From chemistry-request@server.ccl.net Tue Aug 27 01:33:21 2002 Received: from pharmacy.pharm.usyd.edu.au ([129.78.154.1]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g7R5XKr12676 for ; Tue, 27 Aug 2002 01:33:21 -0400 Received: from [129.78.154.44] (pc-012.pharm.usyd.edu.au [129.78.154.44]) by pharmacy.pharm.usyd.edu.au (8.11.3/8.11.0.Beta1) with ESMTP id g7R5XJA14123 for ; Tue, 27 Aug 2002 15:33:19 +1000 (EST) User-Agent: Microsoft-Outlook-Express-Macintosh-Edition/5.02.2022 Date: Tue, 27 Aug 2002 15:35:20 +1000 Subject: DOCK 5.0 on Linux From: Michael Ivery To: Message-ID: Mime-version: 1.0 Content-type: text/plain; charset="US-ASCII" Content-transfer-encoding: 7bit Dear All, I have been trying to operate Dock5.0 under Suse 8 linux without much luck. Grid seems to run fine but when running dock the program gets to the point of reading in the ligand file and then dies with the message Segmentation Fault. I would appreciate any insight from anyone who has got this software operational. Best Wishes Michael Ivery From chemistry-request@server.ccl.net Tue Aug 27 04:26:00 2002 Received: from bute.st-andrews.ac.uk (root@[138.251.12.1]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g7R8Pxr19441 for ; Tue, 27 Aug 2002 04:25:59 -0400 Received: from superintendentchalmers.st-andrews.ac.uk (bmspc-glt2-9 [138.251.94.76]) by bute.st-andrews.ac.uk (8.9.1a/8.9.1) with ESMTP id JAA18034 for ; Tue, 27 Aug 2002 09:20:18 +0100 (BST) Message-Id: <5.1.1.6.0.20020827091902.00a57238@bute.st-andrews.ac.uk> X-Sender: im17@bute.st-andrews.ac.uk X-Mailer: QUALCOMM Windows Eudora Version 5.1.1 Date: Tue, 27 Aug 2002 09:27:47 +0100 To: chemistry@ccl.net From: "Ibrahim M.Moustafa" Subject: GOLD Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed Dear CCL users, We are planning to by a new software for docking and we think about GOLD. I'm wondering if people with experience in using GOLD can tell how they find GOLD in their docking experiment. What is the difference between GOLD, Flexx and DOCK? which of them gives better results? Appreciating your help; all comments are welcomed. regards, Ibrahim Ibrahim M.Mostafa Center for Biomolecular Sciences, Molecular Sciences Building, North Haugh,St.Andrews, Fife,KY16 9ST, Scotland,U.K. Tel. +44-1334-467257 Fax +44-1334-462595 e-mail: im17@st-Andrews.ac.uk From chemistry-request@server.ccl.net Tue Aug 27 06:36:44 2002 Received: from ribotargets.com ([194.129.39.11]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g7RAahr24173 for ; Tue, 27 Aug 2002 06:36:44 -0400 Received: from szilva (helo=localhost) by echo.ribotargets.com with local-esmtp (Exim 3.13 #1) id 17jddf-0006p9-00; Tue, 27 Aug 2002 10:31:59 +0000 Date: Tue, 27 Aug 2002 10:31:59 +0000 (GMT) From: Szilveszter Juhos To: "Ibrahim M.Moustafa" cc: chemistry@ccl.net Subject: Re: CCL:GOLD In-Reply-To: <5.1.1.6.0.20020827091902.00a57238@bute.st-andrews.ac.uk> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII > they find GOLD in their docking experiment. What is the difference between > GOLD, Flexx and DOCK? which of them gives better results? There a very good papers comparing them: Stahl & Rarey: Detailed analysos of Scoring Functions for Virtual Screening J. Med. Chem: 44:1035-1042 (2001) Paul & Rognan: ConsDock: A New Program for the Consensus Analysis.. PROTEINS:47(4):521-533 (2002) Also worth to give a look to Glide (no, I have no any connection to them): http://www.schrodinger.com/Products/glide.html http://www.schrodinger.com/Documents/GlideDataSheet.doc Hope it helps: Szilva From chemistry-request@server.ccl.net Tue Aug 27 04:48:06 2002 Received: from jubilantbiosys.com ([202.144.86.69]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g7R8m2r20358 for ; Tue, 27 Aug 2002 04:48:02 -0400 Received: (from apache@localhost) by jubilantbiosys.com (8.11.6/8.11.6) id g7R8mNu15612; Tue, 27 Aug 2002 14:18:23 +0530 Date: Tue, 27 Aug 2002 14:18:23 +0530 Message-Id: <200208270848.g7R8mNu15612@jubilantbiosys.com> X-Authentication-Warning: jubilantbiosys.com: apache set sender to parthi.s@jubilantbiosys.com using -f From: "parthi.s" To: chemistry@ccl.net Subject: 2D to 3D conversion software X-Mailer: Open WebMail X-OriginatingIP: 192.168.1.56 (parthi.s) MIME-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Dear CClers I would appreciate getting pointers/info on freely available softwares on 2D to 3D conversion of molecular structures. Source code information would be more useful. Also I would like to receive source code info on Molecular Mechanics programs. Thanks in advance. S Parthiban www.jubilantbiosys.com From chemistry-request@server.ccl.net Tue Aug 27 08:00:03 2002 Received: from ifp.ifp.fr ([156.118.212.2]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g7RC03r28138 for ; Tue, 27 Aug 2002 08:00:03 -0400 Received: from irsun165.ifp.fr (irsun165.ifp.fr [156.118.22.211]) by ifp.ifp.fr (8.9.3/8.9.3) with ESMTP id OAA28371 for ; Tue, 27 Aug 2002 14:00:02 +0200 (MET DST) Received: from irnts21.ifp.fr (irnts21 [156.118.15.51]) by irsun165.ifp.fr (8.8.5/8.8.5) with ESMTP id OAA26933 for ; Tue, 27 Aug 2002 14:00:01 +0200 (MET DST) Received: by irnts21.ifp.fr with Internet Mail Service (5.5.2653.19) id ; Tue, 27 Aug 2002 14:00:01 +0200 Message-ID: <3AA99E087354D61185E4002048403CFC59DFC9@irnts23.ifp.fr> From: DE BRUIN theodorus To: "'chemistry@ccl.net'" Subject: SUMMARY: G98: opt=stable and freq Date: Tue, 27 Aug 2002 14:00:01 +0200 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-Type: text/plain; charset="iso-8859-1" Dear All, I would like to thank everybody who replied to my question concerning the instability of the wavefunction and the frequency analysis that I wanted to perform subsequently. I wish to point out that the instability did not have a RHF/UHF origin, since I used (of course) uB3LYP. Initially I used a --link1-- job with guess=read geom=check freq. However in that case I fell back on the old(=instable wavefunction). In my case the combination: guess=(read,mix) geom=check freq resulted in a freq analysis on the stable wavefunction. Thanks again. Theo REPLIES: Frank Jensen [frj@dou.dk]: Try generating the stable wave function (= the one from stable=opt) by e.g. guess=alter or guess=mix. This works if the wave function is RHF --> UHF unstable. If the instability is a symmetry breaking you may need to create your own route card where the wave function is first done with stable=opt, and then immediately continuing onto the frequency. If that is necessary, however, it strongly suggests some (other) problem with your wave function, perhaps it is strongly MCSCF, or the DFT grid is insufficient. Monica Kosa [chmonica@techunix.technion.ac.il]: You can try read optimized wavefunction from the checkpoint file. First you run a job with stable=opt keyword. Than you include the keyword freq (and delete the stable=opt) and guess=read (in the same input file you ran your stable =opt job). Reinaldo Pis Diez [pis_diez@quimica.unlp.edu.ar]: I posted a very similar question even before, in 1999!! Below I send you the "official" answer, that is, that of Gaussian (my original mail is included, too). Note that the suggested recipe is the same you tried!! Note also that an alternative three-step job is proposed: use first stable(opt); then use guess(read) opt to get the true minimum; and finally do the freq calculation. Dr. Diez, There are a couple of points. First, you want to use GUESS=READ and the checkpoint file from the STABLE=OPT calculation to have a chance of recovering the final stable solution. In some nasty cases you may need to use SCF=QC as well. Second, note that if the SCF was unstable for the optimization then the structure no longer corresponds to a minimum and you need to re-optimize to get the true minimum energy structure. You might want to consider changing your protocol and do a STABLE=OPT at the first point, then use GUESS=READ OPT with SCF=QC if needed. This should get you the stable SCF solution to start with and the go from there. > Dear CCL'ers, > > I'm doing some calculations (geometry optimizations) on small systems > using DFT as implemented in Gaussian 94 and 98. > Once the geometry is optimized, I do a stable(opt) job on the wave > function corresponding to that geometry. I find very often that the wf is > unstable, but the opt option in the stable keyword works well and overcome > the unstability problem. > Then, I try a frequency calculation using guess(read) and geom(check) but > the calculation is performed on the unstable wf instead of the stable one!! > How can I perform the frequency job using the stable wf? Which > combination of keywords am I missing? > Thanks in advance. > Regards, > > Reinaldo Laurence Cuffe [Laurence.Cuffe@ucd.ie]: I'm only stepping in with advice here as you say a similar question in the archives remains un-answered. I would use the final geometry from the stable calculation to start an opt=(calcall) calculation with the multiplicity in the input file corrected to correspond to that derived from the stable calculation. Hope this helps Christopher Cramer [cramer@pollux.chem.umn.edu]: We work with unstable wave functions all the time. We find it much more efficient to simply run a "stable" calculation (i.e., no "=opt"). If there is indeed an instability (which the output will tell you), then we proceed to # u[dft method]/[basis] guess=(read,mix) scf=([qc,nosym,direct,cycles=900]) [fopt] [freq] where the brackets indicate wildcards (e.g., the particular DFT method and basis set) or options that may or may not be required to coax the scf to convergence (qc is helpful for difficult cases, nosym is essentially required for molecules that are not C1, but is better used within scf, so that geometry optimization can still take advantage of symmetry, direct may not work depending on the size of the system, number of cycles is a personal choice...) In this case, you can also add optimization and frequency keywords. Note that it is CRITICAL to include the "u" prefix to the DFT method. I seem to recall that the trouble with your approach is that stable=opt usually begins with a restricted wave function, and then if an instability is found, an unrestricted wave function is optimized (although often it seems unable to accomplish this, while guess=mix as listed above is quite robust). HOWEVER, when link 1 is entered again because of your use of the keyword freq, it defaults back to a restricted formalism, so you simply guess the alpha orbitals as an RDFT wave function. My memory may certainly be wrong on this particular point -- I haven't tried it in a long time -- but we usually have excellent success with the protocol I've outlined above. gaussian.com!help@gaussian.com A two-step calculation is necessary. In the second job, the frequency part, use "ub3lyp geom=allcheckpoint guess=read nosymm". If you do not explicitly specify the "u" in ub3lyp, the calculation will converge to the spin-restricted wavefunction. If this doesn't help, please send me your input file and I will attempt to find a set of options for you. Regards, Jim Hess ++++++++++++++++++++++++++ James Hess, Ph.D. Customer Support Scientist Gaussian, Inc. e-mail: help@gaussian.com ++++++++++++++++++++++++++ Stock [mstock@chem.ubc.ca] : You should be able to get the optimized wavefunction with appropriate use of Guess. Try Guess=Mix, which mixes the HOMO and LUMO. If that doesn't work, check out Guess=Alter, G98 user's reference pp. 98 and 101. This will allow you to specify by hand which MOs you want occupied. I'm unfamiliar with the notation used in the manual, so if you end up taking this route and you are familiar with it, I'd be much obliged for an explanation. Perhaps a #P Stable calculation would give you the info you need to correctly choose the alterations to the wavefunction. While you're trying to create the stable wavefunction, you can of course test it with another stable calculation. Juan Pablo Senosiain [senos@Stanford.EDU]: it sounds like you might have a UHF/RHF instability. This is well documented in standard quantum chemistry textbooks. Try the homolytic bond fission using UB3LYP. Patrick Musch [musch@chemie.uni-wuerzburg.de]: as far as I know, the SCF routine in Gaussian uses quatrically convergent (QC) SCF, so try to read in the stable wavefunction from the checkpoint file and do a Link1 for the frequency job GUESS=READ and SCF=QC. This might take a little time, since QC SCF is more time-consuming than the ordinary algortihm. I hope this might work. Olga Dmitrenko [odmitr@UDel.Edu]: Did you try to do first job with opt=stable and link it with the control card # guess=read geom=check freq ? We are doing similar studies on O-O bond elongation in peroxides. Our way is to do UB3LYP with guess=mix. ************************************************** Theodorus de Bruin Institut Français du Pétrole Division Chimie et Physico-Chimie Appliquées Dept. Thermodynamique & Modélisation Moléculaire 1 - 4 Avenue de bois Préau 92852 Rueil-Malmaison Cedex Tel.: +33 (0)1.47.52.54.38 Fax.: +33 (0)1.47.52.70.58 ************************************************** From chemistry-request@server.ccl.net Tue Aug 27 03:49:14 2002 Received: from smtp2.ruc.dk ([130.225.220.70]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g7R7nDr17650 for ; Tue, 27 Aug 2002 03:49:14 -0400 Received: by smtp2.ruc.dk (Postfix, from userid 504) id D781744A2A5; Tue, 27 Aug 2002 09:48:56 +0200 (CEST) Received: from virgil.ruc.dk (virgil.ruc.dk [130.225.220.110]) by smtp2.ruc.dk (Postfix) with ESMTP id 1105B44A2A2 for ; Tue, 27 Aug 2002 09:48:55 +0200 (CEST) Received: from VIRGIL/SpoolDir by virgil.ruc.dk (Mercury 1.47); 27 Aug 02 09:48:56 +0100 Received: from SpoolDir by VIRGIL (Mercury 1.47); 27 Aug 02 09:48:51 +0100 From: "Jens Spanget-Larsen" Organization: Roskilde Universitetscenter To: chemistry@ccl.net Date: Tue, 27 Aug 2002 09:48:43 +0100 Subject: Re: CCL:History question Reply-To: spanget@ruc.dk Priority: normal X-mailer: Pegasus Mail for Windows (v2.23) Message-ID: <3EE2F1A2A92@virgil.ruc.dk> Jan Dillen: > There is a (very good) book by Barbara Lovett Cline: > "The questioners: physicists and the quantum theory" > (Thomas Crowell Co, New York, 1965) where it is said that > a statement of this type was communicated by the "head of the > physics department" to Max Planck when he wanted to enter > the university. The book mentions that this happened in > 1875. No name is given for this departmental head, > but Planck started his studies at Munich, and moved on > to Berlin at a later stage. Dear Jan, thank you for your message. Maybe the "head of physics department" was Phillip von Jolly? Andreas Klamt sent me the following message. Yours, Jens >--< ------------------------------------------------------------------- From: "Dr. Andreas Klamt" Jens, here is the passage from page 9/10 out of the book "Planck", by Armin Hermann, Rowohlt, 1973. "Der vielseitig Begabte (Max Planck im Jahre 1874, Anmerkung A. Klamt) schwankte, ob er Musik, Altphilologie oder Physik studieren sollte. Als er sich nach den Aussichten eines Musikstudiums erkundigte, erhielt er die Antwort: "Wenn Sie schon fragen, studieren Sie was anderes!" Auch der Muenchener Physiker Phillip von Jolly riet dringend ab: In der Physik sei im wesentlichen schon alles erforscht, und es gebe nur noch einige unbedeutende Luecken auszufuellen. AEhnlich betrachtete der Physiologe Emil Du Bois-Reymond die mechanische Theorie, an der Spitze das Energieprinzip, als den Hoehepunkt und endgueltigen Schlussstein der Physik." Regards Andreas NB! Please note new mail address: =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= JENS SPANGET-LARSEN Office: +45 4674 2710 Department of Chemistry Fax: +45 4674 3011 Roskilde University (RUC) Mobile: +45 2320 6246 P.O.Box 260 E-Mail: spanget@ruc.dk DK-4000 Roskilde, Denmark http://virgil.ruc.dk/~spanget =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= From chemistry-request@server.ccl.net Tue Aug 27 09:33:35 2002 Received: from bute.st-andrews.ac.uk (root@[138.251.12.1]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g7RDXYr32289 for ; Tue, 27 Aug 2002 09:33:34 -0400 Received: from superintendentchalmers.st-andrews.ac.uk (bmspc-glt2-9 [138.251.94.76]) by bute.st-andrews.ac.uk (8.9.1a/8.9.1) with ESMTP id OAA26437 for ; Tue, 27 Aug 2002 14:27:55 +0100 (BST) Message-Id: <5.1.1.6.0.20020827142310.072c0798@bute.st-andrews.ac.uk> X-Sender: im17@bute.st-andrews.ac.uk X-Mailer: QUALCOMM Windows Eudora Version 5.1.1 Date: Tue, 27 Aug 2002 14:34:40 +0100 To: chemistry@ccl.net From: "Ibrahim M.Moustafa" Subject: Summary: CCL:GOLD In-Reply-To: <5.1.1.6.0.20020827091902.00a57238@bute.st-andrews.ac.uk> Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed Dear CCL users, Here is a summary of the answers I got on my question concerning docking program GOLD: The question was: At 09:27 27/08/2002 +0100, Ibrahim M.Moustafa wrote: >Dear CCL users, > > We are planning to by a new software for docking and we think about > GOLD. I'm wondering if people with experience in using GOLD can tell how > they find GOLD in their docking experiment. What is the difference > between GOLD, Flexx and DOCK? which of them gives better results? > > Appreciating your help; all comments are welcomed. > > regards, > Ibrahim > > > > > >Ibrahim M.Mostafa >Center for Biomolecular Sciences, >Molecular Sciences Building, >North Haugh,St.Andrews, >Fife,KY16 9ST, >Scotland,U.K. >Tel. +44-1334-467257 >Fax +44-1334-462595 >e-mail: im17@st-Andrews.ac.uk > > >-= This is automatically added to each message by mailing script =- >CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins >Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > The answers came from experts mentioning the papers: Stahl & Rarey: Detailed analysos of Scoring Functions for Virtual Screening J. Med. Chem: 44:1035-1042 (2001) Paul & Rognan: ConsDock: A New Program for the Consensus Analysis.. PROTEINS:47(4):521-533 (2002) and from the experience of people in the field they arrange the docking programs according to the accuracy of results in the order: glide > GOLD > Flexx > > DOCK I think we'll go for glide. Thanks a lot for all who answered my question. Thanks, Ibrahim From chemistry-request@server.ccl.net Tue Aug 27 11:37:25 2002 Received: from smtp1.dti.ne.jp ([202.216.228.36]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g7RFbPr06229 for ; Tue, 27 Aug 2002 11:37:25 -0400 Received: from b159504364 (PPP125.fukuoka-ip.dti.ne.jp [211.132.92.125]) by smtp1.dti.ne.jp (3.08s) with SMTP id g7RFbLYp028732 for ; Wed, 28 Aug 2002 00:37:23 +0900 (JST) Message-ID: <002501c24ddf$89044780$7d5c84d3@b159504364> From: "Telkuni" To: Subject: Gaussian98W's AMBER input --SUMMARY Date: Wed, 28 Aug 2002 00:36:38 +0900 MIME-Version: 1.0 Content-Type: text/plain; charset="Windows-1252" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.50.4133.2400 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4133.2400 Hello, CCLers Last week, I've posted a question: > I'm a novice user of molecular mechanics(MM) and planning to do > Base-Pair's MM calculation with Gaussian98W's AMBER function. > > However, there is a guidance of Gaussian's AMBER on the G98 > user's reference(page122), it is too short to make actual input. > > Maybe, I think, when one want to do AMBER calculation on a molecule, > he must search and apply the molecule's peculiar atomic parameters > such as Fig-5 of "W.D.Cornell et.al, J. Am. Chem. Soc. 117, p5179 (1995)". > (on RNA, it's Fig-6.) > > Is above correct? > > And, must one search and apply the each atomic parameters even a small > molecule? (for example, even though CH3OH ?, where is its parameters?) > > > Any replies I will appreciate and make the summary. Here is the summary of replies. Thank you very much Dr.Nicolas FERRE' and Dr.Chandra U. Singh. --- 1) from Nicolas ------- Hi Telkuni, If you want to use G98 to run some Amber jobs, you always have to write in the Z-matrix part: "Atomic symbol"-"Amber atom type"-"Charge" coordinates ... e.g. C-CT--.0252 for an alpha carbon of a glycin molecule. Actually, the RESP charges defined for Amber are not stored into G98 and you have to write them in the input file. For methanol, you won't find any parameter within this old Amber version which was designed especially for amino-acids. Since this early work, the Amber force-field has been developed to include some parameters for organic molecules also. Maybe you should consider to buy the last version of Amber (7, see http://www.amber.ucsf.edu/amber/), or alternatively you can try to use - free - Tinker that includes Amber, Charmm, MM2/3 ... (http://dasher.wustl.edu/tinker/) If you want to derive the RESP point charges for methanol, consider the procedure described here: http://www.amber.ucsf.edu/amber/charges.txt ... but I'm sure that someone always did it ! Hope this helps. Nicolas --- 2) form Chandra ------- Hello, I have read your e-mail and I am Dr. Singh who developed the AMBER programs in the 80's. If you need to automatic calculations without worrying about parameters, please check our new software GALAXY at www.am-tech.com. Sincerely, Chandra U. Singh ------------------------------------------------------ Telkuni Tsuru telkuni@venus.dti.ne.jp From chemistry-request@server.ccl.net Tue Aug 27 11:06:25 2002 Received: from ChE.UDel.Edu ([128.175.117.64]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g7RF6Pr04423 for ; Tue, 27 Aug 2002 11:06:25 -0400 Received: from che.udel.edu (cognac.che.udel.edu [128.175.117.54]) by ChE.UDel.Edu (8.9.3/8.9.3) with ESMTP id LAA05247 for ; Tue, 27 Aug 2002 11:06:25 -0400 (EDT) Message-ID: <3D6B966C.1000104@che.udel.edu> Date: Tue, 27 Aug 2002 11:10:36 -0400 From: Jeffery Klauda User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.0; en-US; rv:0.9.2) Gecko/20010726 Netscape6/6.1 X-Accept-Language: en-us MIME-Version: 1.0 To: chemistry@ccl.net Subject: Problems with O2 - Carbon Sheet Interaction Energies Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit Dear CCLers, I have been having some problems with calculating interactions energies between diatomic oxygen and a carbon surface of six and seven member rings. All of my calculations correct for BSSE and are at ROMP2/aug-cc-VDZ with a carbon surface that is a singlet in its ground state (hydrogens added to simulate C-C bonds). The problem lies in Hartree-Fock, without changing the initial guess for the orbital occupations the initial INDO guess puts the unpaired electrons on the carbon surface when O2 should have two singly occupied orbitals. Therefore the incorrect spin density is calculated and the interaction energies are extremely repulsive. To alleviate this problem, I thought a better initial guess (one with the singly occupied pi* like orbitals on oxygen) would solve this problem. However, this works only for a limited amount of cases and seems to be more trial and error which orbital to choose than a systematic approach that can be used for other O2 positions and orientations. The correct solution only occurs when at the converged HF energy the spin density is essentially zero on the carbon surface and two on O2. I was wondering if any of you have come across this problem and have a systematic way to solve this. I have tried other approaches to no avail (UMP2, initial guesses of correct wavefunction for other O2 orientations with respect to the carbon surface, other basis sets). Any help in this matter will be greatly appreciated, Jeff Klauda -- *************************************** Jeffery Klauda Ph.D. Candidate in Chemical Eng. University of Delaware 119 Colburn Lab Newark, DE 19702 Phone: (302) 831-6857 Fax: (302) 831-1048 *************************************** From chemistry-request@server.ccl.net Tue Aug 27 19:43:28 2002 Received: from emvasteria.chiron.com ([165.140.4.50]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g7RNhSr30618 for ; Tue, 27 Aug 2002 19:43:28 -0400 Received: from 165.140.4.59 by emvasteria.chiron.com (InterScan E-Mail VirusWall NT); Tue, 27 Aug 2002 16:43:22 -0700 Received: by emvkali.chiron.com with Internet Mail Service (5.5.2655.55) id ; Tue, 27 Aug 2002 16:50:46 -0700 Message-ID: <76914E341621D611ADB5000102758978675E8B@emvshiva.chiron.com> From: "Martin, Eric" To: chemistry@ccl.net Subject: XML and combinatorial chemistry Date: Tue, 27 Aug 2002 16:50:38 -0700 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2655.55) Content-Type: multipart/mixed; boundary="----=_NextPartTM-000-4984a488-ba0e-11d6-87f0-0001032a6990" This is a multi-part message in MIME format. ------=_NextPartTM-000-4984a488-ba0e-11d6-87f0-0001032a6990 Content-Type: text/plain; charset="iso-8859-1" Dear CCL, Does CML or any other chemical XML application support combinatorial chemistry? Specifically, I have in mind Markush or generic structures with lists of R groups. Is specific support for Markush structures necessary or useful, or is there a way to do it with existing CML elements? The CML FAQ (http://www.xml-cml.org/faq/index.html) notes that "Heteromers" e.g. modified proteins, are difficult to represent, which suggests a Markush may be as well. Thanks in advance. Regards, Eric ___________________ Eric Martin Chiron Corp, LSC 4.250 4560 Horton St. Emeryville, CA 94608 (510)923-3306 FAX 923-2010 ------=_NextPartTM-000-4984a488-ba0e-11d6-87f0-0001032a6990 Content-Type: text/plain; name="InterScan_Disclaimer.txt" Content-Transfer-Encoding: 7bit Content-Disposition: attachment; filename="InterScan_Disclaimer.txt" **** ATTENTION! This message contains information (including any appended information, such as copied or forwarded messages and attachments, and any message to which this is appended) which may be confidential and/or privileged. 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Thank you for your assistance. **** ------=_NextPartTM-000-4984a488-ba0e-11d6-87f0-0001032a6990-- From chemistry-request@server.ccl.net Tue Aug 27 17:12:35 2002 Received: from jubilantbiosys.com ([202.144.86.69]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g7RLCVr19675 for ; Tue, 27 Aug 2002 17:12:32 -0400 Received: (from apache@localhost) by jubilantbiosys.com (8.11.6/8.11.6) id g7RLCr503284; Wed, 28 Aug 2002 02:42:53 +0530 Date: Wed, 28 Aug 2002 02:42:53 +0530 Message-Id: <200208272112.g7RLCr503284@jubilantbiosys.com> X-Authentication-Warning: jubilantbiosys.com: apache set sender to parthi.s@jubilantbiosys.com using -f From: "parthi.s" To: chemistry@ccl.net Subject: 2D to 3D conversion software X-Mailer: Open WebMail X-OriginatingIP: 203.90.86.6 (parthi.s) MIME-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Dear CClers I would appreciate getting pointers/info on freely available softwares on 2D to 3D conversion of molecular structures. Source code information would be more useful. Also I would like to receive source code info on Molecular Mechanics programs. Thanks in advance. S Parthiban www.jubilantbiosys.com