From owner-chemistry@ccl.net Thu Sep 16 00:54:00 2010 From: "Eric B. Isaacs ebisaacs-.-gmail.com" To: CCL Subject: CCL: sulfur with 6-31G** and lanl2dz Message-Id: <-42774-100916005131-25310-rUz/hNIDMLPB9Cr1W0poBg~!~server.ccl.net> X-Original-From: "Eric B. Isaacs" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes Date: Wed, 15 Sep 2010 21:51:21 -0700 Mime-Version: 1.0 (Apple Message framework v936) Sent to CCL by: "Eric B. Isaacs" [ebisaacs.|,|.gmail.com] Hi Zineb, As far as I know the LANL2DZ basis set is actually 6-31G for atoms with Z<11, so if all the atoms i quinoxaline n your other derivatives meet this criterion then you should expect the total energies to be pretty close to 6-31G(d,p) -- there should just be some small change > from the addition of polarization functions. In contrast, when you're using the pseudopotential/effective core potential with the sulfur- containing molecule some of the sulfur electrons are not being treated explicitly, so the total energy should change significantly. Eric On Sep 15, 2010, at 7:15 PM, zouzou adnani zinebeladnani-*-hotmail.com wrote: > > Sent to CCL by: "zouzou adnani" [zinebeladnani#,#hotmail.com] > hi > I'm working on the geometry optimisation of the some quinoxaline > derivatives using different basis set , in most of my systems I have > almost the same energies with both 6-31G(d,p) and lanl2dz basis > sets, except in those containing sulfur atoms, can anyone tell me why? > Thanks for taking the time to read this! > Regards, > Zineb el adnani > > > > -= 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/> > From owner-chemistry@ccl.net Thu Sep 16 03:19:00 2010 From: "Maura Mooney mmooney05,+,qub.ac.uk" To: CCL Subject: CCL: Capping termini - protein modeling Message-Id: <-42775-100916031640-5071-JU47sYTc63iuPXMcFSVQEw%%server.ccl.net> X-Original-From: "Maura Mooney" Date: Thu, 16 Sep 2010 03:16:39 -0400 Sent to CCL by: "Maura Mooney" [mmooney05%a%qub.ac.uk] Hi, My question regards peptide caps. I have a few proteins (~25kDa) in which the first and last few residues are truncated. In what circumstances should I cap the protein termini, and apart from stability in small alpha helices, why should we cap protein termini? Thanx, From owner-chemistry@ccl.net Thu Sep 16 03:53:01 2010 From: "Tamas Gunda tgunda2===puma.unideb.hu" To: CCL Subject: CCL: How to make an enantiomer? Message-Id: <-42776-100915031854-18885-BN0hQIvIHpz6NO4f/akd6A=-=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: Wed, 15 Sep 2010 09:18:43 +0200 MIME-Version: 1.0 Sent to CCL by: "Tamas Gunda" [tgunda2 a puma.unideb.hu] Hi! There is a utility program Mol2Mol, it can reverse the coordinates and then output it in many formats. www.gunda.hu/mol2mol Regards Tamas Gunda -------------------------------------------------- > From: "Marcelo Puiatti marcelo.puiatti|*|gmail.com" Sent: Tuesday, September 14, 2010 17:49 PM To: "Gunda, Tamas E " Subject: CCL: How to make an enantiomer? > > Sent to CCL by: Marcelo Puiatti [marcelo.puiatti,+,gmail.com] > Hi, I want to generate an enantiomer of a small molecule from its xyz > coordinates. Is there any program for doing that? > > Thanks in advance> > From owner-chemistry@ccl.net Thu Sep 16 05:24:00 2010 From: "willsd|*|appstate.edu" To: CCL Subject: CCL: ONIOM literature Message-Id: <-42777-100916052026-17161-SE5vIe2fZTIwunGaKuFXgA\a/server.ccl.net> X-Original-From: Content-Disposition: inline Content-Language: en Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii Date: Thu, 16 Sep 2010 09:19:12 GMT MIME-Version: 1.0 Sent to CCL by: [willsd===appstate.edu] The answer is... probably not. ONIOM requires the entire molecule to be calculated at the low level of theory, with a portion of the molecule being also calculated at the high level also. This means that the semi-empirical method you wish to use must include parameters for the transition metals in your compound, and most SE methods do not include such parameters. At least as of a few years ago, I could not perform ONIOM calculations on a rhenium complex with a semi-empirical low level for this reason. Steve Williams ----- Original Message ----- > From: "Michael Dimitrov mich.dimitrov-,-gmail.com" Date: Wednesday, September 15, 2010 7:10 pm Subject: CCL: ONIOM literature To: "Williams, Steve " > > Sent to CCL by: Michael Dimitrov [mich.dimitrov##gmail.com] > Hi, > > In the review J. Mol. Cat. A: Chem. 2010, 324, 104 > (http://dx.doi.org/10.1016/j.molcata.2010.03.015 ) Morokuma has > compiled recent ONIOM calculations and especially Table 1 in the > article is of interest. Looks like DFT:MM or DFT:HF levels were mostly > used for transition metal systems. > > I am wondering, if DFT:Semiempirical can replace DFT:HF with similar > accuracy? (in my system DFT:MM gives unreliable geometry, probably due > to incorrect treatment of electronic effects). > > Best regards, > Michael Dimitrov. > > > > -= 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 /a\ sign. You can > also> Conferences: > http://server.ccl.net/chemistry/announcements/conferences/> > > From owner-chemistry@ccl.net Thu Sep 16 14:58:00 2010 From: "Jamin Krinsky jamink^berkeley.edu" To: CCL Subject: CCL:G: sulfur with 6-31G** and lanl2dz Message-Id: <-42778-100916145543-2614-1Qo/XhKoDVgHGW1RYaGhBg^server.ccl.net> X-Original-From: Jamin Krinsky Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Thu, 16 Sep 2010 11:55:33 -0700 MIME-Version: 1.0 Sent to CCL by: Jamin Krinsky [jamink]^[berkeley.edu] Zineb, For clarification, LANL2DZ uses D95V for Z<11, which is ALMOST comparable to 6-31G(d,p), so it does have polarization. That being said (and I don't think you were suggesting this but just in case), you don't want to compare the energies using the two basis sets anyway. Using an ECP basis for S is not generally ideal (partially because LANL2DZ does NOT put polarization on P, S, etc.), you may want to use 6-31G(d,p) for everything up to Ar and LANL2DZ for the remainder. I assume you're using Gaussian, so you might want to check out a tutorial for setting up custom basis sets here: http://glab.cchem.berkeley.edu/glab/faqs/gauss_custombasis.html Jamin On Wed, Sep 15, 2010 at 9:51 PM, Eric B. Isaacs ebisaacs-.-gmail.com wrote: > > Sent to CCL by: "Eric B. Isaacs" [ebisaacs.|-|.gmail.com] > Hi Zineb, > > As far as I know the LANL2DZ basis set is actually 6-31G for atoms with > Z<11, so if all the atoms i quinoxaline n your other derivatives meet this > criterion then you should expect the total energies to be pretty close to > 6-31G(d,p) -- there should just be some small change >> >> from the addition of polarization functions. In contrast, when you're > > using the pseudopotential/effective core potential with the > sulfur-containing molecule some of the sulfur electrons are not being > treated explicitly, so the total energy should change significantly. > > Eric > > On Sep 15, 2010, at 7:15 PM, zouzou adnani zinebeladnani-*-hotmail.com > wrote: > >> >> Sent to CCL by: "zouzou  adnani" [zinebeladnani#,#hotmail.com] >> hi >> I'm working on the geometry optimisation of the some quinoxaline >> derivatives using different basis set , in most of my systems I have almost >> the same energies with both 6-31G(d,p) and lanl2dz basis sets, except in >> those containing sulfur atoms, can anyone tell me why? >> Thanks for taking the time to read this! >> Regards, >> Zineb el adnani>    >       > > Job: http://www.ccl.net/jobsConferences: > http://server.ccl.net/chemistry/announcements/conferences/>    > > > -- Jamin L Krinsky, Ph.D. Molecular Graphics and Computation Facility 175 Tan Hall, University of California, Berkeley, CA 94720 jamink|-|berkeley.edu, 510-643-0616 http://glab.cchem.berkeley.edu From owner-chemistry@ccl.net Thu Sep 16 19:06:00 2010 From: "Oellien, F (Frank) frank.oellien!^!sp.intervet.com" To: CCL Subject: CCL: Registration for GCC2010 Message-Id: <-42779-100915044643-19540-M4AHrSdxgMvcRhYtj2BaMw],[server.ccl.net> X-Original-From: "Oellien, F (Frank)" Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Wed, 15 Sep 2010 10:46:28 +0200 MIME-Version: 1.0 Sent to CCL by: "Oellien, F (Frank)" [frank.oellien*o*sp.intervet.com] Registration Opened 6th German Conference on Chemoinformatics Hotel 'Der Achtermann', Goslar, Germany 7 - 9 November 2010 Dear Colleagues, The registration for the 6. German Conference on Chemoinformatics (http://www.gdch.de/gcc2010) to be held in Goslar, Germany, November 7 - 9, 2010 is opened. The scientific program will be available on the conference page in the next days. You have still the opportunity to submit last minute posters until October 9, 2010. Invited Speakers this year are: * Colleen Fitzpatrick, Identifiers International, Huntington Beach, USA * Gerhard Klebe, University of Marburg, DE * Holger Gohlke, University of Düsseldorf, DE * Jürgen Gmehling, University of Oldenburg, DE * Hans Fraaije, University of Leiden, NL * Wolfang Guba, Roche, Basel, CH * Andrew R. Leach, GSK, Stevenage, UK Visit the conference website at www.gdch.de/gcc2010 for more information and for the scientific program. Frank Oellien GDCh CIC Chair Mit freundlichen Grüßen / With kind regards Dr. Frank Oellien BioChemInformatics Scientist Intervet Innovation GmbH Zur Propstei 55270 Schwabenheim, Germany E-Mail: frank.oellien%sp.intervet.com Phone: +49 (6130) 948 365 Fax: +49 (6130) 948 517 Home http://www.intervet.com A subsidiary of Merck & Co., Inc., Whitehouse Station, NJ, USA Sitz der Gesellschaft: Schwabenheim Amtsgericht Mainz, HRB 23 166 Geschäftsführer: Dr. Peter Schmid From owner-chemistry@ccl.net Thu Sep 16 21:01:00 2010 From: "Sayed Mesa elsayed.elmes*|*yahoo.com" To: CCL Subject: CCL:G: Induced dipole moment using Gaussian code Message-Id: <-42780-100916205903-440-kVTSkRPlC6H7AxR9lDtQ8Q-.-server.ccl.net> X-Original-From: "Sayed Mesa" Date: Thu, 16 Sep 2010 20:59:02 -0400 Sent to CCL by: "Sayed Mesa" [elsayed.elmes=yahoo.com] Dear CCL community What is the recipe for calculating the induced dipole moment using Gaussian program? Thanks in advance Sayed