knows where I can find the JACS latex style jacs.sty? >reading the notes of jacs to prepare a manuscript using latex, I found that >exist somewhere this jacs.sty style, but I can't find it on internet. I also >have the feeling that jacs tends to discourage to use latex. > >Luca B. > --============_-1067799387==_ma============ Content-Type: text/html; charset="us-ascii" Re: CCL: jacs.sty
Perhaps you could try achemso.sty
Look at http://www.ctan.org/ or (better) at http://texcatalogue.sarovar.org/bytopic.html

Good luck

        F.J. Modrego


Sent to CCL by: "Luca Bertini" [luca.bertini * istm.cnr.it]
Hi folks, does anyone knows where I can find the JACS latex style jacs.sty?
reading the notes of jacs to prepare a manuscript using latex, I found that
exist somewhere this jacs.sty style, but I can't find it on internet. I also
have the feeling that jacs tends to discourage to use latex.
Luca B.
--============_-1067799387==_ma============-- From owner-chemistry@ccl.net Thu Apr 6 11:11:00 2006 From: "Ralf Tonner Tonner.- -.chemie.uni-marburg.de" To: CCL Subject: CCL:G: NBO-Analysis of TurboMole-wavefunctions Message-Id: <-31442-060406092422-26019-hn6Mm5GcMEgzcs3TqPSQBQ- -server.ccl.net> X-Original-From: Ralf Tonner Content-Disposition: inline Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Thu, 6 Apr 2006 14:39:43 +0200 MIME-Version: 1.0 Sent to CCL by: Ralf Tonner [Tonner() chemie.uni-marburg.de] Dear CCLers, I am calculating TurboMole wavefunctions and energies using the fast and reliable RI approximation with DFT methods applying rather large basis sets (TZVPP, QZVPP). As I am now interested in the analysis of the wavefunction (given by the "mos"-file) using NBO and or the AIM methodology there is the ubiquitous problem of different formats for the representation of the wavefunction. Before entering deeply into the user-friendly FORTRAN format I wondered if someone else on the list already tried the same and worked out or found a script converting TurboMole wavefunctions into a format readable either by 1) Gaussian (03 Rev. D or prior, via guess=cards) or directly by the 2) GenNBO (5.0 or prior) standalone program. Unfortunately TurboMole is not directly supported by NBO. And Gaussian is rather slow in calculating the systems I investigate with the choosen level of theory. Any help or suggestions will be greatly appreciated. Thanks in advance Ralf -- Ralf Tonner Philipps Universität Marburg Fachbereich Chemie AK Frenking Hans-Meerwein-Straße 35032 Marburg Germany Tel.: +49-6421/28-27030 Tonner^chemie.uni-marburg.de From owner-chemistry@ccl.net Thu Apr 6 17:52:00 2006 From: "Uwe Huniar uwe.huniar#,#cosmologic.de" To: CCL Subject: CCL:G: NBO-Analysis of TurboMole-wavefunctions Message-Id: <-31443-060406174855-16662-KGPirDs7pYFYj/qRh6cP8g.@.server.ccl.net> X-Original-From: Uwe Huniar Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-15 Date: Thu, 06 Apr 2006 23:48:47 +0200 MIME-Version: 1.0 Sent to CCL by: Uwe Huniar [uwe.huniar||cosmologic.de] Dear Ralf, there are two possibilities to create wfn files for AIM with Turbomole 5.8: 1) add keyword $wfn to the control file (and run 'ridft -proper' if you have converged mos) 2) use tm2molden to convert Turbomole output to molden input and use molden2wfn - a tool that has been written by Anatoliy Volkov some time ago (I do not know if he has a newer version than the one he gave me about a year ago..., please write an email to the Turbomole support to get it or to the Turbomole user mailing list) NBO will be one of the new features of the next Turbomole version, but that does not help you right now... Regards, Uwe > Sent to CCL by: Ralf Tonner [Tonner() chemie.uni-marburg.de] > Dear CCLers, > > I am calculating TurboMole wavefunctions and energies using > the fast and reliable RI approximation with DFT methods > applying rather large basis sets (TZVPP, QZVPP). > > As I am now interested in the analysis of the wavefunction > (given by the "mos"-file) using NBO and or the AIM > methodology there is the ubiquitous problem of different > formats for the representation of the wavefunction. > > Before entering deeply into the user-friendly FORTRAN format > I wondered if someone else on the list already tried the > same and worked out or found a script converting TurboMole > wavefunctions into a format readable either by > 1) Gaussian (03 Rev. D or prior, via guess=cards) > or directly by the > 2) GenNBO (5.0 or prior) standalone program. > > Unfortunately TurboMole is not directly supported by NBO. > And Gaussian is rather slow in calculating the systems I > investigate with the choosen level of theory. > > Any help or suggestions will be greatly appreciated. > > Thanks in advance > > Ralf > From owner-chemistry@ccl.net Thu Apr 6 18:55:00 2006 From: "Christos Deligkaris cdeligka]_[purdue.edu" To: CCL Subject: CCL: Autodock and DNA Message-Id: <-31444-060406164710-8769-ngohC6k91GvMtBQWpl00pQ],[server.ccl.net> X-Original-From: "Christos Deligkaris" Date: Thu, 6 Apr 2006 16:47:08 -0400 Sent to CCL by: "Christos Deligkaris" [cdeligka,+,purdue.edu] Does anyone know why Autodock says that there are missing atoms from all the residues of my DNA pdb file? This is happening even though I have added the polar hydrogens with Autodock Tools. I also used the repairCommands module but still it is not working. And why does Autodock assign Kollman charges for the Oxygens and the Nitrogens of the order of -17 or -24? I used several PDB files I downloaded from the protein data bank but I always have this problem. One PDB file I tried was for example 1BNA. Any comments or suggestions are very welcome. Thank you very much in advance, Christos Deligkaris cdeligka(-)purdue.edu From owner-chemistry@ccl.net Thu Apr 6 19:58:00 2006 From: "Liuming Yan yan.liuming-*-staff.shu.edu.cn" To: CCL Subject: CCL: Compiling CPMD Message-Id: <-31445-060406042952-31782-AA+PzJeLLvMgYVhXJU78SQ|-|server.ccl.net> X-Original-From: "Liuming Yan" Content-Type: multipart/alternative; boundary="----=_Part_17407_19251499.1144308671734" Date: Thu, 6 Apr 2006 15:31:11 +0800 MIME-Version: 1.0 Sent to CCL by: "Liuming Yan" [yan.liuming::staff.shu.edu.cn] ------=_Part_17407_19251499.1144308671734 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline Dear All, I try to compile the cpmd under Suse Linux, however, I have only GNU compiler installed. Is it possible to compile the cpmd or a subset of cpmd using the GNU compiler. Thanks! -- Dr. Liuming Yan Department of Chemistry Shanghai University Tele: 021-6613-2405 Shanghai University Road 99, Shanghai 200444, China, The People's Republic of ------=_Part_17407_19251499.1144308671734 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline
Dear All,
 
I try to compile the cpmd under Suse Linux, however, I have only GNU c= ompiler installed.  Is it possible to compile the cpmd or a subset of = cpmd using the GNU compiler.
 
Thanks!

--
Dr. Liuming Yan

Department = of Chemistry
Shanghai University
Tele: 021-6613-2405
Shanghai Univ= ersity Road 99, Shanghai 200444,
China, The People's Republic of
------=_Part_17407_19251499.1144308671734-- From owner-chemistry@ccl.net Thu Apr 6 20:41:00 2006 From: "Nuno A. G. Bandeira nuno.bandeira%ist.utl.pt" To: CCL Subject: CCL: Compiling CPMD Message-Id: <-31446-060406204034-2666-mfz0FcwEvghhJ6438YYXrw*_*server.ccl.net> X-Original-From: "Nuno A. G. Bandeira" Date: Thu, 6 Apr 2006 20:40:29 -0400 Sent to CCL by: "Nuno A. G. Bandeira" [nuno.bandeira++ist.utl.pt] Liuming Yan yan.liuming-*-staff.shu.edu.cn wrote: > Dear All, > > I try to compile the cpmd under Suse Linux, however, I have only GNU > compiler installed. Is it possible to compile the cpmd or a subset of cpmd > using the GNU compiler. If you use gfortran it's possible. I did it in Windows successfully. 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 --