From owner-chemistry@ccl.net Mon Oct 26 00:37:00 2009 From: "Jimmy Stewart MrMOPAC[a]openmopac.net" To: CCL Subject: CCL: Conformational Analysis of Toxogonine, TMB-4 and HI-6 using PM6!! Message-Id: <-40533-091025222348-32028-bc2gnNhguOl/f2xFqn4yQw^^server.ccl.net> X-Original-From: Jimmy Stewart Content-Type: text/plain; charset="us-ascii"; format=flowed Date: Sun, 25 Oct 2009 19:47:16 -0600 Mime-Version: 1.0 Sent to CCL by: Jimmy Stewart [MrMOPAC()openmopac.net] >Jim Kress said, " Yes, you are correct for pi stacking, ... This is >quite reminiscent of that confusion which arose (and still does) >during the development and application of semi-empirical methods - >although Jimmy Stewart will probably yell at me for bringing that >up, given the latest methodology he has produced, MOPAC 2009 which >features PM6." Reports of high-level calculations of non-covalent interactions in the water dimer: "Anchoring the water dimer potential energy surface with explicitly correlated computations and focal point analyses" G. S. Tschumper, M. L. Leininger, B. C. Hoffman, E. F. Valeev, H. F. Schaefer III, M. Quack, J. Chem. Phys. 116, 690 (2002) http://aros.ca.sandia.gov/~mlleinin/Docs/anchoring_the_water_dimer_potential_energy_surface_with_explicitly_correlated_computations_and_focal_point_analyses.pdf and in biomacromolecules such as that by Cerny and Hobza's "Non-covalent interactions in biomacromolecules " http://www.rsc.org/publishing/journals/CP/article.asp?doi=b704781a provide good theoretical estimates of hydrogen bonding and pi interaction energies. Accurate values of the distances between stacked pi systems can be obtained from the CCDC's Cambridge Structural Database compendium, http://www.ccdc.cam.ac.uk/. So, if needed, there is plenty of readily available high-quality experimental and theoretical reference data for calibrating, i.e., parameterizing, semiempirical methods. Of course, more data are always welcome! Although PM6 does a passable job of modeling the geometries and energies of non-covalent interactions, Rezac, et. al., this year, have developed a quick post-SCF correction, "Semiempirical Quantum Chemical PM6 Method Augmented by Dispersion and H-Bonding Correction Terms Reliably Describes Various Types of Noncovalent Complexes" http://pubs.acs.org/doi/abs/10.1021/ct9000922 that lowers the average error in such interactions for the S22 set from 3.4 kcal/mol to 0.8 kcal/mol, and for pi stacked systems from 3.6 kcal/mol to 1.5 kcal/mol. So the development of accurate theoretical methods such as CCSD(T)/CBS, high-quality X-ray structures, and careful post-SCF corrections have allowed semiempirical methods to predict hydrogen bonding and pi stacking energies and geometries with much greater accuracy than was possible even just a few years ago. Jimmy ( [#] [#] ) .-----------------oOOo----(_)----oOOo--------------------------------------. | James J. P. Stewart | | | Stewart Computational Chemistry | E-mail: MrMOPAC[#]OpenMOPAC.net | | 15210 Paddington Circle | 39/03/15 N, 104/49/29 W | | Colorado Springs CO 80921-2512 | http://openmopac.net/ | | USA | SKYPE: Jimmy.Stewart2 GMT 1500 - 0200| | .ooo0 | Phone: USA +(719) 488-9416 | | ( ) Oooo.| | .-----------------------\ (----( )---------------------------------------. \_) ) / (_/ From owner-chemistry@ccl.net Mon Oct 26 09:33:00 2009 From: "dewdew zhou dewdew[]126.com" To: CCL Subject: CCL: The QCISD error Message-Id: <-40534-091025121624-22448-CE/tPBtwoDgvFNSwERF6Pw(0)server.ccl.net> X-Original-From: "dewdew zhou" Date: Sun, 25 Oct 2009 12:16:19 -0400 Sent to CCL by: "dewdew zhou" [dewdew---126.com] Hi, all, I have used the QCISD method to calculate the geometry of the transition state with the following command: # qcisd/6-311G(d,p) opt(ts,calcfc), freq test But i got the following error: No analytic 2nd derivative for this method. Is there anyone have faced the problem like this? If this is, please tell me how to fix it? Thank you very much! From owner-chemistry@ccl.net Mon Oct 26 11:57:01 2009 From: "Sergio Emanuel Galembeck segalemb]*[usp.br" To: CCL Subject: CCL: The QCISD error Message-Id: <-40535-091026114643-26919-fcIp3GgMp+OCm9qOfA95ZA++server.ccl.net> X-Original-From: Sergio Emanuel Galembeck Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; format="flowed" Date: Mon, 26 Oct 2009 12:46:02 -0200 MIME-Version: 1.0 Sent to CCL by: Sergio Emanuel Galembeck [segalemb.!=!.usp.br] Dear Dewdew, For QCISD and some other methods, as CCSD(T), analytical second derivatives are not available in Gxx, and you are unable to use calcfc keyword. Hope this help you, Sergio Emanuel Galembeck Citando "dewdew zhou dewdew[]126.com" : > > Sent to CCL by: "dewdew zhou" [dewdew---126.com] > Hi, all, > > I have used the QCISD method to calculate the geometry of the > transition state with the following command: > > # qcisd/6-311G(d,p) opt(ts,calcfc), freq test > > But i got the following error: > > No analytic 2nd derivative for this method. > > Is there anyone have faced the problem like this? > > If this is, please tell me how to fix it? > > Thank you very much!> > > From owner-chemistry@ccl.net Mon Oct 26 12:33:01 2009 From: "Rajagopala Reddy Seelam rajagopalaseelam^^gmail.com" To: CCL Subject: CCL: geometry changed during optimization reg Message-Id: <-40536-091026121436-3831-JogCPQK5nTkootXxHc970g===server.ccl.net> X-Original-From: "Rajagopala Reddy Seelam" Date: Mon, 26 Oct 2009 12:14:33 -0400 Sent to CCL by: "Rajagopala Reddy Seelam" [rajagopalaseelam-#-gmail.com] Dear CCL subscribers, I am doing optimization of an anion which is an open shell molecule having one electron being unpaired.I did optimization using ump2 method but it gave a spin contamination of (S**2,0)=.15787D+01 and S**2,1)=.15000D+01 which is quite high for a single unoccupied electron. To get rid of spin contamination I am optimizing by romp2 method . The job is terminated by geometry change from d2h to c2h .How can I do optimization successfully. Thank you, Regards From owner-chemistry@ccl.net Mon Oct 26 13:07:00 2009 From: "lei wang lwang~~tripos.com" To: CCL Subject: CCL: SYBYL-X 1.0 release now available, Windows and Linux Message-Id: <-40537-091026121541-4351-joc6O4FfksehdL8CWzcl7w!A!server.ccl.net> X-Original-From: "lei wang" Date: Mon, 26 Oct 2009 12:15:38 -0400 Sent to CCL by: "lei wang" [lwang . tripos.com] SYBYL-X 1.0 is now available for all supported SYBYL customers. SYBYL-X represents the next generation of the SYBYL suite, with availability on Windows XP as well as on Linux RHEL 4, including all of the robust science available in the original program coupled with improvements in user experience. Enhancements in SYBYL-X 1.0 include release of a new workflow for ligand preparation, allowing users to prepare molecular structures in the chemical representation that is appropriate for submission to a variety of ligand-based design applications, such as docking and topomeric studies. SYBYL also has a new look, as the text console is now docked into the main window. The console and toolbars can be undocked and moved to any location. Navigation within the menu system and dialogs has been simplified. SYBYL has been redesigned to better support task flow in a number of areas, including atom and bond selection and bond expression definition. The UNITY menu has been reorganization to match user task flow, and the SYBYL Sketcher is now driven by a set of toolbars. The Systematic Search dialog has been redesigned to include multiple tabs, providing easy access to all conditions for the run. Surflex-Dock enhancements include the addition of two major new modes: scoring function optimization and multi-structure docking (multiple protein conformations for a single target). In addition, protein pocket flexibility has been added as an experimental option for rescoring docked poses as well as in the final stages of the new mdock_list command. Customers with valid support contracts can download SYBYL-X 1.0 from www.tripos.com/download in the SYBYL section after creating an appropriate profile on the tripos.com website that includes their address and the host id for their SYBYL installation. From owner-chemistry@ccl.net Mon Oct 26 13:42:00 2009 From: "xihai chen quch2006%x%yahoo.com" To: CCL Subject: CCL: The pharmacophore difference between Catalyst and MOE Message-Id: <-40538-091026132949-13553-wkALTZx1620obpeaWUDH8Q*server.ccl.net> X-Original-From: "xihai chen" Date: Mon, 26 Oct 2009 13:29:44 -0400 Sent to CCL by: "xihai chen" [quch2006**yahoo.com] Hello, I remember I read a paper discussing the difference in pharmacophore features between the Catalyst and MOE, maybe including Tripos. I can't not search out now in ACS or google. Could anyone give me a hint or reference? Thank you. Xchen. From owner-chemistry@ccl.net Mon Oct 26 20:28:01 2009 From: "Deepangi Pandit deepangi.pandit%gmail.com" To: CCL Subject: CCL: The pharmacophore difference between Catalyst and MOE Message-Id: <-40539-091026202603-28912-iZl89DEAgTRr054uam0rDA**server.ccl.net> X-Original-From: Deepangi Pandit Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-1 Date: Mon, 26 Oct 2009 20:25:46 -0400 MIME-Version: 1.0 Sent to CCL by: Deepangi Pandit [deepangi.pandit ~~ gmail.com] Are you looking for this one? http://www.ncbi.nlm.nih.gov/sites/entrez Drug Discov Today. 2008 Jan;13(1-2):23-9. Epub 2007 Nov 5. Molecule-pharmacophore superpositioning and pattern matching in computational drug design. Wolber G, Seidel T, Bendix F, Langer T. Three-dimensional (3D) pharmacophore modeling is a technique for describing the interaction of a small molecule ligand with a macromolecular target. Since chemical features in a pharmacophore model are well known and highly transparent for medicinal chemists, these models are intuitively understandable and have been increasingly successful in computational drug discovery in the past few years. The performance and applicability of pharmacophore modeling depends on two main factors: the definition and placement of pharmacophoric features and the alignment techniques used to overlay 3D pharmacophore models and small molecules. An overview of key technologies and latest developments in the area of 3D pharmacophores is given and provides insight into different approaches as implemented by the 3D pharmacophore modeling packages like Catalyst, MOE, Phase and LigandScout. THX Deepa On Mon, Oct 26, 2009 at 1:29 PM, xihai chen quch2006%x%yahoo.com wrote: > > Sent to CCL by: "xihai =A0chen" [quch2006**yahoo.com] > Hello, > > I remember I read a paper discussing the difference in pharmacophore feat= ures between the Catalyst and MOE, maybe including Tripos. I can't not sear= ch out now in ACS or google. Could anyone give me a hint or reference? > > Thank you. > > Xchen. > > > > -=3D This is automatically added to each message by the mailing script = =3D-> =A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message> =A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message> =A0 =A0 =A0http://www.ccl.net/chemistry/sub_unsub.shtml> =A0 =A0 =A0http://www.ccl.net/spammers.txt> > >