From owner-chemistry@ccl.net Mon Apr 23 05:26:01 2007 From: "ucapjcb=-=ucl.ac.uk" To: CCL Subject: CCL: MOLECULE Message-Id: <-34098-070422095835-25481-ITwqf9hzcZYTHBxE0HWfAA . server.ccl.net> X-Original-From: ucapjcb .. ucl.ac.uk Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format="flowed" Date: Sun, 22 Apr 2007 14:08:45 +0100 MIME-Version: 1.0 Sent to CCL by: ucapjcb++ucl.ac.uk I think ArgusLab is really easy to use for building molecules: http://www.planaria-software.com/ and free for windows. Quoting "neeraj misra misraneeraj[]gmail.com" : > WHAT IS THE EASIEST WAY TO BUILD A MOLECULE? > From owner-chemistry@ccl.net Mon Apr 23 08:02:00 2007 From: "Taye Beyene Demissie sene3095~!~yahoo.com" To: CCL Subject: CCL:G: frequency calculation Message-Id: <-34099-070423075115-27414-gaOP29srW/7rZgIXnEq9eQ,server.ccl.net> X-Original-From: "Taye Beyene Demissie" Date: Mon, 23 Apr 2007 07:51:11 -0400 Sent to CCL by: "Taye Beyene Demissie" [sene3095*|*yahoo.com] Dera CCL subscribers, peace for all you. I am calculating frequency of compounds which can polymerize. I used one publishe paper as a standard, but the results for the dimmers is completely different from the results on the paper. Those of you who calculated frequencies for polymers please help me if there is any method of calculation using G03(RHF and ROHF for reuced and oxidized forms) along with the minimal basis set STO-3G. If it is possible please send me related papers that used G03 to calculate frequencies(Thermodynamic properties). Thank you very much. Taye. From owner-chemistry@ccl.net Mon Apr 23 09:15:00 2007 From: "Val Gillet v.gillet(0)sheffield.ac.uk" To: CCL Subject: CCL: Reminder: Fourth Joint Sheffield Conference on Chemoinformatics Message-Id: <-34100-070423091251-23885-9u4y63jukxpa1sb35jZX1g(!)server.ccl.net> X-Original-From: "Val Gillet" Date: Mon, 23 Apr 2007 09:12:46 -0400 Sent to CCL by: "Val Gillet" [v.gillet : sheffield.ac.uk] Fourth Joint Sheffield Conference on Chemoinformatics. University of Sheffield, UK, 18th-20th June 2007. The deadline of April 30th for Early Bird Registration is fast approaching after which the registration fees will increase. Also, note that there is a limit of 200 delegates at the meeting and that we expect to reach capacity soon. Please respond quickly to secure a place. See http://cisrg.shef.ac.uk/shef2007. From owner-chemistry@ccl.net Mon Apr 23 09:49:01 2007 From: "renee~~p.lodz.pl" To: CCL Subject: CCL:G: Basis sets for ONIOM in G03 Message-Id: <-34101-070423040911-18723-tlvfyTwp/KULOfHT0EValw]^[server.ccl.net> X-Original-From: renee*o*p.lodz.pl Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-2 Date: Mon, 23 Apr 2007 09:01:35 +0200 (CEST) MIME-Version: 1.0 Sent to CCL by: renee^p.lodz.pl Hi Rich, Below is a sample input file as an answer to your second question. %chk=trpfs.chk # opt oniom=(UBVP86/gen:amber) nosymm geom=connectivity UBVP86/gen -4 2 0 2 0 2 C-CT--0.366200 -1 -2.437041 -5.543066 -10.826837 L C-C-0.597200 -1 -0.914041 -5.543066 -10.826837 L O-O--0.567900 -1 -0.315041 -4.467066 -10.826837 L N-N--0.415700 0 -0.275936 -6.710835 -10.815907 L C-CT--0.002400 0 1.186333 -6.842008 -10.692168 L C-C-0.597300 0 1.850383 -7.323581 -11.990024 L O-O--0.567900 0 1.264107 -8.098150 -12.747263 L C-CT--0.034300 0 1.519423 -7.810478 -9.542372 L C-CA-0.011800 0 1.601905 -7.230299 -8.139273 L C-CA--0.125600 0 2.307892 -7.955621 -7.160770 L C-CA--0.125600 0 1.023088 -5.990228 -7.793157 L C-CA--0.170400 0 2.438326 -7.450623 -5.858094 L C-CA--0.170400 0 1.152269 -5.486261 -6.489104 L C-CA--0.107200 0 1.857953 -6.217526 -5.520535 L N-N--0.415700 -1 3.107959 -6.910066 -12.207837 L C-CT--0.149000 -1 3.954959 -7.421066 -13.273837 L H-HC-0.029500 0 2.496156 -8.251061 -9.749440 L H-HC-0.029500 0 0.800574 -8.631344 -9.540203 L H-HA-0.133000 0 2.758044 -8.907206 -7.402599 L H-HA-0.133000 0 0.474252 -5.397603 -8.505712 L H-HA-0.143000 0 2.971091 -8.019961 -5.108250 L H-HA-0.143000 0 0.694557 -4.541201 -6.232621 L H-HA-0.129700 0 1.938561 -5.846961 -4.507998 L H-H1-0.097800 0 1.628690 -5.872444 -10.457019 L .... C-CT--0.182500 0 2.431483 7.538542 4.971446 L N-N--0.415700 -1 2.227959 10.539934 6.141163 L C-CT--0.149000 -1 2.582959 11.943934 6.306163 L Fe-FE-0.749 0 -0.729426 2.283450 0.503639 H C-CA--0.528 0 -3.389884 1.649905 -1.364012 H C-CA--0.170 0 1.153828 3.134682 -2.021034 H C-CA--0.089 0 0.852252 4.317127 2.696841 H C-CA--0.266 0 -1.402770 0.072411 2.793948 H N-N6--0.079 0 -1.090184 2.499182 -1.258950 H C-C8-0.284 0 -2.314510 2.246503 -1.959011 H C-CH1--0.397 0 -2.123284 2.480274 -3.374919 H C-C2-0.285 0 -0.777722 2.721954 -3.570160 H C-C9--0.079 0 -0.132761 2.743906 -2.272037 H C-CT2--0.542 0 -0.000824 2.967699 -4.848551 L H-H6 961 C-CT2-0.320 0 -3.207643 2.383069 -4.449323 L H-H6 960 C-CT2--0.230 0 -3.301904 0.992073 -5.070078 L C-CO4-0.851 0 -4.366504 0.922249 -6.147601 L O-OC3--0.830 0 -4.595599 1.892048 -6.877398 L O-OC3--0.830 0 -5.043065 -0.090521 -6.284178 L N-N9-0.031 0 0.676060 3.498059 0.363421 H C-C9--0.069 0 1.542486 3.564017 -0.731039 H C-C3-0.141 0 2.609450 4.440800 -0.450249 H C-C4--0.044 0 2.409429 4.925239 0.862352 H C-C8--0.114 0 1.222412 4.341947 1.331851 H C-CT2--0.312 0 3.696116 4.852446 -1.410160 L H-H6 971 C-CD--0.058 0 3.269766 5.724960 1.750965 L H-H6 972 C-CM--0.491 0 3.974752 6.842915 1.462459 L .... [blank line] connectivity [blank line] c 0 ! c def-SV(P) (7s4p1d) / [3s2p1d] {511/31/1} s 5 1.00 1238.4016938 0.54568832082E-02 186.29004992 0.40638409211E-01 42.251176346 0.18025593888 11.676557932 0.46315121755 3.5930506482 0.44087173314 s 1 1.00 0.40245147363 1.0000000000 s 1 1.00 0.13090182668 1.0000000000 p 3 1.00 9.4680970621 0.38387871728E-01 2.0103545142 0.21117025112 0.54771004707 0.51328172114 p 1 1.00 0.15268613795 1.0000000000 d 1 1.00 0.80000000000 1.0000000000 **** n 0 ! n def-SV(P) (7s4p1d) / [3s2p1d] {511/31/1} s 5 1.00 1712.8415853 -0.53934125305E-02 257.64812677 -0.40221581118E-01 58.458245853 -0.17931144990 16.198367905 -0.46376317823 5.0052600809 -0.44171422662 s 1 1.00 0.58731856571 1.0000000000 s 1 1.00 0.18764592253 1.0000000000 p 3 1.00 13.571470233 -0.40072398852E-01 2.9257372874 -0.21807045028 0.79927750754 -0.51294466049 p 1 1.00 0.21954348034 1.0000000000 d 1 1.00 1.0000000000 1.0000000000 **** h 0 ! h def-SV(P) (6s) / [2s] {51} s 3 1.00 13.010701000 0.19682158000E-01 1.9622572000 0.13796524000 0.44453796000 0.47831935000 s 1 1.00 0.12194962000 1.0000000000 **** o 0 ! o def-SV(P) (11s3p) / [5s1p] {31511/3} s 5 1.00 2266.1767785 -0.53431809926E-02 340.87010191 -0.39890039230E-01 77.363135167 -0.17853911985 21.479644940 -0.46427684959 6.6589433124 -0.44309745172 s 1 1.00 0.80975975668 1.0000000000 s 1 1.00 0.25530772234 1.0000000000 p 3 1.00 17.721504317 0.43394573193E-01 3.8635505440 0.23094120765 1.0480920883 0.51375311064 p 1 1.00 0.27641544411 1.0000000000 d 1 1.00 1.2000000000 1.0000000000 **** s 0 ! s def-SV(P) (15s4p1d) / [5s2p1d] {51153/31/1} s 5 1.00 9184.9303010 -0.22294387756E-02 1381.5105503 -0.16683029937E-01 313.87147580 -0.75262436116E-01 88.053870623 -0.19376827038 27.039914905 -0.17718020803 s 3 1.00 45.648731303 -0.10736062573 4.9664522326 0.65066293018 2.0116242047 0.59712155354 s 1 1.00 0.35661077013 1.0000000000 s 1 1.00 0.13507221477 1.0000000000 p 5 1.00 261.98233439 -0.92729929822E-02 61.306894736 -0.66547669241E-01 19.103729887 -0.24828595903 6.6567720378 -0.48703847402 2.3959635161 -0.39337850312 p 1 1.00 0.61776161679 1.0000000000 p 1 1.00 0.16993376871 1.0000000000 d 1 1.00 0.55000000000 1.0000000000 **** fe 0 ! fe def-SV(P) (19s7p1d) / [6s3p1d] {531163/511/1} s 6 1.00 60923.640643 0.14302254466E-02 9147.8893982 0.10958790038E-01 2081.3505927 0.54332554248E-01 587.55977067 0.18884995009 191.09043990 0.38253069946 65.732730112 0.29308335984 s 3 1.00 127.25891928 -0.10964564925 14.830913010 0.64387631332 6.0653307408 0.45472347323 s 3 1.00 10.449943710 -0.22539639952 1.7245228003 0.72164398156 0.71772177325 0.44985492922 s 1 1.00 0.91449828308E-01 1.0000000000 s 1 1.00 0.33706691021E-01 1.0000000000 p 5 1.00 773.43750995 0.94325735144E-02 182.15149714 0.70029620575E-01 57.547272758 0.26993651996 20.614988935 0.52700011047 7.6348557890 0.34284148028 p 3 1.00 3.8719327990 0.33974402988 1.4924724132 0.56842594005 0.56061284958 0.23649365839 p 4 1.00 38.968133419 0.27879664382E-01 10.800067078 0.14858319982 3.6136457999 0.36905479496 1.2129967888 0.47745100883 d 1 1.00 0.36524393170 0.31418142304 p 1 1.00 0.13491500000 1.0000000000 **** [blank line] Hope this will help you, **** Renata Kwiecien, Ph.D. Université de Nantes > Sent to CCL by: "Richard Huhn" [huhnra-$-mit.edu] > I am using Gaussian 03 to do ONIOM calculations of some very large > molecules containing transition metals. I have a two-part question: > > Is it possible to use two DFT methods in an ONIOM calculation? For > example, the high level could use a different functional than the lower > level(s); or, the high level could use a larger basis set than the lower > level(s). > > If either of these cases are possible, how does one input a general basis > set (as with the GenECP keyword) that will supply the different basis sets > for the different levels? This problem is not encountered in the examples > in the G03 manual, in which only MM or semi-empirical methods are used as > the low layer. An example of a working input file would be greatly > helpful. Thank you for any help or pointers! > > Rich Huhn> > > > From owner-chemistry@ccl.net Mon Apr 23 10:42:00 2007 From: "James Gary Prudhomme jprudhomme[A]healthtech.com" To: CCL Subject: CCL: Registration Deadline: CHI's Structure-Based Design Conference Message-Id: <-34102-070423104036-10729-gG2tyRiavE0YdQF3M/CbWw{}server.ccl.net> X-Original-From: "James Gary Prudhomme" Date: Mon, 23 Apr 2007 10:40:33 -0400 Sent to CCL by: "James Gary Prudhomme" [jprudhomme|,|healthtech.com] Registration Discount Deadline is April 27, 2007. CHI's Structure-Based Design June 6-8, 2007 World Trade Center, Boston, MA Register and view full details at: www.healthtech.com/2007/SBD Registration rates do increase after April 27. From owner-chemistry@ccl.net Mon Apr 23 11:27:01 2007 From: "Yousef Sharifi ysharifi*o*gmail.com" To: CCL Subject: CCL:G: Surface reaction/deposition Message-Id: <-34103-070423112546-3020-zgnCPK5oXeBrT8x/ROY91w++server.ccl.net> X-Original-From: "Yousef Sharifi" Date: Mon, 23 Apr 2007 11:25:43 -0400 Sent to CCL by: "Yousef Sharifi" [ysharifi(0)gmail.com] I like to study adsorption of CO on Pd(111) surface, is it possible to do it in Gaussian 03? If yes, do you have a sample file that I can use as start up? Thanks Yousef From owner-chemistry@ccl.net Mon Apr 23 13:12:01 2007 From: "Ben Shepler bcshepl^emory.edu" To: CCL Subject: CCL: Relativistic and non-relativistic ECPs Message-Id: <-34104-070420134734-30951-IXX7ndskXq28f7gGDhMwWA[]server.ccl.net> X-Original-From: Ben Shepler Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Date: Fri, 20 Apr 2007 13:19:26 -0400 Mime-Version: 1.0 (Apple Message framework v752.3) Sent to CCL by: Ben Shepler [bcshepl||emory.edu] Hi Caroline, This should be no problem. The code will not treat the ECPs any differently. -Ben On Apr 20, 2007, at 5:39 AM, Caroline Norris cn29.:.sussex.ac.uk wrote: > > Sent to CCL by: "Caroline Norris" [cn29*|*sussex.ac.uk] > > Dear CCL, > I was wondering if it's vaild to use a mixture of relativistic > and non-relativistic ECPs within the same calculation? Currently > I'm studying netural vanadium oxide and would like to use a > relativistic ECP on the metal, but a non-relativistic ECP on the > oxygen. Is this valid? Or will it cause complications within the > calculation? > Any comments would be greatly appreciated, > Caroline Norris > > > > -= 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/ > > Search Messages: http://www.ccl.net/htdig (login: ccl, Password: > search)> > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+- > +-+-+ > > > > From owner-chemistry@ccl.net Mon Apr 23 13:46:00 2007 From: "Troy Wymore wymore/a\psc.edu" To: CCL Subject: CCL: QM/MM Workshop at PSC/NRBSC Message-Id: <-34105-070423131616-11957-wjT7iKk1U7JHwX+cYyM5AA]~[server.ccl.net> X-Original-From: "Troy Wymore" Date: Mon, 23 Apr 2007 13:16:11 -0400 Sent to CCL by: "Troy Wymore" [wymore]*[psc.edu] Methods and Applications of Hybrid QM/MM Simulations to Biomolecular Systems Date: September 10-13, 2007 Application Deadline: August 3, 2007 Place: National Resource for Biomedical Supercomputing Pittsburgh Supercomputing Center Primary Instructor: Dr. Martin J. Field (Institut de Biologie Structurale) Website: http://www.nrbsc.org/sb/workshops/qmmm.php Description: The workshop will explore computational approaches for the simulation of enzymatic reactions. The course will present the relevant theoretical background including ab initio and semiempirical molecular orbital methods, density functional theory, molecular mechanics force fields, hybrid Quantum Mechanical/Molecular Mechanical potential energy functions, and simulation techniques on high performance computers. Case studies based on determining the free energy profile for a reaction in the gas phase, in water (using both implicit and explicit solvent) and in an enzyme active site will be presented using primarily the DYNAMO library. Experience with DYNAMO is helpful but not a prerequisite for attendance. The workshop is designed for graduate students, post-doctoral researchers and faculty in computational biophysics and physical organic chemistry who have some experience with computational chemistry methods and seek to enhance their capabilities to include the modeling of enzymatic reactions. Participants are encouraged to discuss and work on biomolecular systems from their own research during the workshop. More details can be found at the workshop website given above. Any questions can be directed to Dr. Troy Wymore (wymore~!~psc.edu) From owner-chemistry@ccl.net Mon Apr 23 15:22:01 2007 From: "Gustavo Seabra gustavo.seabra:gmail.com" To: CCL Subject: CCL: Relativistic and non-relativistic ECPs Message-Id: <-34106-070423151301-3332-SPeJcJZXvF/1F90YGWEP3Q**server.ccl.net> X-Original-From: Gustavo Seabra Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Mon, 23 Apr 2007 15:12:35 -0400 MIME-Version: 1.0 Sent to CCL by: Gustavo Seabra [gustavo.seabra-.-gmail.com] Caroline Norris cn29.:.sussex.ac.uk wrote: > Sent to CCL by: "Caroline Norris" [cn29*|*sussex.ac.uk] > > Dear CCL, > I was wondering if it's vaild to use a mixture of relativistic and non-relativistic ECPs within the same calculation? Currently I'm studying netural vanadium oxide and would like to use a relativistic ECP on the metal, but a non-relativistic ECP on the oxygen. Is this valid? Or will it cause complications within the calculation? > Any comments would be greatly appreciated, > Caroline Norris Hi, Although it may be possible to do (the programs are unlikely to complain), you need to be very careful. Basis sets are ususally designed to work together, and mixing/matching basis sets can lead to unbalanced basis sets. Gustavo. From owner-chemistry@ccl.net Mon Apr 23 16:07:00 2007 From: "zhendong zhao zzhao_._olemiss.edu" To: CCL Subject: CCL: Molecule Optimization Message-Id: <-34107-070423154014-12206-+oDO7YHSS+xBWwf2EYRiIg.:.server.ccl.net> X-Original-From: zhendong zhao Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII Date: Mon, 23 Apr 2007 14:40:21 -0500 Mime-Version: 1.0 Sent to CCL by: zhendong zhao [zzhao(-)olemiss.edu] Dear CCL subscribers, I am doing some calculations on small molecule geometry optimization. I encounter such a problem. A molecule geometry is stable under HF, MP2, CCSD and DFT theoritical methods, but it is unstable under CAS, the optimized geometry goes to another configuration. All calculations use 6-31G(d,p) basis set. I am wondering some one can give me some advices and suggest some good references that discuss why CAS fails but others do not in optimization? Appreciate your help. Zhendong From owner-chemistry@ccl.net Mon Apr 23 17:17:01 2007 From: "Kirk Peterson kipeters|-|wsu.edu" To: CCL Subject: CCL: Relativistic and non-relativistic ECPs Message-Id: <-34108-070423171500-27080-h/982r25HND5dlc134li0w||server.ccl.net> X-Original-From: Kirk Peterson Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Date: Mon, 23 Apr 2007 13:20:51 -0700 Mime-Version: 1.0 (Apple Message framework v752.2) Sent to CCL by: Kirk Peterson [kipeters _ wsu.edu] Caroline, as long as you use the basis set(s) that accompanies the ECP, whether it be a relativistic one or nonrelativistic, this shouldn't be a problem. I'm assuming of course that the basis set for V and the one for oxygen are of similar quality, i.e., both double-zeta or triple- zeta, etc. Probably this is more what Gustavo refers to below. More of a concern for me is using an ECP on a 1st row atom at all. This has been shown to often lead to very large errors (there is a recent Chem. Phys. Lett. paper by Cundari et al. that shows this dramatically for transition metal species). Using a standard all- electron, non-relativistic basis set on oxygen with an ECP-based combination on V would seem to be prefered. just my two cents, Kirk On Apr 23, 2007, at 12:12 PM, Gustavo Seabra gustavo.seabra:gmail.com wrote: > > Sent to CCL by: Gustavo Seabra [gustavo.seabra-.-gmail.com] > Caroline Norris cn29.:.sussex.ac.uk wrote: >> Sent to CCL by: "Caroline Norris" [cn29*|*sussex.ac.uk] >> >> Dear CCL, >> I was wondering if it's vaild to use a mixture of relativistic >> and non-relativistic ECPs within the same calculation? Currently >> I'm studying netural vanadium oxide and would like to use a >> relativistic ECP on the metal, but a non-relativistic ECP on the >> oxygen. Is this valid? Or will it cause complications within the >> calculation? >> Any comments would be greatly appreciated, >> Caroline Norris > Hi, > > Although it may be possible to do (the programs are unlikely to > complain), you need to be very careful. Basis sets are ususally > designed to work together, and mixing/matching basis sets can lead > to unbalanced basis sets. > > Gustavo. > > > > -= This is automatically added to each message by the mailing > script =- > To recover the email address of the author of the message, please > changehttp://www.ccl.net/chemistry/ > sub_unsub.shtmlConferences: http://server.ccl.net/ > chemistry/announcements/conferences/ > > Search Messages: http://www.ccl.net/htdig (login: ccl, Password: > search)> > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+- > +-+-+ > > From owner-chemistry@ccl.net Mon Apr 23 18:32:01 2007 From: "Vedbar Singh khadka vedbar ~ gmail.com" To: CCL Subject: CCL:G: Regarding calculation of second hyperpolarizability using Gaussian Message-Id: <-34109-070423181712-21631-D4wf5evuzSHrKN9jYUzeHQ#,#server.ccl.net> X-Original-From: "Vedbar Singh khadka" Date: Mon, 23 Apr 2007 18:17:07 -0400 Sent to CCL by: "Vedbar Singh khadka" [vedbar!=!gmail.com] Dear CCL, Is it possible to get the second hyperpolarizability directly using ZINDO and sum-over-states (SOS) in Gaussian 03W or we need to do some calculation with the result obtained from Gaussian 03W? Please let me know if you have any procedures to obtain the second hyperpolarizability using Gaussian. Vedbar