From owner-chemistry@ccl.net Wed Sep 10 01:55:00 2008 From: "Renxiao Wang wangrx-*-mail.sioc.ac.cn" To: CCL Subject: CCL: The PDBbind database version 2008 is now released Message-Id: <-37735-080910013939-32720-tQhlV0G4U8YjCAzABbsooA-*-server.ccl.net> X-Original-From: "Renxiao Wang" Date: Wed, 10 Sep 2008 01:39:35 -0400 Sent to CCL by: "Renxiao Wang" [wangrx,mail.sioc.ac.cn] Dear researchers, Here we announce the release of the PDBbind database version 2008. The PDBbind database aims at providing a comprehensive collection of experimentally measured binding affinity data for all biomolecular complexes deposited in the Protein Data Bank. As a new feature of this version, all four major categories of complexes in the Protein Data Bank, including protein-ligand, nucleic acid-ligand, protein-nucleic acid, and protein-protein complexes, are considered. Binding data of a total of 4,300 complexes are included in this version, which is the largest collection of this kind in the world. The PDBbind database version 2008 is now available on the PDBbind-CN server at http://www.pdbbind.org.cn/. The basic information of each complex in PDBbind is totally open for browsing. Users are required to register under a license agreement in order to utilize the full functions provided on this web site. Registration is free of charge to all academic and industrial users. Best regards, Prof. Renxiao Wang Shanghai Institute of Organic Chemistry Chinese Academy of Sciences Shanghai, P. R. China From owner-chemistry@ccl.net Wed Sep 10 05:43:00 2008 From: "Rainer Koch rainer.koch ~~ uni-oldenburg.de" To: CCL Subject: CCL: 2-methyl-tetrahydropyran Message-Id: <-37736-080910045059-22606-8sdgjAkOmJSYgSgCtUH87g*server.ccl.net> X-Original-From: Rainer Koch Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 10 Sep 2008 09:50:44 +0200 MIME-Version: 1.0 Sent to CCL by: Rainer Koch [rainer.koch||uni-oldenburg.de] Dear Ghislain, AM1 (and other semiempirical methods) severely underestimates steric repulsion. Check the original literature on AM1 (JACS, 1985) or PM3 (JCC, 1999) and/or ask Mr Mopac Jimmy Stewart about more details. Cheers, Rainer. Ghislain Deslongchamps ghislain*UNB.ca schrieb: > Hi all, > > We have encountered very strange results for AM1 calculations on the 2 > chair conformers of 2-methyl-tetrahydropyran (CC1CCCCO1). While HF and > MP2 give us energy differences in the 3 kcal/mol range between the axial > and equatorial chair conformers (OK), the same calculations with AM1 > give a 0.17 kcal/mol difference!!! The same result is obtained whether > we use MOPAC or GAMESS. > This is a huge error on an extremely simple system (C6H12O, ether, no > anomeric effect, etc.). Any clues on what is going on with AM1? > > Cheers, > > > Ghislain > > > ----------------------------------------------------------- > Ghislain Deslongchamps, Professor > Department of Chemistry > University of New Brunswick > Fredericton, N.B. CANADA E3B 6E2 > phone: (506) 453-4795 FAX: 453-4981 > e-mail: ghislain*unb.ca WWW: http://taxane.chem.unb.ca > Organic Chemistry Flashware: http://flashchem.nelson.com > ----------------------------------------------------------- From owner-chemistry@ccl.net Wed Sep 10 12:17:01 2008 From: "Edmanuel Torres e.torres[A]mpie.de" To: CCL Subject: CCL: Spectral density for vibrational modes in molecules Message-Id: <-37737-080910085811-25028-seeIlcL0liXAWLhiawBCTg-*-server.ccl.net> X-Original-From: "Edmanuel Torres" Content-Transfer-Encoding: quoted-printable Content-Transfer-Encoding: quoted-printable Content-type: text/plain; charset="utf-8" Content-Type: text/plain; charset="utf-8" Date: Wed, 10 Sep 2008 14:25:31 +0200 MIME-Version: 1.0 Sent to CCL by: "Edmanuel Torres" [e.torres%mpie.de] Hi Cesar=2C I recommend you to give a look to Quantum ESPRESSO=3A http=3A//www=2Equantum-espresso=2Eorg here the capabilities=3A http=3A//www=2Equantum-espresso=2Eorg/whatcanqedo=2Ephp Especially to the section =22Response properties =28density-functional pert= urbation theory=29=22 Best=2C Edmanuel ----- Original Message ----- > From=3A Cesar Augusto Mujica Martinez cesarmujica=23=23=23gmail=2Ecom =5Bmailto=3Aowner-chemistry=40ccl=2Enet=5D= To=3A Torres=2C Edmanuel -id=233in- =5Bmailto=3Ae=2Etorres=40mpie=2Ede=5D Sent=3A Fri=2C 05 Sep 2008 16=3A28=3A01 +0200 Subject=3A CCL=3A Spectral density for vibrational modes in molecules //=20 // Sent to CCL by=3A =22Cesar Augusto Mujica Martinez=22 =5Bcesarmujica=2E= =40=2Egmail=2Ecom=5D // Dear CCLers=2C //=20 // I have a polymeric molecule in a surface and it is excited by a laser=2C= I am // interested in the decay of the excited state =28the energy dissipation= =29 and I // consider that the mean source of dissipation is the electron-phonon // coupling=2C How can I calculate that electron-phonon coupling=3F or how= to // obtain the spectral density function for the vibrational modes given the= IR // or Raman spectra=3F // Any help or reference is highly appreciated=2C //=20 // Thanks in advance=2C //=20 // Cesar Mujica // cesarmujica=28-at-=29gmail=2Ecom // Universidad del Valle // Cali=2C Colombia //=20 //=20 //=20 // -=3D This is automatically added to each message by the mailing script= =3D- // To recover the email address of the author of the message=2C please chan= ge // the strange characters on the top line to the =40 sign=2E You can also= // look up the X-Original-From=3A line in the mail header=2E //=20 // E-mail to subscribers=3A CHEMISTRY=40ccl=2Enet or use=3A // http=3A//www=2Eccl=2Enet/cgi-bin/ccl/send=5Fccl=5Fmessage //=20 // E-mail to administrators=3A CHEMISTRY-REQUEST=40ccl=2Enet or use // http=3A//www=2Eccl=2Enet/cgi-bin/ccl/send=5Fccl=5Fmessage //=20 // Subscribe/Unsubscribe=3A=20 // http=3A//www=2Eccl=2Enet/chemistry/sub=5Funsub=2Eshtml //=20 // Before posting=2C check wait time at=3A http=3A//www=2Eccl=2Enet //=20 // Job=3A http=3A//www=2Eccl=2Enet/jobs=20 // Conferences=3A http=3A//server=2Eccl=2Enet/chemistry/announcements/confe= rences/ //=20 // Search Messages=3A http=3A//www=2Eccl=2Enet/htdig =28login=3A ccl=2C Pa= ssword=3A search=29 //=20 // If your mail bounces from CCL with 5=2E7=2E1 error=2C check=3A // http=3A//www=2Eccl=2Enet/spammers=2Etxt //=20 // RTFI=3A http=3A//www=2Eccl=2Enet/chemistry/aboutccl/instructions/ //=20 //=20 //=20= --- Max-Planck-Institut f=C3=BCr Eisenforschung GmbH Max-Planck-Stra=C3=9Fe 1 D-40237 D=C3=BCsseldorf =20 Handelsregister B 2533=20 Amtsgericht D=C3=BCsseldorf =20 Gesch=C3=A4ftsf=C3=BChrung Prof=2E Dr=2E J=C3=B6rg Neugebauer Prof=2E Dr=2E Anke R=2E Pyzalla Prof=2E Dr=2E Dierk Raabe Prof=2E Dr=2E Martin Stratmann Dipl=2E-Kfm=2E Herbert Wilk =20 Ust=2E-Id=2E-Nr=2E=3A DE 11 93 58 514=20 Steuernummer=3A 105 5891 1000 ------------------------------------------------- From owner-chemistry@ccl.net Wed Sep 10 18:12:00 2008 From: "Cory Pye cpye.:.crux.smu.ca" To: CCL Subject: CCL: COSMORS optimization Message-Id: <-37738-080910180755-5151-Ocq90GxDTFY3wIVwdEnyEg:_:server.ccl.net> X-Original-From: Cory Pye Content-Type: TEXT/PLAIN; charset=US-ASCII Date: Wed, 10 Sep 2008 19:07:38 -0300 (ADT) MIME-Version: 1.0 Sent to CCL by: Cory Pye [cpye%a%crux.smu.ca] Dear Mi, Fluoride has no geometrical parameters to optimize, hence no optimization. -Cory On Tue, 9 Sep 2008, mi yang miyang3790.:.gmail.com wrote: > > Sent to CCL by: "mi yang" [miyang3790,gmail.com] > Hi CCL users > > I am trying to optimize a fluoride ion complex using B3LYP/6-31G* within COSMORS solvent effects. But the job auto end after giving free energy and do not continue Optimization with out giving any error. How I can optimize such complex in COSMORS..?if any body can help I will be highly thankful > > Sample of output End part is here > ******************************* > QIter: Polarization charges converged after 46 iterations. > QIter: iQ= 1 Qconv= 0.10000D-08 Erms= 0.15013D-09 Emax= 0.81243D-09 > Error on nuclear polarization charges = 0.03795 > Error on electronic polarization charges = -0.06614 > SCF Done: E(RB+HF-LYP) = -1412.56728334 A.U. after 6 cycles > Convg = 0.6872D-08 -V/T = 2.0074 > S**2 = 0.0000 > KE= 1.402218561123D+03 PE=-6.800504847581D+03 EE= 2.250829574564D+03 > -------------------------------------------------------------------- > Variational C-PCM results > ========================= > (a.u.) = -1412.467999 > (a.u.) = -1412.567283 > Total free energy in solution: > with all non electrostatic terms (a.u.) = -1412.541683 > -------------------------------------------------------------------- > (Polarized solute)-Solvent (kcal/mol) = -62.30 > -------------------------------------------------------------------- > Cavitation energy (kcal/mol) = 35.69 > Dispersion energy (kcal/mol) = -21.11 > Repulsion energy (kcal/mol) = 1.48 > Total non electrostatic (kcal/mol) = 16.06 > -------------------------------------------------------------------- > Partition over spheres: > Sphere on Atom Surface Charge GEl GCav GDR > 1 C1 13.87 -0.002 -0.03 1.38 -0.79 > 2 C2 12.71 0.013 -0.50 1.27 -0.63 > 3 C3 6.88 0.002 -0.09 0.69 -0.38 > 4 C4 12.07 0.011 -0.40 1.20 -0.67 > 5 C5 5.83 -0.001 0.00 0.58 -0.28 > 6 C6 5.87 0.001 -0.07 0.58 -0.28 > 7 C7 9.74 -0.026 0.55 0.97 -0.53 > 8 C8 9.68 -0.028 0.64 0.96 -0.51 > 9 O9 19.39 0.222 -8.18 2.08 -1.21 > 10 O10 19.64 0.225 -8.87 2.10 -1.22 > 11 N11 2.53 -0.001 0.01 0.26 -0.05 > 12 C12 18.77 -0.034 0.53 1.87 -0.97 > 13 H13 5.56 -0.033 0.52 0.70 -0.37 > 14 H14 6.48 -0.038 0.52 0.81 -0.56 > 15 H15 6.48 -0.038 0.51 0.81 -0.56 > 16 N16 6.14 0.000 0.01 0.64 -0.23 > 17 H17 1.04 -0.013 0.54 0.13 0.00 > 18 C18 9.14 -0.010 0.33 0.91 -0.54 > 19 O19 14.92 0.189 -8.50 1.60 -0.93 > 20 C20 5.84 0.014 -0.51 0.58 -0.27 > 21 C21 12.48 0.030 -1.07 1.24 -0.70 > 22 C22 14.00 0.024 -0.79 1.40 -0.75 > 23 C23 14.05 0.019 -0.68 1.40 -0.74 > 24 C24 13.92 0.026 -0.93 1.39 -0.75 > 25 C25 12.59 0.023 -0.90 1.26 -0.51 > 26 H26 5.41 -0.026 0.63 0.68 -0.42 > 27 H27 6.39 -0.038 0.48 0.80 -0.60 > 28 H28 6.39 -0.039 0.47 0.80 -0.60 > 29 H29 6.38 -0.037 0.86 0.80 -0.57 > 30 H30 1.17 0.000 0.01 0.15 0.00 > 31 H31 4.07 -0.022 0.77 0.51 -0.12 > 32 H32 6.37 -0.047 1.11 0.80 -0.57 > 33 H33 2.52 -0.007 0.30 0.32 -0.02 > 34 Cl34 40.70 0.641 -39.59 4.01 -2.29 > -------------------------------------------------------------------- > After PCM corrections, the SCF energy is -1412.56728334 a.u. > -------------------------------------------------------------------- > > > > > > > > > > > > > > MiYang > Miyang3790 > P.R.China> > ************* ! Dr. Cory C. Pye ***************** ! Associate Professor *** ** ** ** ! Theoretical and Computational Chemistry ** * **** ! Department of Chemistry, Saint Mary's University ** * * ! 923 Robie Street, Halifax, NS B3H 3C3 ** * * ! cpye%crux.stmarys.ca http://apwww.stmarys.ca/~cpye *** * * ** ! Ph: (902)-420-5654 FAX:(902)-496-8104 ***************** ! ************* ! Les Hartree-Focks (Apologies to Montreal Canadien Fans)