From owner-chemistry@ccl.net Thu Mar 9 03:48:01 2006 From: "Ulrike Salzner salzner,+,fen.bilkent.edu.tr" To: CCL Subject: CCL: Norming energies of different entities... Message-Id: <-31156-060309012306-4042-BSDSlnEqxCT3EIxdhbCpRw.@.server.ccl.net> X-Original-From: Ulrike Salzner Content-Transfer-Encoding: 7bit Content-Type: text/plain Date: Thu, 09 Mar 2006 08:22:55 +0200 Mime-Version: 1.0 Sent to CCL by: Ulrike Salzner [salzner{=}fen.bilkent.edu.tr] On Wed, 2006-03-08 at 22:27 -0500, Roy Jensen rjensen^^^consol.ca wrote: > Sent to CCL by: Roy Jensen [rjensen]*[consol.ca] > All > > A pedagogical question... > > Given calculations on a series of diatomic entities -- B2, C2, N2, O2, > and F2 -- is there any way to know how the orbital energies relate > between these species? I want to create a figure that accurately > presents all the MO diagrams. > You are probably asking because you are aware of the MO diagrams in first year chemistry books. I calculated the diagrams with HF and DFT. With DFT the order (sigma-zp vs pi-pz) comes out the way shown in the books. With HF, the HOMO of nitrogen is inconsistent with the experimental state order. > On a second note, what does zero energy (E = 0.0000 Hartree) > correspond to? > Zero energy corresponds to separate electrons and nuclei at 0 K, I suppose because the kinetic energy should be zero as well. > Thanks, > Dr. Roy Jensen > (==========)----------------------------------------- > Chemistry, Grant MacEwan College > Edmonton, AB T5J 4S2 > 780.633.3915> > > > -- Ulrike Salzner Associate Professor Department of Chemistry Bilkent University 06800 Bilkent, Ankara Turkey From owner-chemistry@ccl.net Thu Mar 9 04:43:01 2006 From: "Jens Spanget-Larsen spanget=ruc.dk" To: CCL Subject: CCL:G: Help with Geometry Opt for first singlet excited state usingTDDFT Message-Id: <-31157-060309044018-16194-37K8EDXne2BYxfhFMQsZfQ..server.ccl.net> X-Original-From: Jens Spanget-Larsen Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 09 Mar 2006 10:39:56 +0100 MIME-Version: 1.0 Sent to CCL by: Jens Spanget-Larsen [spanget[A]ruc.dk] Dear CY, TD-DFT geometry-optimization of an excited singlet state is not possible with Gaussian03. Turbomole has this facility. Jens >--< ------------------------------------------------------ JENS SPANGET-LARSEN Office: +45 4674 2710 Department of Chemistry Fax: +45 4674 3011 Roskilde University (RUC) Mobile: +45 2320 6246 P.O.Box 260 E-Mail: spanget*o*ruc.dk DK-4000 Roskilde, Denmark http://www.ruc.dk/~spanget ------------------------------------------------------ Changyong Qin changyong(-)wsu.edu wrote: > Sent to CCL by: "Changyong Qin" [changyong|-|wsu.edu] > Dear All, > > Does anybody have experience in using TDDFT in Gaussian 03 to optimize the first singlet excited state? If yes, could you please share the input file ? Thanks. > > CY From owner-chemistry@ccl.net Thu Mar 9 05:27:03 2006 From: "frisch---gaussian.com (Michael Frisch)" To: CCL Subject: CCL:G: Help with Geometry Opt for first singlet excited state usingTDDFT Message-Id: <-31158-060309052150-7204-JNfsBtS0GKXNRP8Fscb4Qg]=[server.ccl.net> X-Original-From: frisch|a|gaussian.com (Michael Frisch) Content-Disposition: inline Content-Type: text/plain; charset=us-ascii Date: Thu, 9 Mar 2006 05:20:08 -0500 Mime-Version: 1.0 Sent to CCL by: frisch-#-gaussian.com (Michael Frisch) On Thu, Mar 09, 2006 at 04:49:18AM -0500, Jens Spanget-Larsen spanget=ruc.dk wrote: > Sent to CCL by: Jens Spanget-Larsen [spanget[A]ruc.dk] > > Dear CY, > > TD-DFT geometry-optimization of an excited singlet state is not possible > with Gaussian03. Turbomole has this facility. > This statement is false. While TD-DFT geometry optimizations in Gaussian 03 do not use gradients, they are possible. Mike Frisch From owner-chemistry@ccl.net Thu Mar 9 06:06:00 2006 From: "Nuno Loureiro Ferreira nunolf**ci.uc.pt" To: CCL Subject: CCL: Loop prediction - reconstruction of protein missing residues Message-Id: <-31159-060309060347-3140-D93sDSvgnmaRqVcRXGbfVA:+:server.ccl.net> X-Original-From: "Nuno Loureiro Ferreira" Date: Thu, 9 Mar 2006 06:03:42 -0500 Sent to CCL by: "Nuno Loureiro Ferreira" [nunolf*ci.uc.pt] Hi * I have some structures that I want to add some missing loops and reconstruct some protein missing residues (these ones at the terminals of the protein) . My aim is to obtain the whole protein. I'm not so worried about if the loop predictions are in close agreement with known loop structures. Just want to make sure that the added residues/loops are in good stereochemical conditions without steric clashes with neighbouring residues. I'm searching for Linux or SGI software that could do the job. Want to here some feedback on this subject, before choosing the soft pack. Best regards, Nuno From owner-chemistry@ccl.net Thu Mar 9 09:12:01 2006 From: "Mariusz Sterzel m.sterzel,,cyf-kr.edu.pl" To: CCL Subject: CCL:G: Help with Geometry Opt for first singlet excited state usingTDDFT Message-Id: <-31160-060309082920-20188-7jmyIM4OC2ZIyu3UGitcZg#,#server.ccl.net> X-Original-From: Mariusz Sterzel Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed Date: Thu, 9 Mar 2006 13:26:45 +0100 (CET) MIME-Version: 1.0 Sent to CCL by: Mariusz Sterzel [m.sterzel^^^cyf-kr.edu.pl] Hello, I disagree, it is possible to optimize excited states geometry with gaussian but it is computationaly very very expensive. I agree that TURBOMOLE is much better choice since it does have analytical gradients. This also allows you to calculate harmonic frequencies. Anyway going back to gaussian, this question was asked several times. The answer I got some time ago from http://www.ccl.net/chemistry/resources/messages/2002/04/11.009-dir/ is: 1) build _GOOD_ z-matrix for your molecule 2) optimize ground state with opt(z-matrix) 3) calculate frequencies at optimized geometry 4) use following input for say 3rd excited state opimization TD(NStates=5,Singlets,Root=3) Opt(ReadFC,Z-matrix,EnOnly) in addition to your usual gaussian settings. You can also use forces from CIS calculation. Gradients are numerical so use as high symmetry as possible for optimization. And you cannot calculate frequencies so I'd rather use TURBOMOLE (which also have analytical gradients for excited states at CC level). Mariusz -- Mariusz Sterzel Email: m.sterzel/^at^\cyf-kr.edu.pl On Thu, 9 Mar 2006, Jens Spanget-Larsen spanget=ruc.dk wrote: > Sent to CCL by: Jens Spanget-Larsen [spanget[A]ruc.dk] > > Dear CY, > > TD-DFT geometry-optimization of an excited singlet state is not possible > with Gaussian03. Turbomole has this facility. > > Jens >--< > > ------------------------------------------------------ > JENS SPANGET-LARSEN Office: +45 4674 2710 > Department of Chemistry Fax: +45 4674 3011 > Roskilde University (RUC) Mobile: +45 2320 6246 > P.O.Box 260 E-Mail: spanget+*+ruc.dk > DK-4000 Roskilde, Denmark http://www.ruc.dk/~spanget > ------------------------------------------------------ > > Changyong Qin changyong(-)wsu.edu wrote: > >> Sent to CCL by: "Changyong Qin" [changyong|-|wsu.edu] >> Dear All, >> >> Does anybody have experience in using TDDFT in Gaussian 03 to optimize the first singlet excited state? If yes, could you please share the input file ? Thanks. >> >> CY> > > From owner-chemistry@ccl.net Thu Mar 9 09:47:01 2006 From: "Jens Spanget-Larsen spanget[#]ruc.dk" To: CCL Subject: CCL:G: Help with Geometry Opt for first singlet excited state usingTDDFT Message-Id: <-31161-060309092836-7114-mIEgMjoUoCy79UMqIYzFdw+/-server.ccl.net> X-Original-From: Jens Spanget-Larsen Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 09 Mar 2006 15:28:23 +0100 MIME-Version: 1.0 Sent to CCL by: Jens Spanget-Larsen [spanget#%#ruc.dk] Hello Mike, thank you for the correction! - Please answer CYs question and explain us how to perform a TD-DFT excited state geometry optimization with Gaussian03. Yours, Jens >--< ------------------------------------------------------ JENS SPANGET-LARSEN Office: +45 4674 2710 Department of Chemistry Fax: +45 4674 3011 Roskilde University (RUC) Mobile: +45 2320 6246 P.O.Box 260 E-Mail: spanget a ruc.dk DK-4000 Roskilde, Denmark http://www.ruc.dk/~spanget ------------------------------------------------------ frisch---gaussian.com (Michael Frisch) wrote: > Sent to CCL by: frisch-#-gaussian.com (Michael Frisch) > On Thu, Mar 09, 2006 at 04:49:18AM -0500, Jens Spanget-Larsen spanget=ruc.dk wrote: > >>Sent to CCL by: Jens Spanget-Larsen [spanget[A]ruc.dk] >> >>Dear CY, >> >>TD-DFT geometry-optimization of an excited singlet state is not possible >>with Gaussian03. Turbomole has this facility. >> > > > This statement is false. While TD-DFT geometry optimizations in Gaussian 03 > do not use gradients, they are possible. > > Mike Frisch From owner-chemistry@ccl.net Thu Mar 9 10:23:00 2006 From: "Barry Hardy barry.hardy]![tiscalinet.ch" To: CCL Subject: CCL: Advanced Training Workshop Week at Oxford; Early Registration Message-Id: <-31162-060309090428-29070-ijjrHPyRfOjKxies8iwioQ=server.ccl.net> X-Original-From: Barry Hardy Content-Type: multipart/alternative; boundary="=====================_13882207==_.ALT" Date: Thu, 09 Mar 2006 14:01:40 +0100 Mime-Version: 1.0 Sent to CCL by: Barry Hardy [barry.hardy|a|tiscalinet.ch] --=====================_13882207==_.ALT Content-Type: text/plain; charset="us-ascii"; format=flowed Latest Advances in Drug Discovery Design & Planning Methods Virtual screening, structure-based drug design, reaction planning and predictive toxicology supporting decision making for chemists in drug discovery a Hands-on 5 Day eCheminfo Advanced Training Workshop Week, 3-7 July 2006 Chemistry Research Laboratory, Oxford University, Oxford, UK Workshops will be held at the Chemistry Information Technology Center with exercises supported by leading drug discovery software including OpenEye, Schrodinger, ChemAxon, CAChe, Scitegic, Lhasa and Umetrics. 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--=====================_13882207==_.ALT-- From owner-chemistry@ccl.net Thu Mar 9 12:36:00 2006 From: "ReichertD---mir.wustl.edu" To: CCL Subject: CCL: Loop prediction - reconstruction of protein missing residues Message-Id: <-31163-060309120507-16651-ZG50iMomAcDGC3gpU4fH/w|a|server.ccl.net> X-Original-From: ReichertD---mir.wustl.edu Content-type: multipart/related; Boundary="0__=09BBFBBFDFCA62AD8f9e8a93df938690918c09BBFBBFDFCA62AD" Date: Thu, 9 Mar 2006 10:24:03 -0600 MIME-Version: 1.0 Sent to CCL by: ReichertD[]mir.wustl.edu --0__=09BBFBBFDFCA62AD8f9e8a93df938690918c09BBFBBFDFCA62AD Content-type: multipart/alternative; Boundary="1__=09BBFBBFDFCA62AD8f9e8a93df938690918c09BBFBBFDFCA62AD" --1__=09BBFBBFDFCA62AD8f9e8a93df938690918c09BBFBBFDFCA62AD Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: quoted-printable I've been quite happy with the Modeller package from the Sali group (fr= ee for academic use). -david David Reichert, Ph.D. Asst. Professor Radiology Washington University School of Medicine 510 S. Kingshighway, Campus Box 8225 St Louis, MO 63110 e-mail: reichertd_+_wustl.edu http://scoobie.wustl.edu/ voice: (314) 362-8461 fax: (314) 362-9940 = "Nuno Loureiro = Ferreira = nunolf**ci.uc.pt" = To = Sent by: = cc owner-chemistry_+_c = cl.net Subj= ect CCL: Loop prediction - = reconstruction of protein missin= g 03/09/2006 05:28 residues = AM = = = Please respond to = "CCL Subscribers" = = = = Sent to CCL by: "Nuno Loureiro Ferreira" [nunolf*ci.uc.pt] Hi * I have some structures that I want to add some missing loops and reconstruct some protein missing residues (these ones at the terminals = of the protein) . My aim is to obtain the whole protein. I'm not so worried about if the = loop predictions are in close agreement with known loop structures. Just wan= t to make sure that the added residues/loops are in good stereochemical conditions without steric clashes with neighbouring residues. I'm searching for Linux or SGI software that could do the job. Want to here some feedback on this subject, before choosing the soft pa= ck. Best regards, Nuno -=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 chang= ehttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtml= Search Messages: http://www.ccl.net/htdig (login: ccl, Password: searc= h)http://www.ccl.net/spammers.txt-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-= + = --1__=09BBFBBFDFCA62AD8f9e8a93df938690918c09BBFBBFDFCA62AD Content-type: text/html; charset=US-ASCII Content-Disposition: inline Content-transfer-encoding: quoted-printable

I've been quite happy with the Modeller package from the Sali group = (free for academic use).
-david
David Reichert, Ph.D.
Asst. Professor Radiology
Washington University School of Medicine
510 S. Kingshighway, Campus Box 8225
St Louis, MO 63110

e-mail: reichertd_+_wustl.edu
http://scoobie.wustl.edu/
=
voice: (314) 362-8461
fax: (314) 362-9940
3D"Inactive"= ;Nuno Loureiro Ferreira nunolf**ci.uc.pt" <owner-chemistry_+_ccl.= net>


=
          "Nuno Loureiro Ferreira nunolf**ci.uc.pt&q= uot; <owner-chemistry_+_ccl.net>
          Sent by: owner-chemistry_+_ccl.net

          03/09/2006 05:28 AM =
          Please respond to
          "CCL Subscribers" <chemistry_+_ccl.net>

 =

To
3D""
"Reichert, David E. " <reichertd_+_= mir.wustl.edu>

cc
3D""

Subject
3D""
CCL: Loop prediction - reconstruction of protein missi= ng residues
=3D""3D""<= /td>

Sent to CCL by: "Nuno Loureiro Ferreira" [nunolf*ci.uc.pt= ]
Hi *

I have some structures that I want to add some missing loops and recons= truct some protein missing residues (these ones at the terminals of the= protein) .

My aim is to obtain the whole protein. I'm not so worried about if the = loop predictions are in close agreement with known loop structures. Jus= t want to make sure that the added residues/loops are in good stereoche= mical conditions without steric clashes with neighbouring residues.
=
I'm searching for Linux or SGI software that could do the job.
Want to here some feedback on this subject, before choosing the soft pa= ck.
Best regards,
Nuno



-=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 chang= e      http://www.ccl.net/cgi-bin/ccl/send_ccl_message<= /tt>
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I'm not so worried about if > the loop predictions are in close agreement with known loop > structures. Just want to make sure that the added residues/loops are > in good stereochemical conditions without steric clashes with > neighbouring residues. > > I'm searching for Linux or SGI software that could do the job. Want > to here some feedback on this subject, before choosing the soft pack. You could use Modeller (http://salilab.org/modeller/) to achieve this. A missing residues example is at http://salilab.org/modeller/wiki/Missing_residues Ben -- ben{}salilab.org http://salilab.org/~ben/ "It is a capital mistake to theorize before one has data." - Sir Arthur Conan Doyle From owner-chemistry@ccl.net Thu Mar 9 14:32:01 2006 From: "Brian Williams williams#bucknell.edu" To: CCL Subject: CCL: Norming energies of different entities... Message-Id: <-31165-060309114027-13520-ht0dyurEnJR2VyPJHQunJw .. server.ccl.net> X-Original-From: Brian Williams Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1"; format=flowed Date: Thu, 09 Mar 2006 11:39:59 -0500 Mime-Version: 1.0 Sent to CCL by: Brian Williams [williams _ bucknell.edu] Sorry to take up more bandwidth.. A colleague informs me a more recent source for some of this kind of information is "Inorganic Chemistry", Missler and Tarr, 3rd ed. (2004). Table 5-1 gives orbital potential energies and cites a source, "J. B. Mann, T. L. Meek, and L.C. Allen, JACS 2000 122 2780. This source also has some MO diagrams showing the relative energies of the atomic and MO orbitals, along with pictures of the shapes of the orbitals and (sometimes) associated photoelectric spectra. Brian Williams, Bucknell At 10:34 PM 3/8/2006, you wrote: >Sent to CCL by: Roy Jensen [rjensen]*[consol.ca] >All > >A pedagogical question... > >Given calculations on a series of diatomic entities -- B2, C2, N2, O2, >and F2 -- is there any way to know how the orbital energies relate >between these species? I want to create a figure that accurately >presents all the MO diagrams. > >On a second note, what does zero energy (E = 0.0000 Hartree) >correspond to? > >Thanks, > Dr. Roy Jensen >(==========)-----------------------------------------¤ > Chemistry, Grant MacEwan College > Edmonton, AB T5J 4S2 > 780.633.3915 From owner-chemistry@ccl.net Thu Mar 9 15:06:01 2006 From: "D.BIO- Gerard Pujadas gerard.pujadas*urv.net" To: CCL Subject: CCL: Loop prediction - reconstruction of protein missing residues Message-Id: <-31166-060309145156-29867-lSE/tHwMl4VLZ292wxVQgw|*|server.ccl.net> X-Original-From: "D.BIO- Gerard Pujadas" Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" ; format="flowed" Date: Thu, 9 Mar 2006 20:51:11 +0100 Mime-Version: 1.0 Sent to CCL by: "D.BIO- Gerard Pujadas" [gerard.pujadas++urv.net] > From the Sali group, see also the ModLoop server at http://alto.compbio.ucsf.edu/modloop//modloop.html Regards Gerard -- ======================== NOTE: NEW ADDRESS AND E-MAIL ======================== Dr. Gerard Pujadas Grup de recerca en Nutrigenòmica Dept. Bioquímica i Biotecnologia room 106 Campus de Sant Pere Sescelades e-mail: gerard.pujadas.:.urv.net Univ. Rovira i Virgili phone: 34-977 559565 C/ Marcel·lí Domingo fax: 34-977 558232 43007 Tarragona (CATALONIA) State: Spain (European Union) =========================================================================== From owner-chemistry@ccl.net Thu Mar 9 16:48:01 2006 From: "Brian Salter-Duke b_duke ~ octa4.net.au" To: CCL Subject: CCL: Norming energies of different entities... Message-Id: <-31167-060309050301-29204-g9sKEnK9uqFRADQRa4d2bg()server.ccl.net> X-Original-From: Brian Salter-Duke Content-Disposition: inline Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=unknown-8bit Date: Thu, 9 Mar 2006 19:20:46 +1100 Mime-Version: 1.0 Sent to CCL by: Brian Salter-Duke [b_duke,octa4.net.au] On Wed, Mar 08, 2006 at 10:41:35PM -0500, Roy Jensen rjensen^^^consol.ca wrote: > Sent to CCL by: Roy Jensen [rjensen]*[consol.ca] > All > > A pedagogical question... > > Given calculations on a series of diatomic entities -- B2, C2, N2, O2, > and F2 -- is there any way to know how the orbital energies relate > between these species? I want to create a figure that accurately > presents all the MO diagrams. I am not sure what you want here. > On a second note, what does zero energy (E = 0.0000 Hartree) > correspond to? E = 0.000 for the total energy is when all nuclei and all electrons are moved to an infinite distances from each other. Regards, Brian. > Thanks, > Dr. Roy Jensen > (==========)-----------------------------------------¤ > Chemistry, Grant MacEwan College > Edmonton, AB T5J 4S2 > 780.633.3915> > > -- 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 Fellow, Dept. of Medicinal Chemistry, Monash Univ. From owner-chemistry@ccl.net Thu Mar 9 17:22:01 2006 From: "Debasis Sengupta dxs]~[cfdrc.com" To: CCL Subject: CCL:G: parallel G03 in Linux cluster Message-Id: <-31168-060309162719-3526-J8kLAWlb7xpGIGKf7hY5yA{}server.ccl.net> X-Original-From: Debasis Sengupta Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii; format=flowed Date: Thu, 09 Mar 2006 15:29:12 -0600 MIME-Version: 1.0 Sent to CCL by: Debasis Sengupta [dxs]=[cfdrc.com] Hello Everybody, I am planning to buy sixteen AMD64 Athlon dual core machines (with Linux) for running G03 in parallel. They will be connected by ethernet. I never have any experience in running gaussian with Linux cluster. So my questions are the following: 1. Can G03 be run parallel in the above configuration? 2. Do you need to have Linda for running parallel in the above configuration? 3. Do you recommend any other processor? 4. Which brand of Linux is good for running G03 parallel? 5. Pals sharer your experience with running G03 parallel in Linux cluster (like tricks, problems, failure etc). Thanks in advance Debasis