From owner-chemistry@ccl.net Wed Feb 22 02:27:01 2006 From: "Mikael Johansson mikael.johansson[]helsinki.fi" To: CCL Subject: CCL: More imaginary freqs upon isotope substitution Message-Id: <-30970-060222022538-17167-bpIXV2T4DnZqxEt+U50tGw-#-server.ccl.net> X-Original-From: Mikael Johansson Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed Date: Wed, 22 Feb 2006 09:25:23 +0200 (EET) MIME-Version: 1.0 Sent to CCL by: Mikael Johansson [mikael.johansson*helsinki.fi] Hello All! I recently finished a numerical frequency calculation on a largish (from a DFT point of view) part of a protein at BP86 level (with Turbomole). With normal atomic masses, it turned out I still had 2 imaginary frequencies (~40 cm-1). But when I increased the mass of three carbons at the edge of the structure to 200 au, I suddenly had 3 imaginary frequencies, one very small, -7 cm-1. My question is, is isotope substitution supposed to be able to change the number of imaginary frequencies? Is there anything that can be deduced about the system from this effect (except that it didn't converge all the way to a minimum :-) Have a nice day, Mikael J. http://www.helsinki.fi/~mpjohans/ From owner-chemistry@ccl.net Wed Feb 22 08:26:01 2006 From: "Vincent Xianlong Wang xloongw-#-yahoo.com" To: CCL Subject: CCL: 6-31G basis set Message-Id: <-30971-060222024613-28855-0JmAIz969NwWaNOyo3GRzw[]server.ccl.net> X-Original-From: Vincent Xianlong Wang Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-1 Date: Tue, 21 Feb 2006 22:46:07 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: Vincent Xianlong Wang [xloongw .. yahoo.com] --- "Sengen Sun sengensun()yahoo.com" wrote: > Sent to CCL by: Sengen Sun [sengensun+*+yahoo.com] > > I would think a molecule of 10 residue peptides is > too > big to use anything other than HF/3-21G. > > You may try some pure DFT methods (I have very > limited > expereience and cannot tell anything more). But it > might take forever to finish your calculation with > B3LYP. My feeling is that it might not take forever, but only a few days, for a 10 residue peptide at the B3LYP level, using the 6-31G(d) basis set at today's computer condition. Here today's computer condition, I refer to Dell Precision Workstation 650 (dual cpus of 3.06 GHz Xeon). Anyway, a test calcuation will give the answer. Best regards, Vincent > B3LYP is much more time efficient than MP2, > especially > when MP2 requires a very large basis set. > MP2 works significantly better as the basis set gets > larger, but you often cannot afford the cost of your > time. > > Good luck. > > Sengen > > > From: Goedele Roos > > Subject: CCL: 6-31G basis set > > Date: Tue, 21 Feb 2006 09:36:11 +0100 (CET) > > > > > -------------------------------------------------------------------------------- > > > > Sent to CCL by: Goedele Roos [groos/./vub.ac.be] > > I have a large system (a 10-residue peptide) and > I > > was recommended to use rather > > HF/3-21G than HF/6-31G, because -so was said to > me- > > for geometry optimiations, > > hf/6-31G works worser than HF/3-21G, unless there > > were put some polarization > > functions on it... > > Is this coirrect, and why? > > Another point: there is no point in using larger > > basis set with b3LYP. But which > > other functional would you recommand than, with > > which > > larger basis sets are > > usefull? > > Best regards, goedele > > > > > > > > __________________________________________________ > > Do You Yahoo!? > > Tired of spam? Yahoo! Mail has the best spam > > protection around > > http://mail.yahoo.com > > > > > __________________________________________________ > Do You Yahoo!? > Tired of spam? Yahoo! Mail has the best spam > protection around > http://mail.yahoo.com > > > > -= 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 > look up the X-Original-From: line in the mail > header.> > E-mail to administrators: CHEMISTRY-REQUEST[*]ccl.net > or use> > Before posting, check wait time at: > http://www.ccl.net> Conferences: > http://server.ccl.net/chemistry/announcements/conferences/ > > Search Messages: http://www.ccl.net/htdig (login: > ccl, Password: search) > > If your mail bounces from CCL with 5.7.1 error, > check:> > RTFI: > http://www.ccl.net/chemistry/aboutccl/instructions/> > > > __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com From owner-chemistry@ccl.net Wed Feb 22 10:42:00 2006 From: "Jens Thomas j.m.h.thomas(!)dl.ac.uk" To: CCL Subject: CCL: Release of GAMESS-UK version 7.0 Message-Id: <-30972-060222103812-2270-tIpruZfN/d9AYvIOb9Skmg:_:server.ccl.net> X-Original-From: Jens Thomas Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 22 Feb 2006 15:38:03 +0000 MIME-Version: 1.0 Sent to CCL by: Jens Thomas [j.m.h.thomas^-^dl.ac.uk] This email is to announce the release of version 7.0 of GAMESS-UK. GAMESS-UK is a general purpose ab initio molecular electronic structure program for performing SCF-, DFT- and MCSCF-gradient calculations, together with a variety of techniques for post Hartree-Fock calculations. For information on the capabilities and functionality of GAMESS-UK, please visit the CFS website at: http://www.cfs.dl.ac.uk The code is freely available to academic users in the UK. Users of the code that hold a current licence are entitled to receive the updated version of the code. New users, or users whose licence has expired, should apply for a licence by sending an email to: gamess_uk_contact~!~dl.ac.uk A few of the changes introduced in this latest release of the code include: GAMESS-UK finally has its own graphical user interface in the CCP1GUI; a free prototype interface that also includes interfaces to Dalton and Mopac, and with an interface for Molpro in development. For more information on the CCP1GUI, please visit: http://www.cse.clrc.ac.uk/qcg/ccp1gui/index.shtml The Atomic Guess has been extended so it now possible to specify the per-atom electron configuration or charge for the atomic guess, as well as the alpha and beta populations for UHF calculations. Fermi-dirac smearing has been implemented for filling molecular orbitals. Within the newscf_f90 driver, users are now able to define their own SCF convergence schemes for problematic cases. The DFT module has been updated with a range of new functionals, and far more flexible DFT grid specifications are now possible. The MRDCI code is now open-ended in the number of basis functions that can be used, and the Configuration Interaction Transformation between AO and MO basis' has been extended to G functions. MR-ACPF (Multireference Averaged Coupled-Pair-Functional), MR-AQCC (Multi-Reference Average Quadratic Coupled-Cluster) and the CEPA0 coupled electron-pair approximation methods have been added to the MRDCI module. Spherical harmonic basis sets for D,F and G functions can be used within the Valence Bond code and a simple solvation model has also been implemented within this module. A new distributed-data HF and DFT module has been developed using MPI-based tools such as ScaLAPACK to complement the Global Array-based parallel code. A taskfarming harness has been developed for batch processing numerous small calculations on a large parallel machine. A range of new ports have added, including Macintosh OSX, Windows XP, serial and parallel versions for Linux running on AMD Opteron and Athlon, Intel Xeon, EM64T and Itanium processors, and HP-UX on Itanium, as well as for the SGI Altix. Free Windows, Macintosh and Linux demo versions are available for users who wish to try out the code. A GAMESS-UK Forum has been added to the Distributed Computing forums at: http://www.cse.clrc.ac.uk/disco/index.shtml Best wishes, The GAMESS-UK support team From owner-chemistry@ccl.net Wed Feb 22 11:17:00 2006 From: "Rebecca Wade rebecca.wade#,#eml-r.villa-bosch.de" To: CCL Subject: CCL: EMBO Practical Course on Biomolecular Simulation 2006 Message-Id: <-30973-060222035702-10656-emJzYzjKai+dLCL0wdrr4Q]|[server.ccl.net> X-Original-From: "Rebecca Wade" Date: Wed, 22 Feb 2006 03:56:57 -0500 Sent to CCL by: "Rebecca Wade" [rebecca.wade{}eml-r.villa-bosch.de] The 3rd EMBO Practical Course on Biomolecular Simulation will take place from 28th June to 4th July 2006 at the Pasteur Institute in Paris, France. The course topics will include: Molecular and Brownian dynamics simulation, Monte Carlo techniques, electrostatics, free energy calculations, QM/MM, homology modeling, drug design Course organizers: Michael Nilges (Pasteur Institute, Paris) Rebecca Wade (EML Research, Heidelberg) Course lecturers: Arnaud Blondel Valerie Daggett Konrad Hinsen Leslie Kuhn Richard Lavery Tom Simonson Alan Mark Adrian Mulholland Anna Tramontano Registration forms and course details are at: http://cwp.embo.org/pc06-45/ Registration deadline: 1 April 2006 From owner-chemistry@ccl.net Wed Feb 22 11:52:00 2006 From: "John McKelvey jmmckel*attglobal.net" To: CCL Subject: CCL: DFT results as a function of Basis sets Message-Id: <-30974-060222103201-1839-eQDf/0HnEqikT/Cap9txwA^-^server.ccl.net> X-Original-From: John McKelvey Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 22 Feb 2006 10:26:51 -0500 MIME-Version: 1.0 Sent to CCL by: John McKelvey [jmmckel!=!attglobal.net] CCLers I attended a talk where the speaker suggested that H-bond effect /differences/ between functionals [unspecified] tended to become small as quality of basis set quality is increased. Can anyone comment/verify/recommend-a-paper related to this, or if more general, other situations where this might be the case also? Thanks! John McKelvey From owner-chemistry@ccl.net Wed Feb 22 14:31:00 2006 From: "Mike Towler mike_towler|-|postmaster.co.uk" To: CCL Subject: CCL: QMC workshop/summer school - Tuscany Message-Id: <-30975-060222112219-9382-Wd6HoKTgIUg3tbYrWvCE2w]-[server.ccl.net> X-Original-From: "Mike Towler" Date: Wed, 22 Feb 2006 11:22:19 -0500 Sent to CCL by: "Mike Towler" [mike_towler{:}postmaster.co.uk] CCL subscribers interested in using the quantum Monte Carlo method in their quantum chemistry research may find tempting the following two announcements for a workshop and a school for Summer 2006 in Tuscany. There is no particular deadline for registration for either event, but both on-site accommodation and the number of unfilled places are limited, so prompt expressions of interest are recommended. WORKSHOP ANNOUNCEMENT Quantum Monte Carlo in the Apuan Alps II ======================================== Sat 22nd July - Sat 29th July 2006 The Towler Institute, via del Collegio, Vallico Sotto, Tuscany, Italy www.tcm.phy.cam.ac.uk/~mdt26/tti/tti.html Following last year's successful informal workshop (detailed report available on the above website) the Cambridge University Theory of Condensed Matter group is organizing a second International Workshop to discuss the development and application of the continuum quantum Monte Carlo method in condensed matter physics and quantum chemistry. The conference will take place in our 15th Century Tuscan monastery in the Apuan Alps. The format adopted for these events involves formal presentations being restricted to the mornings, with the afternoons and evenings left free for relaxed discussion whilst participating in mountain walks and other healthy outdoor activities. This year's expanded conference will involve up to 25 people, all accommodated on site. Given the limited space most speakers will be specifically invited, but other people who feel they have something to contribute and wish to attend the event should contact Mike Towler (mdt26 at cam.ac.uk) for further details. Confirmed speakers so far: Richard Needs, Cyrus Umrigar, Lubos Mitas, Alan Aspuru-Guzik, Ian Snook, Paolo Umari, Jeff Grossman, Dario Bressanini, Matthew Foulkes, Andrew Williamson, Neil Drummond, Pablo Lopez Rios, Alexander Badinski, Andrea Ma, Matthew Brown, Idoia de Gurtubay, Nick Hine, Ryo Maezono, John Trail, Graham Spink, Samantha Keil, Mike Towler. SUMMER SCHOOL ANNOUNCEMENT Quantum Monte Carlo and the CASINO Program ========================================== Sunday 30th July - Sunday 6th August The Towler Institute, via del Collegio, Vallico Sotto, Tuscany, Italy www.tcm.phy.cam.ac.uk/~mdt26/tti/tti.html August 2006 will see the first Summer School "Quantum Monte Carlo and the CASINO program" hosted by the Cambridge University Theory of Condensed Matter Group in their monastery in the Tuscan Apuan Alps. This course is designed for young scientists with no previous experience in quantum Monte Carlo methodology, although anyone interested is welcome to take part. Many-body quantum theory provides the key ideas for understanding the behaviour of materials at the level of the electrons which bind the atoms together. Describing the complex behaviour of materials at the atomic level requires a sophisticated description of the correlated motion of the electrons, which can be achieved using ab initio computational methods. The quantum Monte Carlo method has many attractive features for probing the electronic properties of real systems. It is an explicitly many-body method which takes electron correlation into account from the outset. It is capable of giving highly accurate results while at the same time exhibiting a very favourable scaling of computational cost with system size. Over the last 15 years, the Cambridge group have been researching QMC methods and we have created a powerful, general computer program - CASINO - to carry them out. The school will focus both on basic theory and on more advanced practical techniques, and will include a thorough introduction to the CASINO program. Instructors will include the authors of the CASINO program (Prof. Richard Needs, Dr. Mike Towler, Dr. Neil Drummond and Dr. Pablo Lopez Rios), along with a number of other speakers to to be confirmed. The monastery is a delightful 15th century building with an attached church which is used as a lecture theatre. It is fully equipped with state of the art presentation and computer technology. All accommodation is on-site and time will be set aside for mountain walking, caving, swimming in thermal baths, eating in fabulous local restaurants, and similar activities. The cost of the school for one week including accommodation will be around 400 GBP. Participants would need to arrange a flight to Pisa airport from where onward transportation will be arranged. Interested parties should contact Mike Towler (mdt26 at cam.ac.uk) for registration and further details (replace the 'at' with an -*- sign). QUOTES FROM LAST YEAR'S EVENTS ============================== "It was easily the most enjoyable conference I have ever attended, and in the most beautiful location" "Each of the days in Tuscany was amazingly wonderful, can I ever imagine Italian lovely place without any crowd of Japanese tourists?" [from a Japanese person] "Thank you many times for the terrific time we (and in particular me) had at the TTI. I think that was my summer highlight for this year, and I suppose that it was the perfect atmosphere for our QMC family to grow closer together!!" "Very educational, very relaxing, just great.. Thanks for this memorable week in Tuscany" From owner-chemistry@ccl.net Wed Feb 22 17:25:00 2006 From: "RICHARD JILL WOOD rwoodphd/a\msn.com" To: CCL Subject: CCL: superimposing molecules Message-Id: <-30976-060222162703-10184-s0jrMEsDJcN5WUWzoWsWzQ!^!server.ccl.net> X-Original-From: "RICHARD JILL WOOD" Content-Type: text/plain; format=flowed Date: Wed, 22 Feb 2006 21:26:55 +0000 Mime-Version: 1.0 Sent to CCL by: "RICHARD JILL WOOD" [rwoodphd^_^msn.com] Hi all, Is there a free program out there that runs under Windows and will allow one to open two pdb files simultaneously, superimpose one on the other easily, and then save the coordinates of the molecule that has been moved? Thanks in advance, Richard _________________________________________________________________ Don’t just search. Find. Check out the new MSN Search! http://search.msn.click-url.com/go/onm00200636ave/direct/01/ From owner-chemistry@ccl.net Wed Feb 22 18:38:00 2006 From: "Ivanciuc, Ovidiu I. oiivanci]-[utmb.edu" To: CCL Subject: CCL: superimposing molecules Message-Id: <-30977-060222182625-7448-pUo12+yGB+SLoLlbQ9rXFA-,-server.ccl.net> X-Original-From: "Ivanciuc, Ovidiu I." Content-Class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="Windows-1252" Date: Wed, 22 Feb 2006 17:26:14 -0600 MIME-Version: 1.0 Sent to CCL by: "Ivanciuc, Ovidiu I." [oiivanci^utmb.edu] >>Is there a free program out there that runs under >> Windows and will allow one >>to open two pdb files simultaneously, >> superimpose one on the other easily, >>and then save the coordinates of the molecule that has been moved? For proteins, there are several posibilities: - use the server CE, http://cl.sdsc.edu/ce.html, and upload the two PDB files - download ProFit for Windows, http://www.bioinf.org.uk/software/ - download PyMol, http://pymol.sourceforge.net/ - download MolMol, http://hugin.ethz.ch/wuthrich/software/molmol/index.html If you want to align chemical compounds, then search in the CCL software list, for a quaternion fit program, or send me an Email. Regards, Ovidiu From owner-chemistry@ccl.net Wed Feb 22 19:39:00 2006 From: "Ross Walker ross|-|rosswalker.co.uk" To: CCL Subject: CCL: superimposing molecules Message-Id: <-30978-060222193113-4125-vS6wvg2lmmd8TdzBoFhOgw.@.server.ccl.net> X-Original-From: "Ross Walker" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Wed, 22 Feb 2006 15:47:20 -0800 MIME-Version: 1.0 Sent to CCL by: "Ross Walker" [ross{=}rosswalker.co.uk] Dear Richard, VMD (http://www.ks.uiuc.edu/Research/vmd/) will do this for you - A tutorial that shows how to do this (section 5) is available here: http://www.rosswalker.co.uk/tutorials/amber_workshop/Tutorial_nine/index.htm All the best Ross /\ \/ |\oss Walker | Department of Molecular Biology TPC15 | | The Scripps Research Institute | | Tel: +1 858 784 8889 | EMail:- ross*o*rosswalker.co.uk | | http://www.rosswalker.co.uk | PGP Key available on request | Note: Electronic Mail is not secure, has no guarantee of delivery, may not be read every day, and should not be used for urgent or sensitive issues. > -----Original Message----- > From: owner-chemistry*o*ccl.net [mailto:owner-chemistry*o*ccl.net] > Sent: Wednesday, February 22, 2006 14:43 > To: Walker, Ross > Subject: CCL: superimposing molecules > > Sent to CCL by: "RICHARD JILL WOOD" [rwoodphd^_^msn.com] > > Hi all, > > Is there a free program out there that runs under Windows and > will allow one > to open two pdb files simultaneously, superimpose one on the > other easily, > and then save the coordinates of the molecule that has been moved? > > Thanks in advance, > Richard > > _________________________________________________________________ > Don't just search. Find. Check out the new MSN Search! > http://search.msn.click-url.com/go/onm00200636ave/direct/01/ > > > > -= 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 Wed Feb 22 21:32:00 2006 From: "Pablo F. Salazar Pablo.Salazar#%#chemail.tamu.edu" To: CCL Subject: CCL: G3B3 Atomization Energy Methane Message-Id: <-30979-060222212448-621-jWki46imozkwhXW+nCj8Ag|,|server.ccl.net> X-Original-From: "Pablo F. Salazar" Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="UTF-8" Date: Wed, 22 Feb 2006 20:24:41 -0600 MIME-Version: 1.0 Sent to CCL by: "Pablo F. Salazar" [Pablo.Salazar||chemail.tamu.edu] It is not fortuitous, it is actually much better: Apparently the singlet was used instead of the triplet for C. Also notice that the data from the log file at 0K and the G3(0K), already contains the ZPE correction . Thus, with the following energies at 0K: H -0.501087 C -37.82845 CH4 -40.458277, the atomization energy for methane at 0K is: (-37.82845+4*-0.501087)- -40.458277 = 1642.20 kJ/mol in perfect agreement with the experiment at 0K(1642.27 kJ/mol). For the atomization energy for methane at 298K, you must use the corrections listed in the log file. So the energy of a molecule (or a atom) at 298K would be: H -0.498727 C -37.82609 CH4 -40.454469 and the atomization energy for methane at 298K is: (-37.82609+4*-0.498727)- -40.454469 = 1663.2 kJ/mol also in perfect agreement with the experiment at 0K(1663.3 kJ/mol). Pablo F Salazar Department Chemical Engineering 3122 TAMU College Station, TX 77843-3122 Phone 979-862-1329 -----Original Message----- > From: "John Bushnell bushnell,+,chem.ucsb.edu" To: "Salazar, Pablo Felix " Date: Mon, 20 Feb 2006 19:43:34 -0500 Subject: CCL: G3B3 Atomization Energy Methane Sent to CCL by: John Bushnell [bushnell**chem.ucsb.edu] I'm not at all familiar with the "G3B3" method, but right off hand I would think that this is very good agreement with experiment. You show an error of 13 kJ/mol at zero K. But the calculation involves the difference of some very large numbers. The difference of only 3 kJ/mol at 298 K seems fortuitously small in fact. If enthalpies of formation could be routinely calculated to this accuracy, we wouldn't have to do so many experiments. :-) Just my offhand impression... - John On Mon, 20 Feb 2006, Roger Kevin Robinson r.robinson .. imperial.ac.uk wrote: > Sent to CCL by: Roger Kevin Robinson [r.robinson,,imperial.ac.uk] > Hi, > > I've asked about this before but i still seem to be having some > trouble. Im just using Methane as an example. > > Using G3B3 methods. > > At 298K I get > > Name G3-Energy(G3B3) ZPE > > C -37.778738 > > H -0.499671 > > CH4 -40.455401 0.043410 > > Using this values to calculate Atomization Energy > > = (-37.778738 + 4* -0.499671) - -40.455401 - 0.043410= 0.634569 = > 1666.06091 kJ/mol > > this fits in well with an experimental value of 1663.3 > > to calculate Enthalpy of formation you need the atomization Energy at 0K > as far as im aware. > > Right at 0K > > > Name G3(0K) - (G3B3) ZPE > > C -37.780154 > > H -0.501087 > > CH4 -40.458277 0.043410 > > = ( -37.780154 +4 * -0.499671) - -40.455401 - 0.043410 = 0.630365 = > 1655.02331. > > But the experimental value is 1642.27 > > Does any one know where im making the mistake ? > > Thanks Rogerhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt