From owner-chemistry@ccl.net Mon Jan 16 01:42:01 2006 From: "Kalju Kahn kalju- -chem.ucsb.edu" To: CCL Subject: CCL: Semiempirical examples for teaching: success stories Message-Id: <-30506-060116002545-21113-ALyIErVk+R1PnUcRnOFAgw:_:server.ccl.net> X-Original-From: Kalju Kahn Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=us-ascii Date: Sun, 15 Jan 2006 21:25:31 -0800 MIME-Version: 1.0 Sent to CCL by: Kalju Kahn [kalju++chem.ucsb.edu] Terry, Please let's keep the discussion within the context of my original question. I was looking for teaching examples, and I think that Dr. Stewart made an excellent point that semi-empirical calculations could be used, among other things, to quickly check for gross errors and suspicious entries in experimental heat of formation data. James gave an useful answer to my question ... and, please, I do not think we need another discussion about *limitations* of semiempirical models. Kalju ------------------- > Sent to CCL by: Terry Frankcombe [T.Frankcombe[]chem.leidenuniv.nl] > > > *cough* *splutter* > > Sorry James, but that's complete nonsense (to put it politely). Since when > have semiempirical extrapolations* been taken over experimental data? > Complete codswallop. A lot of the claims you make in that paper are > questionable at best. What you have shown are best interpreted as FAILURES of > semiempirical and DFT methods, not wins. > > > Terry > > > *I say extrapolations to highlight that semiempirical methods applied outside > their training set are not much more than guesses. Informed guesses, but > guesses nonetheless. > > > -- > Dr Terry Frankcombe > LIC / Theoretical Chemistry > University of Leiden > Postbus 9502, 2300 RA Leiden, The Netherlands > Ph. +31 71 527 4533 Fax +31 71 527 4397 > > > > > > > Sent to CCL by: "James J. P. Stewart" [mrmopac||worldnet.att.net] > > --=====================_177286794==.ALT > > Content-Type: text/plain; charset="us-ascii"; format=flowed > > > > My apologies: My last message re semiempirical methods contained invalid URLs > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Dr. Kalju Kahn Department of Chemistry and Biochemistry University of California, Santa Barbara From owner-chemistry@ccl.net Mon Jan 16 09:04:00 2006 From: "Goedele Roos groos_._vub.ac.be" To: CCL Subject: CCL: reference of the original paper on counterpoise Message-Id: <-30507-060116085814-20908-xKzbG6KgFel021QMEGNd7A|,|server.ccl.net> X-Original-From: Goedele Roos Date: Mon, 16 Jan 2006 14:58:07 +0100 (CET) Sent to CCL by: Goedele Roos [groos\a/vub.ac.be] Dear All, I've tried to find the titel and page numbers and abstract of this article Boys, S. F., Bernardi, F., Mol. Phys. 1970, 19, 553 But I can't find it... Can someone help me out? Thanks a lot, Goedele Drs. Goedele Roos Dienst Algemene Chemie (ALGC) Vrije Universiteit Brussel (VUB) Pleinlaan 2 B-1050 Brussels Tel: 0032-2-629 35 16 Fax: 0032-2-629 33 17 From owner-chemistry@ccl.net Mon Jan 16 10:02:00 2006 From: "Abhik Mukhopadhyay abhikuohyd[-]yahoo.com" To: CCL Subject: CCL: how to use the "field" keyword in gaussian03 for broken symmetry? Message-Id: <-30508-060116060814-1576-jrCl9C53LzcYN7C5MMvWgg%a%server.ccl.net> X-Original-From: "Abhik Mukhopadhyay" Sent to CCL by: "Abhik Mukhopadhyay" [abhikuohyd*o*yahoo.com] Dear users I want to know how i should use this "field" and "symm" keyword when doing calculation of broken symmetry. I saw some input files with field value "X+50" , "X+.01" etc. What do they signify? I am working on a dinuclear metal complex system having two unpaired electron on metal which are not directly bridged. In this case how i should define the "field" value and based on what it should be defined. Thnaks in advance. With regards Abhik Mukhopadhyay Research Scholar University of Hyderabad Hyd-500046 From owner-chemistry@ccl.net Mon Jan 16 10:37:01 2006 From: "Michael Devereux michael.devereux .. student.manchester.ac.uk" To: CCL Subject: CCL: PROAIMV question... Message-Id: <-30509-060116084858-20005-R8w/DBiVEzp/ly4wIDIJTw ~ server.ccl.net> X-Original-From: Michael Devereux Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-15 Date: Mon, 16 Jan 2006 13:12:22 +0000 MIME-Version: 1.0 Sent to CCL by: Michael Devereux [michael.devereux .. student.manchester.ac.uk] Dear CCLers, I have a quick question for anyone familiar with Bader's 'PROAIMV' program. As atoms theoretically extend to infinity where not bounded by an interatomic surface, what is the default practical boundary used to cap atoms during integration? It doesn't appear to be the 'VOL2' rho surface, which is quite close to the nucleus anyway. Is it the max distance criterion, set at 9au, or is this only applied as an absolute cutoff for very large atoms? Many thanks to anyone who can help me clear this up! Mike Devereux From owner-chemistry@ccl.net Mon Jan 16 11:12:00 2006 From: "John Hearns john.hearns{=}streamline-computing.com" To: CCL Subject: CCL: Randell Mills Message-Id: <-30510-060116031132-11930-bhJbchNlhv4aCWXSfdMMXQ..server.ccl.net> X-Original-From: John Hearns Content-Transfer-Encoding: 7bit Content-Type: text/plain Date: Mon, 16 Jan 2006 07:14:20 +0000 Mime-Version: 1.0 Sent to CCL by: John Hearns [john.hearns,,streamline-computing.com] On Sun, 2006-01-15 at 19:42 -0500, Brian Salter-Duke b_duke===octa4.net.au wrote: > Sent to CCL by: Brian Salter-Duke [b_duke:-:octa4.net.au] > Randell Mills is famous for coming up with the theory that the H atom > can be made smaller than in its ground state and that this can be used > to generate cheap power. http://www.englishteastore.com/cafrnutchbar.html I guess its true if you substitute a muon in there, but that's a different story. "Since this gas is lighter than air, it may also be safely vented and allowed to diffuse into space. " I guess atmospheric hydrogen will eventually diffuse off into space. (Actually, that's quite an interesting topic. Does anyone have a reference on the mean time for this process? I would guess years). From owner-chemistry@ccl.net Mon Jan 16 11:47:00 2006 From: "Jim Pfaendtner pfaendtner##northwestern.edu" To: CCL Subject: CCL: reference of the original paper on counterpoise Message-Id: <-30511-060116093837-12457-WCEfqx7TYwjIc6ieQoo9kg:+:server.ccl.net> X-Original-From: Jim Pfaendtner Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Mon, 16 Jan 2006 08:38:33 -0600 MIME-Version: 1.0 Sent to CCL by: Jim Pfaendtner [pfaendtner%x%northwestern.edu] From Jensen's book, I got this: F.B. van Duijneveldt et al. Chem Rev, 94 (1994), p.1873 good luck Goedele Roos groos_._vub.ac.be wrote: >Sent to CCL by: Goedele Roos [groos\a/vub.ac.be] >Dear All, >I've tried to find the titel and page numbers and abstract of this article >Boys, S. F., Bernardi, F., Mol. Phys. 1970, 19, 553 >But I can't find it... >Can someone help me out? > >Thanks a lot, >Goedele > >Drs. Goedele Roos >Dienst Algemene Chemie (ALGC) >Vrije Universiteit Brussel (VUB) >Pleinlaan 2 >B-1050 Brussels >Tel: 0032-2-629 35 16 >Fax: 0032-2-629 33 17> > > > From owner-chemistry@ccl.net Mon Jan 16 12:22:00 2006 From: "Pieter vanGrootel p.w.v.grootel . student.tue.nl" To: CCL Subject: CCL:G: Examine results by Gaussian Message-Id: <-30512-060116075144-13468-kQaPmukqzVRHC1ZkulcnKg*server.ccl.net> X-Original-From: "Pieter vanGrootel" Sent to CCL by: "Pieter vanGrootel" [p.w.v.grootel[-]student.tue.nl] Dear CCL Subscribers, I'm examining a system containing a transition-metal with Gaussian03/Linda. I'm familiar with the theory behind Gaussian, but so far Gaussian is a black box to me. Gaussian provides me with several results, but I don't want to take these results as a truth, I want to check the results before accepting them as a true result. I want to ask those of you who are familiar with these calculations, some references to articles or sites, where I can find some standard tools or procedures to check whether the given results are results. With kind regards, Pieter van Grootel p[dot]w[dot]v[dot]grootel[at]student[dot]tue[dot]nl From owner-chemistry@ccl.net Mon Jan 16 12:57:00 2006 From: "Terry Frankcombe T.Frankcombe|*|chem.leidenuniv.nl" To: CCL Subject: CCL:G: how to use the "field" keyword in gaussian03 for broken symmetry? Message-Id: <-30513-060116101339-31684-skPRL3w4qbbqkNcaM5MC5g : server.ccl.net> X-Original-From: Terry Frankcombe Content-Type: text/plain; charset=us-ascii Date: Mon, 16 Jan 2006 16:13:29 +0100 Mime-Version: 1.0 Sent to CCL by: Terry Frankcombe [T.Frankcombe^^^chem.leidenuniv.nl] Have you read this: ? > Sent to CCL by: "Abhik Mukhopadhyay" [abhikuohyd*o*yahoo.com] > Dear users > I want to know how i should use this "field" and "symm" keyword when doing ca lculation of broken symmetry. I saw some input files with field value "X+50" , "X+.01" etc. What do they signify? > I am working on a dinuclear metal complex system having two unpaired electron on metal which are not directly bridged. In this case how i should define the "field" value and based on what it should be defined. > > Thnaks in advance. > > With regards > Abhik Mukhopadhyay > Research Scholar > University of Hyderabad > Hyd-500046> > From owner-chemistry@ccl.net Mon Jan 16 13:31:01 2006 From: "Tanja van Mourik t.vanmourik#ucl.ac.uk" To: CCL Subject: CCL: reference of the original paper on counterpoise Message-Id: <-30514-060116102109-7436-sGUO2sZgdih+gQ+9RbyHhg|*|server.ccl.net> X-Original-From: Tanja van Mourik Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii Date: Mon, 16 Jan 2006 14:40:43 +0000 (GMT) MIME-Version: 1.0 Sent to CCL by: Tanja van Mourik [t.vanmourik(~)ucl.ac.uk] Dear Goedele, > I've tried to find the titel and page numbers and abstract of this article > Boys, S. F., Bernardi, F., Mol. Phys. 1970, 19, 553 > But I can't find it... > Can someone help me out? I don't have the abstract, but here are the title and page numbers of this article: Title: CALCULATION OF SMALL MOLECULAR INTERACTIONS BY DIFFERENCES OF SEPARATE TOTAL ENERGIES - SOME PROCEDURES WITH REDUCED ERRORS Molecular Physics 19 (issue 4), pp 553-566. Best wishes, Tanja -- ================================================================= Tanja van Mourik Royal Society University Research Fellow Chemistry Department University College London phone: +44 (0)20-7679-4663 20 Gordon Street e-mail: work: T.vanMourik..ucl.ac.uk London WC1H 0AJ, UK home: tanja..van-mourik.me.uk http://www.chem.ucl.ac.uk/people/vanmourik/index.html ================================================================= From owner-chemistry@ccl.net Mon Jan 16 14:06:00 2006 From: "Mario Citra citra]=[syrres.com" To: CCL Subject: CCL: Randell Mills Message-Id: <-30515-060116102117-7472-DZuXyjDIq5ZRCSkF9O66hA]|[server.ccl.net> X-Original-From: Mario Citra Content-Type: text/plain; charset="us-ascii"; format=flowed Date: Mon, 16 Jan 2006 09:38:06 -0500 Mime-Version: 1.0 Sent to CCL by: Mario Citra [citra_+_syrres.com] Thats really the problem - no one does. A few years ago when I looked at his claims, I remember being less than impressed with his arguments. He went through great lengths to re-derive Bohr's model of the hydrogen atom and claimed it represented some new understanding of the quantum universe (grand unified theory of classical QM). I stopped reading shortly thereafter. I believe Robert Park has reviewed and debunked much of Mills work. He has a book called Voodoo Science that might address this topic. At 07:50 PM 1/15/2006 -0500, you wrote: >I really do not have time to wade through this sludge in Mills' online >book. I really want to know whether anyone else has done so. > >Regards, Brian. Regards, Mario J. Citra Ph.D. Syracuse Research Corporation (315) 452-8406 citra::syrres.com http://esc.syrres.com/ From owner-chemistry@ccl.net Mon Jan 16 14:42:01 2006 From: "Pedro Salvador pedro.salvador%%udg.es" To: CCL Subject: CCL: reference of the original paper on counterpoise Message-Id: <-30516-060116104508-17196-GPeGhtM3VydbLUalULyE0w]*[server.ccl.net> X-Original-From: Pedro Salvador Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Mon, 16 Jan 2006 15:47:11 +0100 MIME-Version: 1.0 Sent to CCL by: Pedro Salvador [pedro.salvador:+:udg.es] Dear Godele, This is what I got from ISI: *CALCULATION OF SMALL MOLECULAR INTERACTIONS BY DIFFERENCES OF SEPARATE TOTAL ENERGIES - SOME PROCEDURES WITH REDUCED ERRORS* Author(s): BOYS SF , *BERNARDI F* Source: MOLECULAR PHYSICS 19 (4): 553-& 1970 Document Type: Article Language: English *Cited References:* 5 *Times Cited:* 5336 Publisher: TAYLOR & FRANCIS LTD, ONE GUNPOWDER SQUARE, LONDON EC4A 3DF, ENGLAND Subject Category: PHYSICS, ATOMIC, MOLECULAR & CHEMICAL IDS Number: H3964 ISSN: 0026-8976 Hope it helps, Pedro Goedele Roos groos_._vub.ac.be wrote: >Sent to CCL by: Goedele Roos [groos\a/vub.ac.be] >Dear All, >I've tried to find the titel and page numbers and abstract of this article >Boys, S. F., Bernardi, F., Mol. Phys. 1970, 19, 553 >But I can't find it... >Can someone help me out? > >Thanks a lot, >Goedele > >Drs. Goedele Roos >Dienst Algemene Chemie (ALGC) >Vrije Universiteit Brussel (VUB) >Pleinlaan 2 >B-1050 Brussels >Tel: 0032-2-629 35 16 >Fax: 0032-2-629 33 17> > > > From owner-chemistry@ccl.net Mon Jan 16 15:17:00 2006 From: "FyD fyd,,u-picardie.fr" To: CCL Subject: CCL: Release of RESP ESP charge DDatabase Message-Id: <-30517-060116111235-10192-eswlZp+ibq/Bsw4umt0DaA|*|server.ccl.net> X-Original-From: FyD Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Mon, 16 Jan 2006 17:12:18 +0100 MIME-Version: 1.0 Sent to CCL by: FyD [fyd()u-picardie.fr] Dear CCL users, I am pleased to announce the release of the RESP ESP charge DDataBase (or R.E.DD.B.) [-] http://www.u-picardie.fr/labo/lbpd/REDDB/. RESP and ESP charges centered on atoms are needed in many molecular mechanics and docking studies, and used in many force field based simulations. These atomic charges are recognized as highly efficient to reproduce many molecular properties. However, no real system allows to rigorously define the charge derivation conditions, and store, compare and distribute the corresponding charge values. The RESP ESP charge DDataBase is a new source of RESP or ESP charge values for small structures and model systems. Its goals are multiple. R.E.DD.B. allows to freely store and distribute RESP and ESP charges of high quality and high reproduciblility in the scientific community. However, R.E.DD.B. can also be seen as a tool devoted to reproduce, compare, criticize and improve the different RESP and ESP models. Many different procedures are used to derive such RESP or ESP charges, and the charge values are affected by many parameters (QM programs, algorithms, molecular orientation, molecular conformation, human errors, etc...). Thus, R.E.DD.B. not only stores RESP or ESP charge values, but also the structures (Cartesian coordinates optimized by QM) and detailed information about the method used to derive the charges. Two types of the data or projects can be found in R.E.DD.B. * WHOLE MOLECULE type projects, "W-$n", which corresponds to an intact (un-broken) molecule. Examples are small organic or inorganic molecules such as solvent molecules (Dimethylsulfoxide, Ethanol, Cyclohexane etc...), or ligands of proteins or nucleic acids. * MOLECULE FRAGMENT type projects, "F-$n", which corresponds to a part (or fragment) of an organic or inorganic macro-molecule. Examples are amino-acid fragments 'NH-CH(R)-CO' (AA) where the atomic charges are generally derived using capped amino acids 'ACE-AA-NME', nucleotide fragments originating from the fusion between dimethylphosphate and the corresponding nucleosides, or monosaccharide fragments. These fragments are generally compatible with previously existing ones (available in force field topology databases), and used to construct macro-molecules such as proteins, nucleic acids or polysaccharides. DESCRIPTION OF R.E.DD.B.: - A R.E.DD.B. project code is automatically attributed to each project submitted in R.E.DD.B. once it has been sucessfully uploaded. This code should to be used by its author(s) to reference the R.E.DD.B. project in the corresponding publication. Consequently, the R.E.DD.B. project code provides a rigorous link between the charge values and the corresponding publication insuring the definition/reproducibility of the published results. - A tool has been developped allowing the author(s) of a project (i) to fully describe the computational conditions she/he used in the charge derivation procedure and (ii) to upload the files required to characterize this project. - A second tool has been written to efficiently search projects within R.E.DD.B. and download the corresponding projects. - FAQ are available to describe the project submission procedure, the data and files required for a submission, the ways of searching projects in R.E.DD.B. and much more. - A list of references about RESP and ESP charges is also available. - Each whole molecule and molecule fragment and its corresponding charge values is visualized within HTML pages using the Jmol program, http://jmol.sourceforge.net/, and J2SE Runtime Environment, http://java.sun.com/j2se/1.5.0/download.jsp. - For each molecule name and project name provided in a project a link to Wikipedia, the Free Encyclopedia, http://en.wikipedia.org/wiki/Main_Page/ is generated providing general information. - The R.E.DD.B.2t ("bis & test") internet site, http://www.u-picardie.fr/labo/lbpd/REDDB2t/ has been designed to track bugs in the system. It can also be used by anyboby interested in learning how to submit projects in the official RESP ESP charge DDatabase. Thus, this "bis & test" web site is useful for knowing the information required before/for an official R.E.DD.B. by performing and recording blind tests. EXAMPLES OF PROJECT AVAILABLE IN R.E.DD.B.: We have already submitted close to 140 projects involving multi-orientation, multi-conformation and/or multi-molecule RESP or ESP fit. Below, is a short listing of some projects available in R.E.DD.B.: * RESP atomic charges for 10 solvent molecules based on the Connolly surface algorithm and the HF/6-31G* theory level: Project "W-46", http://www.u-picardie.fr/labo/lbpd/REDDB/up/W-46/info.html with many links to Wikipedia: http://en.wikipedia.org/wiki/Organic_solvent, http://en.wikipedia.org/wiki/Ethanol, http://en.wikipedia.org/wiki/Dimethylsulfoxide etc... * RESP atomic charges for 10 solvent molecules based on the CHELPG algorithm and the HF/6-31G* theory level: Project "W-47". * ESP atomic charges for 10 solvent molecules based on the Connolly surface algorithm and the HF/6-31G* theory level: Project "W-48". * ESP atomic charges for 10 solvent molecules based on the CHELPG algorithm and the HF/6-31G* theory level: Project "W-49". * RESP atomic charges for the 4 DNA and RNA nucleosides based on the Connolly surface algorithm and the HF/6-31G* theory level: Projects "W-69" and "W-74". * RESP atomic charges for the 4 DNA and RNA nucleosides based on the CHELPG algorithm and the HF/6-31G* theory level (following a strategy similar to that applied in the GLYCAM 2004 force field, http://glycam.ccrc.uga.edu/index.jsp): Projects "W-73" and "W-78". * RESP atomic charges for the central, (+)NH3-terminal, (-)OOC-terminal, NH2-terminal and HOOC-terminal fragments of the dimethylalanine amino acid based on the Connolly surface algorithm and the HF/6-31G* theory level: Project F-3, http://www.u-picardie.fr/labo/lbpd/REDDB/up/F-3/info.html and Projects "F-7", "F-11", "F-15" "F-19", respectively. * Similar data are available for the O-methyl-L-tyrosine amino acid, http://www.scripps.edu/newsandviews/e_20011029/schultz1.html involving the Connolly surface and the CHELPG algorythm (RESP and ESP charges): Projects "F-23" up to "F-44". * RESP atomic charges based on the Connolly surface algorithm and the HF/6-31G* theory level for the 16 components of a force field topology database useful for modeling regular DNA: Project "F-45", http://www.u-picardie.fr/labo/lbpd/REDDB/up/F-45/info.html with a LEaP script, http://www.u-picardie.fr/labo/lbpd/REDDB/up/F-45/leaprc-mol2tooff.ff to convert the library precursors (Tripos format) into OFF files. * RESP atomic charges based on the CHELG algorithm and the HF/6-31G* theory level for the 16 components of a force field topology database useful for modeling regular DNA (following a strategy similar to that applied in the GLYCAM 2004 force field): Project "F-49". * Same as project F-45, but the phosphate is located at the O3' position instead of the O5' one: Project "F-50". * RESP atomic charges based on the Connolly surface algorithm and the HF/6-31G* theory level for the 16 components of a force field topology database useful for modeling regular RNA: Project "F-51" with a LEaP script to convert the library precursors (Tripos format) into OFF files (up to "F-56" for other RNA force field topology databases). * Unusual nucleotide projects: "F-57", "F-58" and "F-59". More projects are available, see the download section... These projects have been carried out using the R.E.D. program (version III), http://www.u-picardie.fr/labo/lbpd/RED/. We hope the community will find R.E.DD.B. interesting and will participate to its development. We encourage researchers to submit projects in R.E.DD.B. involving multi-orientations, multi-conformations and multi-molecules and not only single-orientation, single-conformation and single molecule projects which are more limited. This email is available [-] http://www.u-picardie.fr/labo/lbpd/REDDB/release.php with all the links to the R.E.DD.B. projects reported. Best regards, Francois -- * F.-Y. Dupradeau * DMAG EA 3901 & Faculte de Pharmacie, Amiens, France **** http://www.u-picardie.fr/labo/lbpd/FyD.htm From owner-chemistry@ccl.net Mon Jan 16 15:52:01 2006 From: "Guosheng Wu wu_guosheng2002%%yahoo.com" To: CCL Subject: CCL: Questions on the protonations of a HIV-1 protease (1aaq) Message-Id: <-30518-060116113042-30332-y61vv+pQ8sfQ2u9ulwMnXw_._server.ccl.net> X-Original-From: Guosheng Wu Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-1 Date: Mon, 16 Jan 2006 07:30:34 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: Guosheng Wu [wu_guosheng2002[*]yahoo.com] Dear listers, I am puzzled in assigning protonation states for some HIV-1 protease complexes, and 1aaq(pdb code) is a typical complex of many structures. > From this structure, one can see all of the 5 oxygen atoms (from Asp 25 & Asp 125, and ligand OH) are very close to each other(2.7~3.1), and almost in the same plane. Also each of the Gly 27 is not far away(about 3.3 Angstrom) from the Asp 25, although the angle of H-bond is not very good (the Xray resolution is 2.5 Angstrom, exp. done in 1992; only one water is given, but not close to this part). Since the OO contact between Asp 25 and Asp 125 is 2.5 Angstrom, which is about the distance of OO in H5O2+ ion(2.4), one would like to assign a proton between them. However, it seems very difficulty to rationalize other polar interactions. One possible explanation may have something to do with quantum effect, which may lead to some modifications over the hybridization of the ligand Oxygen atom, as well as some of the C-O-H bond angles. Certainly, some kind of minimizations may be able to help on some directions, but it seems to me typical current force field would have trouble for this case. I wonder if you have done any study on this special complex, or similar cases (actually many pdb structures are like this one). I would really appreciate if you could share some of your insights with me. Best regards, Guosheng __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com From owner-chemistry@ccl.net Mon Jan 16 16:27:00 2006 From: "Xu Wang xwang6+*+uky.edu" To: CCL Subject: CCL:G: PES for 4,4'-bipyridine Message-Id: <-30519-060116120847-23198-7h+0ITqyyx1mi5cFVsm06A^^^server.ccl.net> X-Original-From: "Xu Wang" Sent to CCL by: "Xu Wang" [xwang6[#]uky.edu] Hey, Before I had the question about the PES (potential energy surface) scan for the 2,2'-bipyridine with respect to the dihedral angle of both pyridine rings. Some of you helped me out about that at the time. I really appreciate it! These days, I am doing a similar calculation for 4,4-bipyridine. I have gotten the PES curve using the B3LYP method. When I was trying to perform the scan with the MP2 method and practically the same input file, I got an error message as follows: PROGRAM ABORTED : IEEE inexact result PROCEDURE TRACEBACK: (0) 0x4000000000156a50 FTN_GETARITRAP + 0x570 [/opt/cluster/apps/g03-C.02.M1/g03/l801.exe] (1) 0x40000000001577d0 U_CATCH_ARITHMETIC_TRAP + 0x3b0 [/opt/cluster/apps/g03-C.02.M1/g03/l801.exe] (2) 0xe000000190002660 _user_sendsig + 0x2660 [***_Kernel_Gateway_***] (3) 0x40000000005a8262 ipopvc_ + 0xe2 [/opt/cluster/apps/g03-C.02.M1/g03/l801.exe] (4) 0x4000000000597ab0 caldsu_ + 0x46d0 [/opt/cluster/apps/g03-C.02.M1/g03/l801.exe] (5) 0x40000000008432d0 harfok_ + 0xb90 [/opt/cluster/apps/g03-C.02.M1/g03/l801.exe] (6) 0x40000000007f8bd0 atharmo_ + 0xd00 [/opt/cluster/apps/g03-C.02.M1/g03/l801.exe] (7) 0x40000000007f2180 findco_ + 0x3c0 [/opt/cluster/apps/g03-C.02.M1/g03/l801.exe] (8) 0x4000000000153fe0 window_ + 0x3dd0 [/opt/cluster/apps/g03-C.02.M1/g03/l801.exe] (9) 0x40000000000f77c0 _start + 0x1c0 [/opt/cluster/apps/g03-C.02.M1/g03/l801.exe] (10) 0xc00000000004e070 main_opd_entry + 0x50 [/usr/lib/hpux64/dld.so] I dont have any idea about this. Any suggestions or comments are appreciated! FYI, OPT=ModRedundant and Nosymm were used. The basis set was 6-311+G(d,p). Thanks, Xu --- Wang Xu Department of Chemistry, University of Kentucky (O)859-257-6150 From owner-chemistry@ccl.net Mon Jan 16 17:02:00 2006 From: "Nuno A. G. Bandeira nuno.bandeira%%ist.utl.pt" To: CCL Subject: CCL:G: Examine results by Gaussian Message-Id: <-30520-060116131607-11932-3kdgZWOeiMAJ+iavF1t5mw]*[server.ccl.net> X-Original-From: "Nuno A. G. Bandeira" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii; format=flowed Date: Mon, 16 Jan 2006 18:16:02 +0000 MIME-Version: 1.0 Sent to CCL by: "Nuno A. G. Bandeira" [nuno.bandeira###ist.utl.pt] Pieter vanGrootel p.w.v.grootel . student.tue.nl wrote: > Sent to CCL by: "Pieter vanGrootel" [p.w.v.grootel[-]student.tue.nl] > Dear CCL Subscribers, > > I'm examining a system containing a transition-metal with Gaussian03/Linda. > > I'm familiar with the theory behind Gaussian, but so far Gaussian is a black box to me. > Gaussian provides me with several results, but I don't want to take these results as a truth, I want to check the results before accepting them as a true result. > > I want to ask those of you who are familiar with these calculations, some references to articles or sites, where I can find some standard tools or procedures to check whether the given results are results. What exactly did you run in Gaussian ? -- Nuno A. G. Bandeira, AMRSC Graduate researcher and molecular sculptor Inorganic and Theoretical Chemistry Group, Faculty of Science University of Lisbon - C8 building, Campo Grande, 1749-016 Lisbon,Portugal http://cqb.fc.ul.pt/intheochem/nuno.html Doctoral student ^^ IST,Lisbon -- From owner-chemistry@ccl.net Mon Jan 16 17:37:00 2006 From: "Ewald Pauwels ewald.pauwels.:.UGent.be" To: CCL Subject: CCL: CCL G: internal rotation in hydrocarbons Message-Id: <-30521-060116120712-22737-i0W/ixatjXjgw7zchvKdRA/a\server.ccl.net> X-Original-From: Ewald Pauwels Content-Type: multipart/mixed; boundary="=======AVGMAIL-43CBC3986700=======" Date: Mon, 16 Jan 2006 17:02:31 +0100 Mime-Version: 1.0 Sent to CCL by: Ewald Pauwels [ewald.pauwels:-:UGent.be] --=======AVGMAIL-43CBC3986700======= Content-Type: multipart/alternative; boundary=------------000100050205070803090208 --------------000100050205070803090208 Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit Dear Jim, Our research group (see http://molmod.ugent.be/ ) has a lot of experience in treating large amplitude motions, or more specifically internal rotations. Currently, there is a program available ('HRpublic.v1'), which is designed to treat the one-dimensional hindered rotor (HR-1D) in a consistent way. The program evaluates the HR-1D partition function, which is the key quantity for further study of thermochemical quantities and reaction kinetics. The HR-1D partition function is evaluated within the classical limit and corrected with the Pitzer-Gwinn values. [Copyright program source code : Center for Molecular Modeling (CMM) - Ghent University - Belgium] The program is free from licence for scientific purposes. The source code and accompanying ReadMe file can be obtained after simple request to the CMM. It is also possible to obtain a quantum mechanically based program to calculate energy levels. It requires the input of a fourier fit, and of a moment of inertia (which can be calculated with the other program). For more info, feel free to contact Peter Vansteenkiste: http://molmod.ugent.be/people/peter.xml Sincerely, Ewald. -- Ewald Pauwels Center for Molecular Modeling Laboratory of Theoretical Physics Ghent University Proeftuinstraat 86 B-9000 Gent Belgium http://molmod.ugent.be ewald.pauwels!^!UGent.be +32 9 264 65 76 --------------000100050205070803090208 Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit

Dear Jim,

Our research group (see http://molmod.ugent.be/ ) has a lot of experience in treating large amplitude motions, or more specifically internal rotations.

Currently, there is a program available ('HRpublic.v1’), which is designed to treat the one-dimensional hindered rotor (HR-1D) in a consistent way. The program evaluates the HR-1D partition function, which is the key quantity for further study of thermochemical quantities and reaction kinetics. The HR-1D partition function is evaluated within the classical limit and corrected with the Pitzer-Gwinn values.

[Copyright program source code : Center for Molecular Modeling (CMM) - Ghent University - Belgium]
The program is free from licence for scientific purposes. The source code and accompanying ReadMe file can be obtained after simple request to the CMM.

It is also possible to obtain a quantum mechanically based program to calculate energy levels. It requires the input of a fourier fit, and of a moment of inertia (which can be calculated with the other program).

For more info, feel free to contact Peter Vansteenkiste: http://molmod.ugent.be/people/peter.xml

Sincerely,
Ewald.

-- 
Ewald Pauwels
Center for Molecular Modeling
Laboratory of Theoretical Physics
Ghent University
Proeftuinstraat 86
B-9000 Gent
Belgium
http://molmod.ugent.be
ewald.pauwels!^!UGent.be
+32 9 264 65 76
--------------000100050205070803090208-- --=======AVGMAIL-43CBC3986700======= Content-Type: text/plain; x-avg=cert; charset=us-ascii Content-Transfer-Encoding: quoted-printable Content-Disposition: inline Content-Description: "AVG certification" No virus found in this outgoing message. Checked by AVG Free Edition. Version: 7.1.371 / Virus Database: 267.14.18/230 - Release Date: 14/01/2006 = --=======AVGMAIL-43CBC3986700=======-- From owner-chemistry@ccl.net Mon Jan 16 18:12:00 2006 From: "Connie Chang cc236++cornell.edu" To: CCL Subject: CCL: Gaussian03 error, stuck Message-Id: <-30522-060116140109-2715-ec560bvR4haebhExvjWupQ(0)server.ccl.net> X-Original-From: Connie Chang Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Mon, 16 Jan 2006 13:04:22 -0500 MIME-Version: 1.0 Sent to CCL by: Connie Chang [cc236]~[cornell.edu] Hi, I know I've asked this question in the past, but I'm not sure if I got many responses from it. I'm running a 56 atom B3LYP 6311G frequency calculation. Here is the relevant input line: %mem=1800Mb %rwf=t1,200MW,t2,200MW,t3,200MW,t4,200MW,t5,200MW,t6,200MW,t7,200MW, t8,200MW,t9,200MW,t10,200MW,t11,-1 %chk=/a/cc236/polycharge56.chk #T B3LYP 6-311G Geom=Allcheck Guess=Read Freq Test And it gets stuck on this step: Symmetrizing basis deriv contribution to polar: IMax=3 JMax=2 DiffMx= 0.00D+00 Calling FoFCou, ICntrl= 3107 FMM=T I1Cent= 0. Calling FoFCou, ICntrl= 3107 FMM=T I1Cent= 0. Calling FoFCou, ICntrl= 3107 FMM=T I1Cent= 0. FoFCou: FMM=T IPFlag= 0 FMFlag= 100000 FMFlg1= 8193 NFxFlg= 0 DoJE=F BraDBF=F KetDBF=F FulRan=T. Symmetry not used in FoFCou. FMM levels: 10 Number of levels for PrismC: 9 PrismC: NFx= 2048 NFxT= 41 NFxU= 40. PrismC: NFx= 2048 NFxT= 41 NFxU= 41. Does anyone know why it's stuck here? Is it because I'm splititng up my rwf files improperly? Is there some way I can check where I'm getting stuck? I don't think using #P gives me any more output info. Thanks in advance... -Connie From owner-chemistry@ccl.net Mon Jan 16 18:47:00 2006 From: "Kalju Kahn kalju---chem.ucsb.edu" To: CCL Subject: CCL: reference of the original paper on counterpoise Message-Id: <-30523-060116134037-27998-6Rw5uW0NhbZK4J0M7JDS4g#%#server.ccl.net> X-Original-From: Kalju Kahn Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=us-ascii Date: Mon, 16 Jan 2006 10:21:01 -0800 MIME-Version: 1.0 Sent to CCL by: Kalju Kahn [kalju[#]chem.ucsb.edu] Dear Goedele, I have the title and page numbers. Boys, S. F. Bernardi, F. The calculation of small molecular interactions by the differences of separate total energies. Some procedures with reduced errors. Mol. Phys. 19, 553-566 (1970) Hope this helps. Kalju ------------------- > Sent to CCL by: Goedele Roos [groos\a/vub.ac.be] > Dear All, > I've tried to find the titel and page numbers and abstract of this article > Boys, S. F., Bernardi, F., Mol. Phys. 1970, 19, 553 > But I can't find it... > Can someone help me out? > > Thanks a lot, > Goedele > > Drs. Goedele Roos > Dienst Algemene Chemie (ALGC) > Vrije Universiteit Brussel (VUB) > Pleinlaan 2 > B-1050 Brussels > Tel: 0032-2-629 35 16 > Fax: 0032-2-629 33 17> > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ -+ > > > > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Dr. Kalju Kahn Department of Chemistry and Biochemistry University of California, Santa Barbara From owner-chemistry@ccl.net Mon Jan 16 19:21:00 2006 From: "Charles Hu umchhu~~yahoo.com" To: CCL Subject: CCL: Heating Locally in MD Message-Id: <-30524-060116170034-2196-/OPCiZJpfbZAuHI1LWn7lQ.:.server.ccl.net> X-Original-From: Charles Hu Content-Transfer-Encoding: 8bit Content-Type: multipart/alternative; boundary="0-1539825457-1137445232=:78507" Date: Mon, 16 Jan 2006 13:00:32 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: Charles Hu [umchhu]=[yahoo.com] --0-1539825457-1137445232=:78507 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Dear CCLers, I am novice user here and would like to do some molecular dynamics calculation of an enzyme, with special requirement that only heating a part of the protein and freeze the rest. i.e., after minimizing and equilibrating the whole protein at 10K, only thermalize the active site of the enzyme to 300K. I am wondering which MD package could that. If possible, I prefer to free software such as TINKER. Thank you very much! --------------------------------- Yahoo! Photos – Showcase holiday pictures in hardcover Photo Books. You design it and we’ll bind it! --0-1539825457-1137445232=:78507 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: 8bit
Dear CCLers,

I am novice user here and would like to do some molecular dynamics calculation of an enzyme, with special requirement that only heating a part of the protein and freeze the rest. i.e., after minimizing and equilibrating the whole protein at 10K, only thermalize the active site of the enzyme to 300K. 

I am wondering which MD package could that. If possible, I prefer to free software such as TINKER.

Thank you very much!

Yahoo! Photos – Showcase holiday pictures in hardcover
Photo Books. You design it and we’ll bind it! --0-1539825457-1137445232=:78507-- From owner-chemistry@ccl.net Mon Jan 16 19:56:00 2006 From: "Brian Salter-Duke b_duke/a\octa4.net.au" To: CCL Subject: CCL: Randell Mills Message-Id: <-30525-060116165743-1977-Rh2jL7hlJZwsIaCle2cEyw%server.ccl.net> X-Original-From: Brian Salter-Duke Content-Disposition: inline Content-Type: text/plain; charset=us-ascii Date: Tue, 17 Jan 2006 08:57:39 +1100 Mime-Version: 1.0 Sent to CCL by: Brian Salter-Duke [b_duke-,-octa4.net.au] On Mon, Jan 16, 2006 at 02:13:54PM -0500, Mario Citra citra]=[syrres.com wrote: > Sent to CCL by: Mario Citra [citra_+_syrres.com] > Thats really the problem - no one does. A few years ago when I looked at > his claims, I remember being less than impressed with his arguments. He > went through great lengths to re-derive Bohr's model of the hydrogen atom > and claimed it represented some new understanding of the quantum universe > (grand unified theory of classical QM). I stopped reading shortly > thereafter. I believe Robert Park has reviewed and debunked much of Mills > work. He has a book called Voodoo Science that might address this topic. I think the hydrino stuff has been debunked quite well and I think that means his calculations on many electron atoms and molecules like H2O, H3+, CN, O2 have to be faulty too. Certainly the molecule stuff is too recent to be in Park's book. It is this month. The accuracy of his numbers is attracting some people. We need to know why they are accurate. I will look to see if I can find "Voodoo Science", but it might not be in Austrtalia. Thanks for your help, Brian. > At 07:50 PM 1/15/2006 -0500, you wrote: > >I really do not have time to wade through this sludge in Mills' online > >book. I really want to know whether anyone else has done so. > > > >Regards, Brian. > > > Regards, > Mario J. Citra Ph.D. > Syracuse Research Corporation > (315) 452-8406 > citra#syrres.com > http://esc.syrres.com/> > > -- Brian Salter-Duke (Brian Duke) b_duke _ octa4.net.au Post: 626 Melbourne Rd, Spotswood, VIC, 3015, Australia Phone 03-93992847. http://members.iinet.net.au/~linden1/brian/ Honorary Researcher Fellow, Dept. of Medicinal Chemistry, Monash Univ. From owner-chemistry@ccl.net Mon Jan 16 20:32:01 2006 From: "Ross Walker ross,,rosswalker.co.uk" To: CCL Subject: CCL: Heating Locally in MD Message-Id: <-30526-060116200224-467-ZTMc2PzYj5EypmkBfjxFrg^-^server.ccl.net> X-Original-From: "Ross Walker" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Mon, 16 Jan 2006 17:01:55 -0800 MIME-Version: 1.0 Sent to CCL by: "Ross Walker" [ross]=[rosswalker.co.uk] Dear Charles, If you have a copy of AMBER then you can do this using a number of methods, probably the most reliable being restraints. You could first of all minimise the entire protein, then heat it to 10K with no restraints. Then you could add weak harmonic restraints say 5 KCal/mol/A to everything you want to fix and then heat the system to 300K. By doing things this way you should attain the correct kinetic energy ensemble for the enzyme since. A tutorial on how to do this sort of thing in AMBER is available here: http://www.rosswalker.co.uk/tutorials/amber_workshop/Tutorial_one/index.htm All the best Ross /\ \/ |\oss Walker | Department of Molecular Biology TPC15 | | The Scripps Research Institute | | Tel: +1 858 784 8889 | EMail:- ross#,#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#,#ccl.net [mailto:owner-chemistry#,#ccl.net] > Sent: Monday, January 16, 2006 16:32 > To: Walker, Ross > Subject: CCL: Heating Locally in MD > > Sent to CCL by: Charles Hu [umchhu]=[yahoo.com] > --0-1539825457-1137445232=:78507 > Content-Type: text/plain; charset=iso-8859-1 > Content-Transfer-Encoding: 8bit > > Dear CCLers, > > I am novice user here and would like to do some molecular > dynamics calculation of an enzyme, with special requirement > that only heating a part of the protein and freeze the rest. > i.e., after minimizing and equilibrating the whole protein at > 10K, only thermalize the active site of the enzyme to 300K. > > I am wondering which MD package could that. If possible, I > prefer to free software such as TINKER. > > Thank you very much! > > > > > --------------------------------- > Yahoo! Photos - Showcase holiday pictures in hardcover > Photo Books. You design it and we'll bind it! > --0-1539825457-1137445232=:78507 > Content-Type: text/html; charset=iso-8859-1 > Content-Transfer-Encoding: 8bit > >
Dear CCLers,

I am novice user > here and would like to do some molecular dynamics calculation > of an enzyme, with special requirement that only heating a > part of the protein and freeze the rest. i.e., after > minimizing and equilibrating the whole protein at 10K, only > thermalize the active site of the enzyme to 300K.  >

I am wondering which MD package could that. If > possible, I prefer to free software such as TINKER. >

Thank you very much!

>

Yahoo! Photos - Showcase holiday > pictures in hardcover
> href="http://us.rd.yahoo.com/mail_us/taglines/photobooks/*http ://pa.yahoo.com/> *http://us.rd.yahoo.com/mail_us/taglines/photos/evt=38088/*htt p://pg.photos.yahoo.com/ph//page?.file=photobook_splash.html">> Photo Books. You design it and we'll bind it! > --0-1539825457-1137445232=:78507-- > > > > -= This is automatically added to each message by the mailing > script =- > To recover the email address of the author of the message, > please change> > > http://www.rosswalker.co.uk/star_wars_sounds/ > http://www.rosswalker.co.uk/adsense_alternatives/> > Search Messages: http://www.ccl.net/htdig (login: ccl, > Password: search)> > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > -+-+-+-+-+ > > > >