From owner-chemistry@ccl.net Fri Feb 2 01:40:01 2007 From: "Jean-Francois Truchon jeanfrancois_truchon_+_merck.com" To: CCL Subject: CCL: GLARE: a free software for combinatorial library design Message-Id: <-33503-070202001059-24779-K40iFuXtNDW4kFKUxe5wmg^_^server.ccl.net> X-Original-From: "Jean-Francois Truchon" Date: Fri, 2 Feb 2007 00:10:56 -0500 Sent to CCL by: "Jean-Francois Truchon" [jeanfrancois_truchon..merck.com] Dear chemists, As of January 2007, I posted a new and freely available software called GLARE (Global Library Assessment of Reagents) on the sourceforge.net website (http://glare.sourceforge.net). GLARE can be really useful for those of you who design combinatorial libraries of compounds since it can optimize list of commercially available reagents leading to 10E12 or more products in a few seconds time scale. Developed at Merck & Co, this software has been useful in real pharmaceutical library designs, improving desired properties of the products while reducing the time a chemist spends selecting the reagents. The algorithm behind GLARE has been published in: Journal of Chemical Information and Modeling, 46 (4), 1536-1548, 2006. The use of GLARE has lead to an interesting paper on the generality of single reagent lists: Australian Journal of Chemistry, 59, 879-882, 2006. Finally, Elsevier MDL has reviewed our work in an article in their magazine: Molecular Connections Vol. 24 No. 4, 2006. GLARE is filling a gap where chemists had to make very crude approximations: pruning large lists of reagents (100-20000) by inferring the properties of products (for instance the Lipinski rule of five) they would make when combined with other dimensions of the combinatorial set. This usually comes before the more refined diversity optimization, which GLARE does not tackle directly. The reason to make this software available is to help the community to improve the process of library design, letting others to re-use the hard work involved in the development of GLARE. Sincerely, Jean-Francois Truchon. From owner-chemistry@ccl.net Fri Feb 2 06:02:01 2007 From: "Lukasz Cwiklik lukasz.cwiklik_-_uochb.cas.cz" To: CCL Subject: CCL: Changing Parameters in AMBER Message-Id: <-33504-070202051539-910-fV4R8CxEwlVrfle3iJseDw%%server.ccl.net> X-Original-From: "Lukasz Cwiklik" Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Fri, 2 Feb 2007 10:14:47 +0100 MIME-Version: 1.0 Sent to CCL by: "Lukasz Cwiklik" [lukasz.cwiklik!A!uochb.cas.cz] On 2/1/07, Mary Veronica O Connor moconnor(_)westliberty.edu > Sent to CCL by: "Mary Veronica O Connor" [moconnor||westliberty.edu] > I have a set of parameters (bond lengths, etc.) for heme iron that I would like to insert into my copy of the AMBER program. Can anyone tell me how to go about doing this? > Thanks, > Mary Hi Mary, Take, for example, a look at my minitutorial at: http://www.molecular.cz/~cwiklik/materials/amb_residues.html The procedure for polarizable force-field is described there. Also the tutorials on Antechamber's web page can be useful for you: http://amber.scripps.edu/antechamber/example.html Best, Lukasz Cwiklik -- Lukasz Cwiklik http://www.molecular.cz/~cwiklik From owner-chemistry@ccl.net Fri Feb 2 06:55:00 2007 From: "FyD fyd^u-picardie.fr" To: CCL Subject: CCL: Changing Parameters in AMBER Message-Id: <-33505-070202032629-25683-PdULFzC6YswvX2dF6WYsXw!^!server.ccl.net> X-Original-From: FyD Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; format="flowed" Date: Fri, 02 Feb 2007 08:33:02 +0100 MIME-Version: 1.0 Sent to CCL by: FyD [fyd|-|u-picardie.fr] Quoting "Mary Veronica O Connor moconnor(_)westliberty.edu" : > I have a set of parameters (bond lengths, etc.) for heme iron that I > would like to insert into my copy of the AMBER program. Can anyone > tell me how to go about doing this? Create a FRCMOD file http://amber.scripps.edu/formats.html#frcmod and lead it in LEaP using the following command: FRCMOD = loadAmberParams Your-frcmod.fille regards, Francois From owner-chemistry@ccl.net Fri Feb 2 07:28:01 2007 From: "neeraj misra misraneeraj _ gmail.com" To: CCL Subject: CCL: software Message-Id: <-33506-070202071307-10684-13p+nQGW1Lzsg+fSkLjSBQ..server.ccl.net> X-Original-From: "neeraj misra" Date: Fri, 2 Feb 2007 07:13:03 -0500 Sent to CCL by: "neeraj misra" [misraneeraj]-[gmail.com] I AM LOOKING FOR A SOFTWARE (PREFERABLY WINDOWS) WHICH CAN CALCULATE THERMODYNAMIC PROPERTIES OF A MOLECULE IN DETAIL. THANKS IN ADVANCE From owner-chemistry@ccl.net Fri Feb 2 08:03:00 2007 From: "Sergio Emanuel Galembeck segalemb%a%usp.br" To: CCL Subject: CCL:G: [NBO problem] Message-Id: <-33507-070131135034-19485-FkCz/tYjyjhwyw8TFGyrIg]*[server.ccl.net> X-Original-From: Sergio Emanuel Galembeck Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Wed, 31 Jan 2007 15:49:01 -0200 MIME-Version: 1.0 Sent to CCL by: Sergio Emanuel Galembeck [segalemb=usp.br] Dear Albert, The list of numbers means the basis functions in the same order that are listed in the main electronic structure program. Unfortunately I am not observed the second error. I suggest you to write to Professor Weinhold. He is a nice person and answered all my questions. Hope this help you, Sergio ============================================================== Sergio Emanuel Galembeck Assistant Professor in Physical Chemistry Departamento de Quimica Faculdade de Filosofia, Ciencias e Letras de Ribeirao Preto Universidade de Sao Paulo Av Bandeirantes, 3900 Ribeirao Preto, SP Brasil phone: +55-16-3602-37-65 fax: +55-16-3602-48-538 e-mail: segalemb_at_usp.br ============================================================== Citando "ALBERT POATER TEIXIDOR albert.poater\\a/udg.es" : > > Sent to CCL by: "ALBERT POATER TEIXIDOR" [albert.poater~!~udg.es] > Dear NBO experts, > I have a problem of ignorancy. I do not know how to interprete the meaning > of the information given by a NBO analysis. I would like to know which is > the contribution of each d orbital but I do not understant de meaning of > the numbers. The list of numbers means: 1s, 2s, 2px, 2py, 2pz, 3s...? > > 85. (0.00015) RY*( 4) C 2 s( 87.28%)p 0.05( 4.51%)d 0.09( > 8.22%) > 0.0000 -0.0063 0.9342 -0.0179 > 0.1035 > 0.0000 0.0000 -0.0158 -0.1838 > 0.0000 > 0.0040 -0.0001 -0.2427 -0.1525 > 86. (0.00012) RY*( 5) C 2 s( 3.01%)p28.88( 86.82%)d 3.38( > 10.17%) > 0.0000 -0.0022 0.1734 -0.0032 > -0.4856 > 0.0000 0.0001 -0.0031 0.7952 > 0.0000 > 0.0961 0.0000 -0.2494 0.1740 > I have to observe the output file because when I put the keyword > pop=(nbo,savenbo) the calculation fails (it has 41 atoms and it is an > unrestricted calculation, I say the dimension because the same calculation > for a simple molecule as H2 is possible): > > > Sorting of NBOs: 157 139 148 200 179 207 88 191 > 193 120 > Sorting of NBOs: 129 110 101 130 121 249 87 107 > 98 196 > Sorting of NBOs: 198 199 147 195 190 189 194 192 > NBStor is confused about NOcc. > Error termination via Lnk1e in /estufa/soft/g03pedro/g03/l607.exe at Wed > Jan 24 02:01:33 2007. > Job cpu time: 0 days 0 hours 48 minutes 39.7 seconds. > File lengths (MBytes): RWF= 104 Int= 0 D2E= 0 Chk= 11 > Scr= 1 > > Thanks for your comments, and I would be pleased if there is any other > option to visualize or way to explain the contributions of each orbital > Best regards, > Albert > > > > Dr. Albert Poater Teixidor > University of Salerno> > > > From owner-chemistry@ccl.net Fri Feb 2 09:44:00 2007 From: "Wai-To Chan chan,,curl.gkcl.yorku.ca" To: CCL Subject: CCL:G: using Gaussian to write wavefunction file. Message-Id: <-33508-070202093923-15381-2Z2evf40bvRHciCvbCNepA!=!server.ccl.net> X-Original-From: Wai-To Chan Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii Date: Fri, 2 Feb 2007 09:57:26 -0500 (EST) MIME-Version: 1.0 Sent to CCL by: Wai-To Chan [chan_._curl.gkcl.yorku.ca] You show in your message these coefficients: <<<<<<<<<< 1.54328967E-01 5.35328142E-01 4.44634542E-01 1.54328967E-01 5.35328142E-01 4.44634542E-01 >>>>>>>>>>>>>> which are contraction coefficients of the basis set employed. The coefficients from thw wfn file you show: <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< 0.15199328D+00 0.14700128D+00 0.45813880D-01 0.15199328D+00 0.14700128D+00 0.45813880D-01 >>>>>>>>>>>>>>>>>>>>> which are actually molecular obital coefficients not basis set coefficients I don't have an easy answers to your question: <<<< Does anyone know how Gaussian transforms these coefficients for writing the wfn file?>>> Here are some thoughts that could might be useful. The way I understand what the MOs in the wfn file means is that the electron density rho is generated from rho = summation n_i summation |c_j|^2 i j where n_i is the occupancy of the ith MO in the wfn file and j sums over the coefficients of the MO. It doesn't look like that the wfn file contains the contraction coefficients of the basis set. It seems to contain only the exponents. Looks like the contraction coefficients of the basis set are already merged into the coefficients of the MOs in the wfn file. What I am not sure about is whether the original MOs in the wfn file are actually the Hartree-Fock orbitals or the DFT orbitals Gaussian printed out in the output file. If the procedure of generating rho is indeed the summation of the squares of the individual coefficients (and the associated phi) for each MO and then combine together the summations for all of the MOs then it is possible that the MOs in the wfn file are derived > from natural orbitals. In fact if you want to obtain electron density from a post-Hartree-Fock calclation like MP2 an QCISD you have to specify density=current which also enables generation of the natural orbitals. Without this option you will obtain the same wfn file for a Hartree-Fock run for a post-hartree-fock job. The formulae above I used to illustrate the procedure for the transformation the MOs in the wfn file to rho is based on my understanding of how the AIMPAC code works. This is from a rather casual study of the code nearly a decade ago so I could be wrong. But if I have to figure out the precise details about the how the MOs in a wfn file are generated I would look to the code of AIMPAC as a starting point. Wai-To Chan From owner-chemistry@ccl.net Fri Feb 2 10:23:01 2007 From: "Wai-To Chan chan*_*curl.gkcl.yorku.ca" To: CCL Subject: CCL: using Gaussian to write wavefunction file. (correction) Message-Id: <-33509-070202095326-20746-sXWv6zCFLUbBRLDabqUdVw~!~server.ccl.net> X-Original-From: Wai-To Chan Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii Date: Fri, 2 Feb 2007 10:11:32 -0500 (EST) MIME-Version: 1.0 Sent to CCL by: Wai-To Chan [chan:-:curl.gkcl.yorku.ca] > From my previous post: rho = summation n_i summation |c_j|^2 should read: rho = summatin n_i summation |c_j*phi_j|^2 phi_j refers to the basis set component associated with c_j. Wai-To Chan From owner-chemistry@ccl.net Fri Feb 2 10:53:00 2007 From: "taye beyene beyene sene3095|,|yahoo.com" To: CCL Subject: CCL: software Message-Id: <-33510-070202101218-30102-/sJF2B0kYRkqBwnBe+4mmQ:_:server.ccl.net> X-Original-From: taye beyene beyene Content-Transfer-Encoding: 8bit Content-Type: multipart/alternative; boundary="0-1616982850-1170429127=:46917" Date: Fri, 2 Feb 2007 07:12:07 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: taye beyene beyene [sene3095],[yahoo.com] --0-1616982850-1170429127=:46917 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit You can use Gauassian03 or Gaussitan98 programm packages to calculae the frequency of ur compound and extract thermodynamic properties. "neeraj misra misraneeraj _ gmail.com" wrote: Sent to CCL by: "neeraj misra" [misraneeraj]-[gmail.com] I AM LOOKING FOR A SOFTWARE (PREFERABLY WINDOWS) WHICH CAN CALCULATE THERMODYNAMIC PROPERTIES OF A MOLECULE IN DETAIL. THANKS IN ADVANCEhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt--------------------------------- Don't get soaked. Take a quick peak at the forecast with theYahoo! Search weather shortcut. --0-1616982850-1170429127=:46917 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: 8bit
You can use Gauassian03 or Gaussitan98 programm packages to calculae the
frequency of ur compound and extract thermodynamic properties.

"neeraj misra misraneeraj _ gmail.com" <owner-chemistry|,|ccl.net> wrote:

Sent to CCL by: "neeraj misra" [misraneeraj]-[gmail.com]
I AM LOOKING FOR A SOFTWARE (PREFERABLY WINDOWS) WHICH CAN CALCULATE THERMODYNAMIC PROPERTIES OF A MOLECULE IN DETAIL.
THANKS IN ADVANCE


http://www.ccl.net/cgi-bin/ccl/send_ccl_message
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Don't get soaked. Take a quick peak at the forecast
with theYahoo! Search weather shortcut. --0-1616982850-1170429127=:46917-- From owner-chemistry@ccl.net Fri Feb 2 16:57:01 2007 From: "Noel M. O Boyle baoilleach-*-gmail.com" To: CCL Subject: CCL:G: Basis set coefficients in Jaguar Message-Id: <-33511-070202121746-31762-egZt7QSKu18nkgup2XZMNw[]server.ccl.net> X-Original-From: "Noel M. O Boyle" Date: Fri, 2 Feb 2007 12:17:42 -0500 Sent to CCL by: "Noel M. O Boyle" [baoilleach||gmail.com] Dear CCLers, I am wondering where the basis set coefficients used by Jaguar come from, or how they are derived. For example, the coefficients and exponents used for a H atom in STO-3G are usually (e.g. in Gaussian, GAMESS): exponent coefficient 0.3425250914D+01 0.1543289673D+00 0.6239137298D+00 0.5353281423D+00 0.1688554040D+00 0.4446345422D+00 Jaguar (4.2) has the same exponents, but different coefficients: H6 1 2 0 1 25 3.4252509 0.2405014 0.4315658 H6 2 -1 0 1 25 0.6239137 0.8342385 0.4173916 H6 3 1 0 1 25 0.1688554 1.0000000 0.1877355 (I think that the final column are normalised coefficients for individual primitives, but it's hard to be sure) Does anyone know how the Gaussian/GAMESS coefficients are related to those used by Jaguar? Regards, Noel From owner-chemistry@ccl.net Fri Feb 2 17:32:01 2007 From: "Petrina Kamya petrina.k]~[gmail.com" To: CCL Subject: CCL: Error when writing wfn on gaussian 03 Message-Id: <-33512-070202115314-29719-YFhVYmupf9miDiQXlN/oKA . server.ccl.net> X-Original-From: "Petrina Kamya" Date: Fri, 2 Feb 2007 11:53:10 -0500 Sent to CCL by: "Petrina Kamya" [petrina.k_+_gmail.com] Hi, I am trying to write a wfn of a system that has 118 atoms. The job terminates successfully however when I try to open the wfn file using AIM 2000 I get an error message that says 'illegal primitive centre'. When I looked in the log file from the calculation I noticed that when the Eigenvalues are being calculated, after the 999th eigenvalue, there are 'stars' in the place of numbers. Please see below: 999 4PY 0.76339 0.15138 *** 4PZ 0.21947 0.21647 *** 5XX 0.03700 0.00049 *** 5YY -0.05772 0.00006 *** 5ZZ 0.01998 0.00153 *** 5XY -0.01770 0.00140 *** 5XZ -0.05053 -0.00123 *** 5YZ -0.03949 -0.00136 *** 79 C 1S -0.00532 -0.00030 *** 2S -0.02011 0.01378 etc... Has anyone seen this problem before, and if so,would you know how to circumvent it? Thank you! Petrina From owner-chemistry@ccl.net Fri Feb 2 18:15:00 2007 From: "Frank Neese neese*thch.uni-bonn.de" To: CCL Subject: CCL:G: New ORCA Version Message-Id: <-33513-070202180726-25960-f4LV2Dbs3gGyu38QZflnmg{=}server.ccl.net> X-Original-From: Frank Neese Content-Type: text/plain; charset="us-ascii"; format=flowed Date: Sat, 03 Feb 2007 00:06:49 +0100 Mime-Version: 1.0 Sent to CCL by: Frank Neese [neese()thch.uni-bonn.de] Dear CCL'ers, we are happy to announce that we have just uploaded a new version of the ORCA program onto our hompage: http://www.thch.uni-bonn.de/tc/orca/ ORCA is an easy-to-use, efficient and general purpose electronic structure program that is free of charge for academic users. The latest version (released in binary form for windows, generic x86, optimized versions for p4, amd64/em64t and ia64) has the following new features: - Enhanced user friendliness - Much improved efficiency, in particular for RI-DFT (rewritten numerical integration scheme, modified cut-offs -> much higher efficiency; RI calculations now default to SplitRIJ with acompanying improvements in efficiency). Example: Penicilin with 42 atoms and 567 basis functions takes about 5 minutes to converge on a standard PC (~2 GHz CPU; ~13 iterations) - More reliable and usually faster convergence. - Full second order Newton-Raphson convergence in HF, DFT, and RI-DFT - DFT meta-GGA functionals (TPSS, TPSSh) - mPW functional + hybrids and double hybrids - Accurate double hybrid functional energies + gradients (B2PLYP, mPW2PLYP from Stefan Grimme's group) - Semi-empirical van der Waals corrections to DFT from Stefan Grimme's ideas (energies and gradients) - SCS-MP2 again according to Stefan Grimme's ideas - MP2 and RI-MP2 gradients, SCS-MP2 +/- COSMO and external potentials - Implementation of spin-orbit coupling and spin-spin coupling contributions to the zero-field splitting using DFT - MRCI + Spin orbit coupling - CASSCF program (+RI trafo for second order) + gradients (including "unfolded" two step procedure + very efficient CI step) - New AutoStart feature - input check on syntax lines - less output by default - RI now default for pure functionals - New optimizer keywords - Enable/disable of MO orthogonalization/renormalization - New basis sets: QZVP, QZVP/C, def2-TZVPP - Improved trajectory calculations (spectroscopic parameters for diatomics) - CIS gradients (TD-DFT (still) underway) - NRVS spectra and (ahem) - Countless bug fixes.... - we are now "banned by Gaussian" and can no longer support the interface to the Gaussian optimizer (Gau_external) that was previously available please enjoy the program - we enjoy positive and negative feedback as well as suggestions how to improve the code, all the best, Frank Neese and Frank Wennmohs on behalf of the ORCA development team