From owner-chemistry@ccl.net Tue Mar 6 00:19:00 2007 From: "Zhijian WU zjwu _ ciac.jl.cn" To: CCL Subject: CCL:G: how to write this input file? Message-Id: <-33741-070305222538-6587-vOKITbvbVlvDirihK9C+4w~!~server.ccl.net> X-Original-From: "Zhijian WU" Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="gb2312" Date: Tue, 6 Mar 2007 10:55:08 +0800 Mime-Version: 1.0 Sent to CCL by: "Zhijian WU"[zjwu*ciac.jl.cn] Hi, there, It should be the LANL2DZ basis set. As defined, it is a double theta basis set. In addition, you may also try SDD basis set which is triple theta basis set. The input file looks like: #B3lyp/lanl2dz opt freq .... Regards, Sincerely, -- Z. J. Wu ======= 2007-03-05 23:03:00 you write£º======= >Sent to CCL by: "Bingxing Wang" [wangbx[-]dicp.ac.cn] >Dear all ccler, > In an article, it said,"The relativistic effective core potential (ECP) of the Los Alamos National Laboratory 2 ( LANL2)was used to describe the 60 core electrons of a Pt atom. The 5s, 5p, 5d, and 6s valence electrons of the Pt atom were described with split-valence (double-zeta) basis sets." G03 program is used. I want to know how to write the input file. Is it LanL2DZ basis set? Then how about the 5s,5p,5d, and 6s valence electrons? Any suggestion is helpful. Thanks a lot. > > > >¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡ > >¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡wangbx[-]dicp.ac.cn >¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡2007-03-05> > > = = = = = = = = = = = = = = = = = = = = From owner-chemistry@ccl.net Tue Mar 6 04:37:01 2007 From: "Val Gillet v.gillet(!)sheffield.ac.uk" To: CCL Subject: CCL: Fourth Joint Sheffield Conference on Chemoinformatics:Registration Message-Id: <-33742-070306043401-22943-62q+mcOdTVhGie3Iq3WBzg(_)server.ccl.net> X-Original-From: "Val Gillet" Date: Tue, 6 Mar 2007 04:33:58 -0500 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. See http://cisrg.shef.ac.uk/shef2007 for the Preliminary Programme, and details on Registration, Student Bursaries and the Commercial Exhibition. Programme: The list of oral presentations is now available. Note that there will also be a large number of high quality posters (details to be posted later) following the very healthy response to the call for papers. Registration is now open with early bird discounts available until April 30th. Note that early registration is encouraged since there is a limit on delegate numbers. Student bursaries are available through generous sponsorship provided by the Chemical Computing Group, the Chemical Structure Association Trust and the Molecular Graphics and Modelling Society. Note the deadline for bursary applications is March 31st, 2007. See conference website for details on how to apply. Commercial exhibition: A list of exhibitors is available via the conference website. To secure the remaining exhibition slots please email the conference organisers at cheminf2007__shef.ac.uk. From owner-chemistry@ccl.net Tue Mar 6 05:54:01 2007 From: "Silviu Polosan Spol68^^^yahoo.com" To: CCL Subject: CCL: adding a perturbation Message-Id: <-33743-070306050842-6478-6hgIRLTauDmQzBOHDi/flQ~~server.ccl.net> X-Original-From: "Silviu Polosan" Date: Tue, 6 Mar 2007 05:08:37 -0500 Sent to CCL by: "Silviu Polosan" [Spol68::yahoo.com] Hi friends, Is someone who can tell me how can I add a constant perturbation (number, like an external field) to a job type B3LYP/6-31 G Any answer will be appreciate Thank you Silviu From owner-chemistry@ccl.net Tue Mar 6 06:17:00 2007 From: "=?ISO-8859-1?Q?=D6d=F6n?= Farkas farkas---chem.elte.hu" To: CCL Subject: CCL: Free Tool for conformer generation Message-Id: <-33744-070306061506-510-LTWGvo9v0EpuGEdDzMOg9g###server.ccl.net> X-Original-From: =?ISO-8859-1?Q?=D6d=F6n?= Farkas Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=UTF-8 Date: Tue, 06 Mar 2007 12:12:56 +0100 Mime-Version: 1.0 Sent to CCL by: =?ISO-8859-1?Q?=D6d=F6n?= Farkas [farkas-#-chem.elte.hu] Hi Raphael, Chemaxon's Marvin has conformer generation, which is free for academia. It has GUI, command line tool and API for Java. You can find more details at: http://www.chemaxon.com/marvin Best wishes, Odon On Mon, 2007-03-05 at 20:45 -0600, Brunsteiner, Michael micb(~)uic.edu wrote: > Sent to CCL by: "Brunsteiner, Michael" [micb#,#uic.edu] > On Mon, March 5, 2007 10:31, Raphael A. Bauer raphael.bauer{:}charite.de > wrote: > > > > Sent to CCL by: "Raphael A. Bauer" [raphael.bauer,charite.de] > > Hi CC List, > > > > I am wondering if anybody of you knows a tool for the generation of > > conformers. Pretty much what Catalyst does. But - for my project I would > > need something "free" (open source) and scriptable (command line version > > maybe). > > > > Any recommendations for good tools? > > omega2 from openeye (www.eyesopen.com) > its fast, quite versatile, and can (only) be used > > from the command-line. > for academia/non-profit its free. > mic > > > > Many thanks in advance! > > > > Raphael> > > -- Ödön Farkas Associate professor Deparment of Organic Chemistry and Laboratory of Chemical Informatics, Institute of Chemistry, Eötvös Loránd University, Budapest Address: 1/A Pázmány Péter sétány, H-1117 Budapest, Hungary Phone: +36-1-372-2570 Cell phone: +36-30-255-3111 Fax: +36-1-372-2620 URL: http://organ.elte.hu/farkas From owner-chemistry@ccl.net Tue Mar 6 06:52:00 2007 From: "Stefan.Guessregen.|,|.sanofi-aventis.com" To: CCL Subject: CCL: 21st "Darmstadt" Molecular Modelling Workshop - May 15-16, 2007 in Erlangen Message-Id: <-33745-070306050734-5949-4GL2XjaGBWuL3N92sQYL4g|,|server.ccl.net> X-Original-From: Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Tue, 6 Mar 2007 11:07:04 +0100 MIME-Version: 1.0 Sent to CCL by: [Stefan.Guessregen###sanofi-aventis.com] 21st "Darmstadt" Molecular Modeling Workshop Computer-Chemie-Centrum, 91052 Erlangen, Germany Tuesday, May 15 - Wednesday, May 16, 2007 Dear Colleagues, I would like to bring to your attention that the 21st "Darmstadt" Molecular Modeling Workshop will be taking place in Erlangen on May 15th and 16th 2007. The goal of the Workshop is to give young scientists, especially PhD students and Post-Docs, the chance to present their current research, industrial colleagues are able to gain an overview about ongoing academic research. Contributions from all areas of molecular modelling, life sciences to materials, are highly welcome. We are pleased to announce that the following scientists have agreed to give plenary lectures: Prof. Thierry Langer (University of Innsbruck) Prof. Wilfred van Gunsteren (ETH Zurich) For any further information regarding the program, registration, location, and accomodation, please refer to the following website: http://www.chemie.uni-erlangen.de/ccc/darmstadt.html The deadline for registration is 13th April 2007. Best regards Stefan Guessregen Dr. Stefan Guessregen Sanofi-Aventis Deutschland GmbH Scientific & Medical Affairs / Drug Design Industriepark Hoechst, Building G 878 D-65926 Frankfurt am Main Germany Phone: +49 (69) 305 26 616 Fax: +49 (69) 305 942 333 E-Mail: stefan.guessregen*aatt*sanofi-aventis.com ************************************************************************************************************************************************************** Sanofi-Aventis Deutschland GmbH, Sitz der Gesellschaft: Frankfurt am Main, Handelsregister: Frankfurt am Main, Abt. B Nr. 40661 Vorsitzender des Aufsichtsrats: Hanspeter Spek - Geschäftsführer: Dr. Heinz-Werner Meier (Vorsitzender), Dr. Matthias Braun, Hervé Gisserot, Dieter Kohl, Prof. Dr. Dr. Werner Kramer, Dr. Martin Siewert ************************************************************************************************************************************************************** From owner-chemistry@ccl.net Tue Mar 6 07:28:01 2007 From: "Przemyslaw G. Czyryca pczyryca]![allosterix.com" To: CCL Subject: CCL: Eyring equation for the transition state more stable than the rea Message-Id: <-33746-070305192128-30644-ii+tHa2knB4WMSV54aO/WA . server.ccl.net> X-Original-From: "Przemyslaw G. Czyryca" Date: Mon, 5 Mar 2007 19:21:25 -0500 Sent to CCL by: "Przemyslaw G. Czyryca" [pczyryca^-^allosterix.com] Hmm, it may be a silly suggestion, but I think the rate-limiting step is from the Intermediate (I) through the TS to P. This step's energetics is quite typical (the energy of the TS is higher then the intermediate's), so why bother with the reactant (R) at all? Regards, Przemek From owner-chemistry@ccl.net Tue Mar 6 08:02:00 2007 From: "CCL CCL computationalchemist .. gmail.com" To: CCL Subject: CCL: free energy of hydration from free energy of solvation Message-Id: <-33747-070306074010-4124-oi5U55ZMI6MpbsYRzXcN3w(-)server.ccl.net> X-Original-From: "CCL CCL" Content-Type: multipart/alternative; boundary="----=_Part_179031_17892142.1173183254404" Date: Tue, 6 Mar 2007 12:14:14 +0000 MIME-Version: 1.0 Sent to CCL by: "CCL CCL" [computationalchemist**gmail.com] ------=_Part_179031_17892142.1173183254404 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Content-Disposition: inline Dear Friends, this may be a naive question, but i'm very new to the field. so, forgive me if i'm wrong. I was struggling with a problem, since morning. Could be fine if any one helps me to come out. I, have a system say,, A+B ---> TS ---> C I computed the free energy of solvation [ delG(solv) ] for all these species ( chemsol - online programe) and they are ( solvent being water), A = -19.9 B = -9.6 TS = -36.3 C = -50.9 My question is how to calculate free energy of hydration, [ delG(hyd) ] from these value. Any pointers or suggestions will be greatly apprciated. -- Regards, Dr. Sanjay ------=_Part_179031_17892142.1173183254404 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline
Dear Friends,
 
this may be a naive question, but i'm very new to the field. so, forgive me if i'm wrong.
 
I was struggling with a problem, since morning. Could be fine if any one helps me to come out.
 
I, have a system  say,,   A+B ---> TS ---> C
 
I computed the free energy of solvation [ delG(solv) ] for all these species ( chemsol - online programe) and they are ( solvent being water),
 
 A  = -19.9
 B  = -9.6
 TS = -36.3
 C   =  -50.9
My question is how to calculate free energy of hydration, [ delG(hyd) ]  from these value.
 
Any pointers or suggestions will be greatly apprciated.
 

 


--
Regards,
Dr. Sanjay ------=_Part_179031_17892142.1173183254404-- From owner-chemistry@ccl.net Tue Mar 6 09:05:00 2007 From: "James Gary Prudhomme jprudhomme[]healthtech.com" To: CCL Subject: CCL: CHI's Structure-Based Design Conference, June 6-8, Boston Message-Id: <-33748-070306083159-8251-srxlf36j4ks5FWNxgT1EGA[A]server.ccl.net> X-Original-From: "James Gary Prudhomme" Date: Tue, 6 Mar 2007 08:31:55 -0500 Sent to CCL by: "James Gary Prudhomme" [jprudhomme===healthtech.com] Dear Colleagues, Below is the distinguished faculty participating at CHI's Structure-Based Design conference which is scheduled for June 6-8, 2007 at the World Trade Center in Boston, MA. Discounted registration rates are available until March 9. To view speaker abstracts and to register, visit www.healthtech.com/2007/SBD Wenyan Wang, Ph.D., Principal Scientist, Protein Engineering and Biochemistry Group, Structural Chemistry Department,Schering-Plough Research Institute Celerino Abad-Zapatero, Ph.D., Associate Research Fellow, Protein Crystallography Laboratory, Abbott Laboratories N. Claude Cohen, Ph.D., Founder & Chief Executive Officer, Synergix Ltd. David Moskowitz, M.D., Chief Executive Officer, GenoMed, Inc. Mark Murcko, Ph.D., Vice President & Chief Technology Officer, Scientific Advisory Board, Vertex Pharmaceuticals Inc. Anthony Trippe, Ph.D., Senior Innovation Manager, NPD, CAS Woody Sherman, Ph.D., Application Scientist, Schrdinger, Inc. Jeremy L. Jenkins, Ph.D., Research Investigator, Lead Discovery Center, Novartis Institutes for BioMedical Research Inc. Gergely Toth, Ph.D., Chemistry, Elan Pharmaceuticals, plc Ulrich Rester, Ph.D., Senior Research Scientist, Medicinal Chemistry, Bayer HealthCare AG Arthur M. Doweyko, Ph.D., Macromolecular Structure, CADD, Pharmaceutical Research Institute, Bristol-Myers Squibb Richard A. Friesner, Ph.D., Professor, Chemistry, Columbia University Sid Topiol, Ph.D., Associate Director, Computational Chemistry, Lundbeck Research, USA, Inc. Debananda Das, Ph.D., Senior Research Fellow, HIV & AIDS Malignancy Branch, National Cancer Institute, National Institutes of Health John P. Priestle, Ph.D., Discovery Technologies, Novartis Institute for BioMedical Research N. Claude Cohen, Ph.D., President & Chief Executive Officer, Synergix, Ltd. Kent Stewart, Ph.D., Research Fellow, Structural Biology, Abbott David Claremon, Ph.D., Vice President of Chemistry, Vitae Pharmaceuticals I hope you will be able to join us. Best regards, Jim Prudhomme Cambridge Healthtech Institute www.healthtech.com/2007/sbd From owner-chemistry@ccl.net Tue Mar 6 11:25:00 2007 From: "Norge Cruz Hern ndez norge*us.es" To: CCL Subject: CCL: mpirun in LSF queue system. Message-Id: <-33749-070306112127-1388-kJWn53U4EtQKeaOM5hrX0A _ server.ccl.net> X-Original-From: "Norge Cruz Hern ndez" Date: Tue, 6 Mar 2007 11:21:23 -0500 Sent to CCL by: "Norge Cruz Hern ndez" [norge+*+us.es] Hi, Does anyone know how to submit MPI job by LSF queue system in quadrics inter-connection? I am not able to run my job with the following command line in my job script. mpirun -np 8 -machinefile machine.file ./test I received this error from error log - "mpirun: error: elan netids not given in machinefile or MPIRUN_ELANIDMAP_FILE" My machine.file looks like: node1:4 node2:4 Pls help. Thanks Norge From owner-chemistry@ccl.net Tue Mar 6 15:09:01 2007 From: "Giulio Vistoli giulio.vistoli-x-unimi.it" To: CCL Subject: CCL: VEGA ZZ 2.0.8 Message-Id: <-33750-070306092603-1336-lky+hEg5/08k3IUVy/1BDw++server.ccl.net> X-Original-From: Giulio Vistoli Content-transfer-encoding: 7bit Content-type: text/plain; format=flowed; charset=iso-8859-1; reply-type=original Date: Tue, 06 Mar 2007 14:35:18 +0100 MIME-version: 1.0 Sent to CCL by: Giulio Vistoli [giulio.vistoli#%#unimi.it] Dear CCLers, We are proud to announce that VEGA ZZ 2.0.8 is now available for download at: http://www.ddl.unimi.it/vega/download.htm ***** Outstanding New Features **** - Conformational analysis (grid scan, random search and Boltzmann jump). - Cluster analysis of the trajectory files (cluster by coordinates, by torsion and by torsion RMSD). **** New Features **** - Mol2 multi-model trajectory saver. - X-Plor PSF loader. - ChemSol loader and saver. - CML 1.0 & 2.0 loader and saver. - PQR saver. - CHARMM 22 force field for AMMP. - Improved the rendering speed of solid surfaces with OpenGL 1.5 compliant graphic cards (2x time faster). - Mopac 2007 support (not included in the package). - PSF saver totally rewritten and new improper angle detection. - HyperDrive K8 for AMD Opteron, Athlon 64/FX and Sempron 64 CPUs. - 64 bit version of AMMP, ESCHER NG, InpMerge, PropKa, Top2Tem, Vega command line version, WarpBench, WarpGate, WarpKeyGen and WarpTel for Windows XP Professional x64 Edition, Windows Server 2003 x64 Editions and Windows Vista x64 Editions. - Slow motion function converting a trajectory to a video stream. - Gasteiger charges and the ATDL engine use the new parallel code. - ATDL template cache for a faster atom typing. - Added the possibility to compute manually the total charge in the Mopac dialog window. - PowerNet plug-in: script description feature. - Tutorials for most common molecular modelling problems. - Fix: Excel driver. - Fix: Gromos/Gromacs loading of very big files. - Fix: connectivity merge. - Fix: WarpGate access violation if an invalid host name is found in the configuration file. - Auto-installation utility for the license file (LicInst). - Updated the CPU detection to recognize the Intel Core 2 CPUs. - AMMP 2.2.0. - WarpGate 1.1. - New extended commands: AmmpSetFF, AmmpUpdateFreq, CTorClear, CTorGet, CTorFind. - New system variable: TotCTor. - New scripts: Database logP.c (calculate the logP for each molecule in the database), SDF export.c (export a trajectory in a SDF database), Dump backbone torsions.c (dump the phi and psi backbone torsion values). - InpMerge: utility to merge the CHARMM/NAMD parameter files. - Italian localization of the setup procedure. - Updated the gl2ps library to 1.3.2. - Updated the libbzip2 library to 1.0.3. - Updated the ziplib library to 1.0.1. - Updated the zlib library to 1.2.3. - Demo music remastered with surround effects. **** Update procedure **** If you installed the VEGA ZZ Live CD Creator uninstall it from the control panel before the setup of the new release. **** Other updated VEGA packages **** VEGA 1.5.8 for Linux x86 32 bit VEGA 1.5.8 for Linux x86 64 bit VEGA 1.5.8 for AmigaOS VEGA 1.5.8 Localization Pack Best regards VEGA Developer Team From owner-chemistry@ccl.net Tue Mar 6 18:31:01 2007 From: "Aniel Aron anisamron+*+yahoo.com" To: CCL Subject: CCL:G: G03 Optimization problem Message-Id: <-33751-070306180712-25653-XF4pxY5lL6qDWJ/X00zYDw~!~server.ccl.net> X-Original-From: Aniel Aron Content-Type: multipart/alternative; boundary="0-604122861-1173218817=:83065" Date: Tue, 6 Mar 2007 14:06:57 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: Aniel Aron [anisamron..yahoo.com] --0-604122861-1173218817=:83065 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable =0AHi All,=0AI have one problem and one question; first on "optimization" a= nd second on "IOps".=0A=0A1) I was trying to optimize a small metallic clus= ters (6-8 atoms) using SDD basis set and PBE1PBE using G03. However, I enco= unter some problems with the optimization and quit the calculation with the= following error. =0AError termination request processed by link 9999.=0A= =0AThe energy is very close to converge, but the Maximum Force and RMS Forc= e do not converge.=0AThe error message is: =0A Item = Value Threshold Converged?=0A Maximum Force = 0.002180 0.000450 NO=0A RMS Force = 0.000952 0.000300 NO=0A Maximum Displacement 0.000010 = 0.001800 YES=0A RMS Displacement 0.000005 0.001200 = YES=0A Predicted change in Energy=3D-2.455189D-05=0A Optimization s= topped.=0A -- Number of steps exceeded, NStep=3D 31=0A -- Flag rese= t to prevent archiving.=0A=0Agrep "SCF D" {last 4 steps}=0A SCF Done: E(UP= BE+HF-PBE) =3D -1017.54917094 A.U. after 3 cycles=0A SCF Done: E(U= PBE+HF-PBE) =3D -1017.54917094 A.U. after 2 cycles=0A SCF Done: E(= UPBE+HF-PBE) =3D -1017.54917095 A.U. after 4 cycles=0A SCF Done: E= (UPBE+HF-PBE) =3D -1017.54917094 A.U. after 4 cycles=0A=0AI restart= ed the calculation from chk file; but again, the Max/RMS Force do not conve= rge. Could you please tell me what modifications I should include in the "i= nput" file?=0A(input details for 6 atoms: =0A#P pbe1pbe/SDD opt=3D(calcfc,m= axstep=3D50) symm=3D(PG=3DOh) geom=3Dcheckpoint guess=3Dread)=0A=0A2) What = exactly is IOps? I checked the G03 manual, but did not understand the logic= behind in choosing the correct numerator and denominator and integer after= the "=3D" sign. How can I find out the correct/proper values/numbers to us= e in IOps? For example, Does the following IOp statement has any special me= aning?=0AIOp(5/42=3D10000428,5/43=3D05720572,5/44=3D10001000)=0A=0AI would = really take any feedback from you. Thanks in advance.=0A=0ASincerely,=0AAni= el=0A=0A=0A=0A=0A=0ASend instant messages to your online friends http://uk.= messenger.yahoo.com --0-604122861-1173218817=:83065 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable

Hi All,
I have one problem and one question;= first on "optimization" and second on "IOps".

1) I was trying to op= timize a small metallic clusters (6-8 atoms) using SDD basis set and PBE1PB= E using G03. However, I encounter some problems with the optimization and q= uit the calculation with the following error. 
Error termination request processed by link 9999.
The energy is very close to converge, but the Maximum Force and RMS F= orce do not converge.
The error message is:
              &nbs= p;  Item          &n= bsp;          Value        =    Threshold   Converged?
 Maximum Force  &n= bsp;             0.002180 = ;    0.000450         NO
 RMS=         Force      &= nbsp;         0.000952     0.0= 00300         NO
 Maximum Displacement =     0.000010     0.001800    &= nbsp;    YES
 RMS     Displacement        0.000005  = ;   0.001200         YES
 Predicte= d change in Energy=3D-2.455189D-05
=  Optimization stopped.
 &nbs= p;  -- Number of steps exceeded,  NStep=3D  31
  =   -- Flag reset to prevent archiving.

grep "SCF D" {last= 4 steps}
 SCF Done:  E(UP= BE+HF-PBE) =3D  -1017.54917094     A.U. after = ;   3 cycles
 SCF Done:  E(UPBE+HF-PBE) =3D  -10= 17.54917094     A.U. after    2 cycles
<= span style=3D"font-style: italic;"> SCF Done:  E(UPBE+HF-PBE) =3D=   -1017.54917095     A.U. after    = 4 cycles
 SCF Done:  E(UPBE+HF-PBE) =3D  -1017.54917094&nbs= p;    A.U. after    4 cycles

I = restarted the calculation from chk file; but again, the Max/RMS Force do no= t converge. Could you please tell me what modifications I should include in= the "input" file?
(input details for 6 atoms:
#P pbe1pbe/SDD opt=3D(calcfc,maxstep=3D50) symm=3D(PG=3DOh) = geom=3Dcheckpoint guess=3Dread)

2) What exactly is IOps? I ch= ecked the G03 manual, but did not understand the logic behind in choosing t= he correct numerator and denominator and integer after the "=3D" sign. How = can I find out the correct/proper values/numbers to use in IOps? For example, Does the following IOp stateme= nt has any special meaning?
IOp(5/42=3D10000428,5/43=3D05720572,5/44=3D1= 0001000)

I would really take any feedback from you. Thanks in advanc= e.

Sincerely,
Aniel



Send instant messa= ges to your online friends http://uk.messenger.yahoo.com --0-604122861-1173218817=:83065-- From owner-chemistry@ccl.net Tue Mar 6 19:05:01 2007 From: "David Gallagher gallagher.da[#]gmail.com" To: CCL Subject: CCL: mopac NOREOR Message-Id: <-33752-070306143723-15529-0+AbhS9wttQ/mlzuVX9k4Q]_[server.ccl.net> X-Original-From: David Gallagher Content-Type: text/plain; charset="us-ascii"; format=flowed Date: Tue, 06 Mar 2007 10:41:38 -0800 Mime-Version: 1.0 Sent to CCL by: David Gallagher [gallagher.da : gmail.com] I believe that the old MOPAC 6 did not support Cartesian coordinates and converted everything to internals, leading to reorientation. Short of rewriting MOPAC 6, you could try the new MOPAC2007 which is based on MOPAC 6 but also supports Cartesian coordinates which should solve the problem. MOPAC2007 still includes AM1 and PM3 as well as the new PM6 method, and is free to academics at mopac2007.com . Regards, David Gallagher CACheResearch.com At 06:48 AM 3/5/2007, Marcelo Zaldini zaldini-,-ufpe.br wrote: >Sent to CCL by: "Marcelo Zaldini" [zaldini^^^ufpe.br] >Dear CCLers, >Is it possible to setup the mopac 6.10 to NOT reorient the molecular >geometry before calculations, using keyword or even any change in >source code ? The RE-ORIENTATION is normally used for symmetry purposes. >In mopac93 manual, there is a keyword named NOREOR, but it doesn't >work in mopac 6.10. > >Best Regards, >Marcelo. From owner-chemistry@ccl.net Tue Mar 6 19:42:00 2007 From: "Eric Scerri scerri]=[chem.ucla.edu" To: CCL Subject: CCL: Foundations of Chemistry, volume 9, #1 Message-Id: <-33753-070306194034-5663-wD1k5Vk4wruUQrt6jCzHGQ(a)server.ccl.net> X-Original-From: Eric Scerri Content-Type: multipart/alternative; boundary=Apple-Mail-4--500074001 Date: Tue, 6 Mar 2007 16:42:17 -0800 Mime-Version: 1.0 (Apple Message framework v752.2) Sent to CCL by: Eric Scerri [scerri~!~chem.ucla.edu] --Apple-Mail-4--500074001 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=WINDOWS-1252; delsp=yes; format=flowed > > > > FOUNDATIONS OF CHEMISTRY, VOLUME 9, NUMBER 1 > > http://springerlink.metapress.com/content/m52644274770/?=20 > p=3D86dac8fa8c6c4640a5df2b6d7399d775&pi=3D0 > > > > Editorial 25 > Eric R. Scerri, > > > Wilhelm Ostwald=92s Energetics 1: Origins and Motivations > R.J. Deltete > > > The closure of the Department of Chemistry at the University of =20 > Exeter =96 An insider=92s view > Klaus Jacob > > > The need for the historical understanding of nature in physics and =20 > chemistry > Leo Napinen > > > Letter to the Editor: The concept of chemical bond =96 some like it =20= > fuzzy but others concrete (letter to the editor) > Shant Shahbazian and Mansour Zahedi > > > BOOK REVIEW > Carmen Giunta on Richard Morris, The Last Sorcerers: The Path =46rom =20= > Alchemy to the Periodic Table. > > > BOOK REVIEW > Janet Stemwedl on D. Baird, E.R. Scerri, L. McIntyre, The =20 > Philosophy of Chemistry: The Synthesis of a New Discipline. > > > > > > ----------------------------------------------------------------------=20= > ----------------------------------------------------------------------=20= > ----------------- > The Periodic Table: Its Story and Its Significance, by Eric Scerri, =20= > Oxford University Press, 2006. > > "An absolutely gorgeous book. I put it on my bedside table =20 > and then stayed up half the night reading it - it is immensely =20 > readable." > ---Oliver Sacks, author of The Man Who Mistook his Wife =20 > for a Hat, Awakenings etc. > ----------------------------------------------------------------------=20= > ----------------------------------------------------------------------=20= > ------------------------------------------------- > > Dr. Eric Scerri > Department of Chemistry & Biochemistry, > Charles Young Drive, > Los Angeles, > CA 90095-1569. > > 310 206 7443 > fax: 310 206 2061 > > UCLA faculty web page: http://www.chem.ucla.edu/dept/Faculty/scerri/ > > Editor of Foundations of Chemistry, > http://www.springer.com/sgw/cda/frontpage/=20 > 0,11855,4-40399-70-35545882-detailsPage%253Djournal%=20 > 257CmostViewedArticles%257CmostViewedArticles,00.html > > International Society for the Philosophy of Chemistry, > http://ispc.sas.upenn.edu/ > > > ------------------------------------------------------------------------=20= ------------------------------------------------------------------------=20= ------------- The Periodic Table: Its Story and Its Significance, by Eric Scerri, =20 Oxford University Press, 2006. "An absolutely gorgeous book. I put it on my bedside table =20 and then stayed up half the night reading it - it is immensely =20 readable." ---Oliver Sacks, author of The Man Who Mistook his Wife =20 for a Hat, Awakenings etc. ------------------------------------------------------------------------=20= ------------------------------------------------------------------------=20= --------------------------------------------- Dr. Eric Scerri Department of Chemistry & Biochemistry, Charles Young Drive, Los Angeles, CA 90095-1569. 310 206 7443 fax: 310 206 2061 UCLA faculty web page: http://www.chem.ucla.edu/dept/Faculty/scerri/ Editor of Foundations of Chemistry, http://www.springer.com/sgw/cda/frontpage/0,11855,4-40399-70-35545882-=20= detailsPage%253Djournal%257CmostViewedArticles%257CmostViewedArticles,=20= 00.html International Society for the Philosophy of Chemistry, http://ispc.sas.upenn.edu/ --Apple-Mail-4--500074001 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=WINDOWS-1252

=


FOUNDATIONS OF CHEMISTRY, VOLUME 9, NUMBER = 1

=



Eric R. Scerri,


R.J. = Deltete


Klaus Jacob
=A0

Leo Napinen

=A0
Shant Shahbazian and Mansour Zahedi=A0 = =A0


Carmen Giunta = on=A0=A0Richard Morris, The Last Sorcerers: The Path =46rom = Alchemy to the Periodic = Table.


BOOK = REVIEW
Janet Stemwedl on = D. Baird, E.R. Scerri, L. McIntyre,=A0 The Philosophy of Chemistry: The = Synthesis of a New Discipline.





The Periodic Table: Its = Story and Its Significance, by Eric Scerri, Oxford University Press, = 2006.
=A0=A0 =A0=A0 = =A0
=A0=A0 =A0=A0 = =A0"An absolutely = gorgeous book.=A0=A0I put it on my bedside = table and then stayed up half the night reading it - it is immensely = readable."=A0=A0 =A0=A0 =A0=A0 = =A0
=A0 =A0 =A0=A0 =A0=A0 =A0---Oliver Sacks, author of The Man Who Mistook his Wife for a = Hat,=A0Awakenings etc.
-----------------------------------------------------------------= --------------------------------------------------------------------------= --------------------------------------------------

Dr. Eric Scerri
Department of Chemistry & = Biochemistry,
Charles Young = Drive,
Los = Angeles,
CA = 90095-1569.

310 206 7443
fax: 310 206 2061

UCLA faculty web page:=A0=A0=A0http://www.chem.ucla.edu/dept/Faculty/scerri/

Editor of Foundations of Chemistry,

International Society for the Philosophy of = Chemistry,

<= /SPAN>

=


The Periodic Table: Its = Story and Its Significance, by Eric Scerri, Oxford University Press, = 2006.
=A0=A0 =A0=A0 = =A0
=A0=A0 =A0=A0 = =A0"An absolutely = gorgeous book.=A0=A0I put it on my bedside = table and then stayed up half the night reading it - it is immensely = readable."=A0=A0 =A0=A0 =A0=A0 = =A0
=A0 =A0 =A0=A0 =A0=A0 =A0---Oliver Sacks, author of The Man Who Mistook his Wife for a = Hat,=A0Awakenings etc.
-----------------------------------------------------------------= --------------------------------------------------------------------------= --------------------------------------------------

Dr. Eric Scerri
Department of Chemistry & = Biochemistry,
Charles Young = Drive,
Los = Angeles,
CA = 90095-1569.

310 206 7443
fax: 310 206 2061

UCLA faculty web page:=A0=A0=A0http://www.chem.ucla.edu/dept/Faculty/scerri/

Editor of Foundations of Chemistry,

International Society for the Philosophy of = Chemistry,

<= /SPAN>


= --Apple-Mail-4--500074001-- From owner-chemistry@ccl.net Tue Mar 6 21:40:00 2007 From: "John Merle jkmerle+*+yahoo.com" To: CCL Subject: CCL: Eyring equation for the transition state more stable than the rea Message-Id: <-33754-070306174641-23530-qqHXYKBQ6c4gMdSaXqlvww#%#server.ccl.net> X-Original-From: John Merle Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-1 Date: Tue, 6 Mar 2007 13:46:30 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: John Merle [jkmerle^_^yahoo.com] This situation is seen in reactions between polar molecules in the gas phase. You could treat the situation as a two step process. 1. Equilibrium between the reactants and the first intermediate. 2. Reaction through TS. In the end if you bypass the first intermediate (separated reactants through TS) the result will be the same. This will work for standerd TST rate calculations. The result of this low TS barrier is that the rate is inversely proportional with temperature at lower temperatures; until G for the barrier becomes greater than G for reactants. Regards, John --- "Przemyslaw G. Czyryca pczyryca]![allosterix.com" wrote: > > Sent to CCL by: "Przemyslaw G. Czyryca" > [pczyryca^-^allosterix.com] > Hmm, it may be a silly suggestion, but I think the > rate-limiting step is from the Intermediate (I) > through the TS to P. This step's energetics is quite > typical (the energy of the TS is higher then the > intermediate's), so why bother with the reactant (R) > at all? > > Regards, > Przemek > > > > -= 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/> > > > ____________________________________________________________________________________ Don't get soaked. Take a quick peek at the forecast with the Yahoo! Search weather shortcut. http://tools.search.yahoo.com/shortcuts/#loc_weather