From owner-chemistry@ccl.net Mon Aug 29 03:52:05 2005 From: "CCL" To: CCL Subject: CCL: Software convert 3D structure .sd file to 2D structure Message-Id: <-29028-050829034700-7867-sY0f/B+VKit+lcn3g2/sLw%a%server.ccl.net> X-Original-From: Carsten Detering Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Mon, 29 Aug 2005 09:46:52 +0200 MIME-Version: 1.0 Sent to CCL by: Carsten Detering [detering%a%biosolveit.de] William, our software tool 2Ddraw can draw molecular sketches even under constraints. Have look at it here: http://www.biosolveit.de/2ddraw Hope this helps. Best regards, Carsten -- =================================================================== The 3rd FlexX DOCKING WORKSHOP will take place November 10-11, 2005 in Bonn-Cologne, Germany (TBA) Register today! Space is limited. More information on this high-quality workshop and how to register: http://www.biosolveit.de/workshops/2005 =================================================================== -- BioSolveIT GmbH - An der Ziegelei 75 - 53757 St.Augustin - Germany Dr. Carsten Detering detering%a%biosolveit.de Phone: +49-2241-2525-0 / Fax: -525 www.biosolveit.de CCL wrote: > Hi all, > > Could anybody suggest a software could convert 3D structure file (.sd or > .mol) to a 2D structure file for synthetic chemists reading? > > Thanks in advance, > William > > -------------------------------- > William Wei, Ph.D. > Computational Chemist > Lorus Therapeutics Inc. > 2 Meridian Road > Toronto, On, M9W 4Z7 > 416-798-1200 Ext. 374 > wwei%a%lorusthera.com > > > ------------------------------------------------------------------------ > This message contains CONFIDENTIAL INFORMATION intended solely for the > use of the addressee(s) named above. > Any review, disclosure, distribution, copying or use of the information > by others is strictly prohibited. > If you have received this message in error, please advise the sender by > immediate reply and delete the original message. > From owner-chemistry@ccl.net Mon Aug 29 07:56:41 2005 From: "CCL" To: CCL Subject: CCL: CCL question about limitations of PCM Message-Id: <-29029-050829032223-6208-sY0f/B+VKit+lcn3g2/sLw|*|server.ccl.net> X-Original-From: Alessandro Contini Content-transfer-encoding: 8BIT Content-type: text/plain; charset=ISO-8859-15 Date: Mon, 29 Aug 2005 09:20:55 +0200 MIME-version: 1.0 Sent to CCL by: Alessandro Contini [alessandro.contini|*|unimi.it] Hi, the problem refers to the model used for deriving the atomic radius. Indeed the UAO model consider every hydrogen as bounded to an heavy atom, and in the case of a proton transfer the hydrogen results unbounded and the program does not know how to set a sphere on that atom. You can solve this by settign the keyword "pcm=read" and at the end of the geometry specifications you have to place the keyword "SPHEREONH=N" where N is the number assigned to the migrating hydrogen. Alternatively you could try explicit hydrogens models, like uff, pauling, bondi. Hope this help Alessandro -- Alessandro Contini, Ph.D. Istituto di Chimica Organica "Alessandro Marchesini" Università degli Studi di Milano, Facoltà di Farmacia Via Venezian, 21 20133 Milano Tel. +390250314480 Fax. +390250314476 e-mail alessandro.contini|*|unimi.it From owner-chemistry@ccl.net Mon Aug 29 08:39:16 2005 From: "CCL" To: CCL Subject: CCL: Restored missed CCL messages to CCL archives Message-Id: <-29030-050829013132-32050-sY0f/B+VKit+lcn3g2/sLw(~)server.ccl.net> X-Original-From: janl(~)speakeasy.net Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="iso-8859-1" Date: Mon, 29 Aug 2005 05:31:26 +0000 MIME-Version: 1.0 Sent to CCL by: janl(~)speakeasy.net Dear CCL, When I was away from CCL, many replies to messages posted to CCL messages from you did not get to subscribers. I processed all these messages and placed them in the CCL list archives rather than reposting them. So please check the archives for July and August, and you may find there an answer to the question that you posted on CCL: http://server.ccl.net/chemistry/resources/messages/index.shtml Why the messages were not posted. Blame me... The Reply-To: field was not set to chemistry(~)ccl.net to avoid all the "I am away from my office" to go back to list (some went anyhow, sorry). Many of you did not look on your To: line when responding to the message from CCL. If you just clicked on [reply] in your mail software, it responded to the From: address. The From: address on CCL is now set to: owner-chemistry(~)ccl.net to avoid exposing the original sender of the message to spyware that collects addresses for spammers. Unfortunately, spyware is so popular on Windows computers that I had to protect the kind and gentle people who post to CCL. Since I am back "in town" and can monitor the CCL often, I restored the Reply-To: and did more changes to the CCL distribution scripts to avoid the "I am away > from office" messages, though they may occasionally creep in. I will use this occasion to give you more details on how the posting to CCL works nowadays. Note, you do not have to be a subscriber to CCL, to post to it. I found early on that constraining posting to the list of subscribers does not work that well, since we all have many different e-mail addresses, and I personally do not remember where I am subscriber with which address. How to post to CCL subscribers? 1) Send your message to: chemistry(~)ccl.net (if you reply to CCL message, please always check if chemistry(~)ccl.net is on the To: line, since some mail packages ignore the Reply-To: header line.). You can also use the Web form: http://www.ccl.net/cgi-bin/ccl/send_ccl_message to send the message to CCL subscribers. 2) After sending the message, you should receive a computer generated message asking you to confirm that you posted the message. You may sometimes wait a few hours for the response (CCL uses greylisting: http://www.ccl.net/cca/software/UNIX/greylisting/README.shtml if you want to learn more). This step is necessary since spammers usually put phony addresses on the From: line (you would not want to see your name associated with running an off-shore pharmacy, would you?). 3) You have to respond to confirmation request to have your message posted (though, when I am by the computer, I often use my little gizmo, to post your message on the CCL before you get to confirming it, but do not count on it...). The instruction for confirming the message are given in the confirmation request. You have two choices: 1) click on the link within a message (preferred and faster method) 2) Respond to the message, but YOU HAVE TO ADD a string: [CCL] (i.e., CCL embraced in square brackets) on the beginning of the subject line, and you should not to change anything else in the message. Make sure that your confirmation message goes to: confirm(~)ccl.net (this should be automatically displayed in your mail software, but again, some mailers to not respect the Reply-To: header). 4) If you are posting for the first time from your e-mail address, the message will not be posted to CCL automatically. But next messages from this address will. I will need to bless your address first, since ANYONE can send to CCL. And even if I used the subscriber lists, I have no way of checking if you are who you tell you are. I had a few Joe Schmoe's subscriber before. And beside... Your computer can be hacked. So it is all a compromise, but at least, I am less worried, if I the software lets message through automatically after I already received a responsible posting from the given address. 5) Now, your message should be distributed on CCL. You can check if it went through by looking up the CCL message archives at: http://www.ccl.net/chemistry/resources/messages/index.shtml Your e-mail address is obfuscated (the (~) sign is replaced by random characters). It also does not appear on the From: line of the CCL message, so the spyware that harvests e-mail addresses on your friend's infected computer does not send it to the collection agency on some Caribbean island. Well... You will miss all these opportunities from the African countries you will not be notified about big prizes you won without buying a ticket. 6) Your message is sent individually to each CCL subscriber, so I can process bounces automatically when your puny mailbox is filled up, or you got (or lost) a job, or when your company merged/split again and you have a new domain before you even know it, or when they cut your fiber optics by mistake again. More comments and explanations, if you care to read. The chemistry ((~)ccl.net) is not a real user id, but an alias that sends mail to a script. The script does a lot of checks to see if message is not a spam, virus from your friend infected windows computer, or some message like: "I am on vacations" or "Thank you for your message". But it is a catch-up game and you will see an occasional mishap since exploits and responders are the bulk of the mail CCL receives. Moreover, legitimate messages can go to a black hole, since I use Spamassassin, and blacklists to fight thousands of spam and malware messages that CCL gets every day. If sending e-mail to chemistry(~)ccl.net does not work, try the Web form. Messages posted to CCL through Web interface do not go through spam/access control, though even there I am blocking some IP addresses from posting. While there are now many emerging standards for verifying the sender of the mail, there is no consensus. Part of the problem is that the only way to do it, is to require that each of us has the digital certificate in his/her name issued by the agency that is trusted (i.e., will not give certificates to "just anyone") and discrete (i.e., will not share this information with our tax/debt collectors, former boyfriends, and army recruiters, for example...). Apart from the privacy issues, and the fact that in some poor countries even border routers are not secured, ho will pay for it and who will manage PKI? Moreover, with the lax security of many home and office computers and the omnipresence of Windows that were never meant to be on the Internet, and their security model (that has to be backward compatible) is just orthogonal to the one required by the real multiuser operating system, makes the idea of PKI infrastructure a wishful thinking. We will be in this mess for a long time, until we decide to go back to paper mail {:-(}. Sometimes, however, the message that you sent to CCL will not go through, and you will not even get a confirmation request. Long messages (larger than 20k) are not allowed. The CCL does not allow certain attachments to be posted (e.g., application/something). Checking the mail message for viruses and exploits in image formats, is an inexact science, and with so many infected computers and so many inferior life forms using the Internet nowadays, I just cannot risk sending malware to thousands of people. Not only that I do not want the lawyers chasing my ambulance (after I was beaten up by CCL subscribers), but I would feel bad if I was responsible for your misery of cleaning your boxes or loosing you data. Jan Labanowski CCL Admin jkl(~)ccl.net From owner-chemistry@ccl.net Mon Aug 29 08:40:19 2005 From: "CCL" To: CCL Subject: CCL: PC windows codes for electronic properties of crystals Message-Id: <-29031-050829043221-22464-sY0f/B+VKit+lcn3g2/sLw(~)server.ccl.net> X-Original-From: may abdelghani Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-1 Date: Mon, 29 Aug 2005 10:32:14 +0200 (CEST) MIME-Version: 1.0 Sent to CCL by: may abdelghani [may01dz(~)yahoo.fr] Hell, CCLers Can someone point me toward an code, which can calculate the properties of crystals(crystal structure, phonons ,band structure, DOS, COOP...), but work on PC windows( not in linux ) ... and why not a free one. Best regards may abdelghani ___________________________________________________________________________ Appel audio GRATUIT partout dans le monde avec le nouveau Yahoo! Messenger Téléchargez cette version sur http://fr.messenger.yahoo.com From owner-chemistry@ccl.net Mon Aug 29 08:53:13 2005 From: "CCL" To: CCL Subject: CCL: ESP grid in Gaussian without QM? Message-Id: <-29034-050829055822-31396-sY0f/B+VKit+lcn3g2/sLw*|*server.ccl.net> X-Original-From: "Hugo G. de Teran" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Mon, 29 Aug 2005 11:02:09 +0200 MIME-Version: 1.0 Sent to CCL by: "Hugo G. de Teran" [hteran*|*xray.bmc.uu.se] You can try GRID program from Peter Goodford. It uses MM to calculate interaction energies at discretized grid points with any selected chemical probe. It is available at http://www.moldiscovery.com Hope it helps, Hugo CCL wrote: >Sent to CCL by: Anselm.Horn]![chemie.uni-erlangen.de >Dear all, > >a Gaussian question: >Is it possible to print out the electrostatic potential grid used for >population analysis e.g. via pop=MK iop(6/33=2) iop(6/42=6) without >performing any QM calculation, i.e. use the Gaussian program as plain grid >creator? > >I tried to run an MM calculation with the above keywords, but that failed. > >In my case, the molecule of interest is rather large, so any QM >calculation is not feasible. > >Best regards, > >Anselm Horn> > > > > > -- Hugo G. de Teran, PhD. Department of Cell and Molecular Biology Uppsala University BMC, Box 596 Tel: +46 (0)18 471 5057 SE-751 24 Uppsala Fax: +46-(0)18 53 69 71 SWEDEN e-mail: hteran*|*xray.bmc.uu.se http://xray.bmc.uu.se/~aqwww From owner-chemistry@ccl.net Mon Aug 29 08:53:13 2005 From: "CCL" To: CCL Subject: CCL: Looking for Chemistry software running on PDA/Pocket PC Message-Id: <-29033-050828110441-24467-sY0f/B+VKit+lcn3g2/sLw%a%server.ccl.net> X-Original-From: e-Chemistry Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-1 Date: Sun, 28 Aug 2005 07:04:37 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: e-Chemistry [echemistry%a%yahoo.com] ChemIH 1.0 beta 1 is released (http://www.chemih.com/) Feature Hightlight 1. Draw organic structures 2. Stereochemistry 3. Text notes 4. Predrawn templates 5. Free-hand drawing 6. Multiple-step Undo/Redo system 7. Support many popular file formats And more ... ____________________________________________________ Start your day with Yahoo! - make it your home page http://www.yahoo.com/r/hs From owner-chemistry@ccl.net Mon Aug 29 08:53:13 2005 From: "CCL" To: CCL Subject: CCL: Inaccurate quadrature in caldsu Message-Id: <-29035-050826130048-15760-sY0f/B+VKit+lcn3g2/sLw|a|server.ccl.net> X-Original-From: Oluwakemi.Oloba|a|mail.uh.edu Content-transfer-encoding: 7BIT Content-type: text/plain; charset=ISO-8859-1 Date: Fri, 26 Aug 2005 09:33:25 -0500 (CDT) MIME-version: 1.0 Sent to CCL by: Oluwakemi.Oloba|a|mail.uh.edu Hello Pls can anyone help me with this i am runiung a a calculation on g03 with the Bq atoms but it keeps coming out with the error "inaccurate quadrature in caldsu" i have tried using guess=indo but it still does not work Thanks a lot Kemi Oloba From owner-chemistry@ccl.net Mon Aug 29 08:53:13 2005 From: "CCL" To: CCL Subject: CCL: tinker maximum allowed vibrations Message-Id: <-29037-050828091720-20913-sY0f/B+VKit+lcn3g2/sLw:_:server.ccl.net> X-Original-From: "Michael Schnieders" Content-Type: multipart/alternative; boundary="----=_NextPart_000_0012_01C5ABA2.9AB015D0" Date: Sun, 28 Aug 2005 07:32:11 -0500 MIME-Version: 1.0 Sent to CCL by: "Michael Schnieders" [mike_schnieders:_:hotmail.com] This is a multi-part message in MIME format. ------=_NextPart_000_0012_01C5ABA2.9AB015D0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hi I'm a graduate student with Jay Ponder so I spend quite a bit of time = using TINKER. When a dimension in "sizes.i" changes, all of the FORTRAN code needs to = be re-compiled (not just relinked). This is my guess for what be = happening here, although it depends on what you mean by "compiles fine". = If the FORTRAN modules are not recompiled, the programs will still = compile, but seg faults would result. If this doesn't help, let me know - what you want to do should = definitely not be a problem.=20 - Mike PS. Also, I would move maxvib above maxhess in the header file just to = be safe, because I'm not sure how the preprocessor resolves = dependencies. ----- Original Message -----=20 From: CCL=20 To: Schnieders, Michael =20 Sent: Saturday, August 27, 2005 5:34 PM Subject: CCL: tinker maximum allowed vibrations Dear CCL users, I have been trying to change the maximum allowed vibrations in the = program TINKER by modifying the variable maxvib=3D1000 in "sizes.i". If I change maxvib to be 1001, the program compiles fine, by I get a = segmentation fault when I run the program "vibrate". It doesn't help to change = maxhess=3Dmaxvib**2. Does anyone know how to change the maximum allowed vibrations, = successfully? =20 Any help will be greatly appreciated. Jose A. Gascon Postdoctoral Associate,=20 Chemistry Department=20 Yale University.=20 jose.gascon at yale.edu ------=_NextPart_000_0012_01C5ABA2.9AB015D0 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Hi
 
I'm a graduate student with Jay Ponder = so I spend=20 quite a bit of time using TINKER.
 
When a dimension in "sizes.i" changes, = all of the=20 FORTRAN code needs to be re-compiled (not just relinked). This is my = guess for=20 what be happening here, although it depends on what you mean by = "compiles fine".=20 If the FORTRAN modules are not recompiled, the programs will still = compile, but=20 seg faults would result.
 
If this doesn't help, let me know - = what you want=20 to do should definitely not be a problem.
- Mike
 
PS. Also, I would move maxvib above = maxhess in the=20 header file just to be safe, because I'm not sure how the = preprocessor=20 resolves dependencies.
----- Original Message -----
From:=20 CCL=20
Sent: Saturday, August 27, 2005 = 5:34=20 PM
Subject: CCL: tinker maximum = allowed=20 vibrations

Dear CCL = users,
I have been trying to change the maximum allowed vibrations = in the=20 program TINKER
by modifying the variable maxvib=3D1000 in = "sizes.i".
If I=20 change maxvib to be 1001, the program compiles fine, by I get a=20 segmentation
fault when I run the program "vibrate". It doesn't = help to=20 change maxhess=3Dmaxvib**2.
Does anyone know how to change the = maximum=20 allowed vibrations, successfully? 
Any help will be greatly = appreciated.

Jose A. Gascon
Postdoctoral Associate, =
Chemistry=20 Department
Yale University.
jose.gascon at=20 yale.edu
------=_NextPart_000_0012_01C5ABA2.9AB015D0-- From owner-chemistry@ccl.net Mon Aug 29 08:53:12 2005 From: "CCL" To: CCL Subject: CCL: CCL question about limitations of PCM Message-Id: <-29032-050826235431-3140-sY0f/B+VKit+lcn3g2/sLw|a|server.ccl.net> X-Original-From: "CHUNG Lung Wa" Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-1 Date: Sat, 27 Aug 2005 11:11:12 +0800 (HKT) MIME-Version: 1.0 Sent to CCL by: "CHUNG Lung Wa" [choscar|a|ust.hk] Hello, I faced the same problem before, due to default United Atom Topological Model in G03 (UA0), different from G98. You can use UAHF or UAKS and you need to type two more keywords. 1. add "read" in SCRF SCRF=(PCM, solvent=XXX, read) 2. add "radii=UAXX" in the last line, UAXX is type of United Atom Topological Model you choose. For details, you can check the manual. You also can check a recent paper about United Atom Topological Model: "Benchmarking the Conductor-like Polarizable Continuum Model (CPCM) for Aqueous Solvation Free Energies of Neutral and Ionic Organic Molecules" Takano, Y.; Houk, K. N.; J. Chem. Theory and Comput. ; (Article); 2005; 1(1); 70-77. Best Wishes, Oscar P.S. I am not an expert, but share with my experience. Welcome to give comment! > > Sent to CCL by: khunter#%#mta.ca > We are investigating a transition state of a proton transfer mechanism. We successfully > modelled such a state in the gas phase and are now looking at the solvation effects using the > PCM method. However, the transfering hydrogen is unbound (according to the gas phase) and upon > trying to do a solvation calculation we receive the following error. > > United Atom Topological Model (UA0 parameters set). > UA0: Hydrogen 21 is unbound. Keep it explicit at all point on the UA0: potential energy > surface to get meaningful results. > > Is this error a limitation of the PCM or does anyone have advice on how to correct this error? > Any assistance would be greatly appreaciated.To send e-mail to > subscribers of CCL put the string CCL: on your Subject: line and send your message to: > CHEMISTRY|a|ccl.netHOME Page: > http://www.ccl.net | Jobs Page: http://www.ccl.net/jobsuse the Web based form > from CCL Home Page From owner-chemistry@ccl.net Mon Aug 29 08:53:13 2005 From: "CCL" To: CCL Subject: CCL: Molecular dynamics w/ 2D PBC Message-Id: <-29036-050826191121-27642-sY0f/B+VKit+lcn3g2/sLw*|*server.ccl.net> X-Original-From: Kramer Campen Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed Date: Fri, 26 Aug 2005 18:10:51 -0400 (EDT) MIME-Version: 1.0 Sent to CCL by: Kramer Campen [campen*|*geosc.psu.edu] Possibly of interest along these lines is a paper from Klaus Schulten's group describing the interaction of a protein with a gold surface using the CHARMM parameters for the protein, some novel parameters of the gold surface (as I recall) and simulating the whole thing using NAMD. Abstract and paper are at, http://www.ks.uiuc.edu/Publications/Papers/paper.cgi?tbcode=BRAU2002 regards, Kramer On Fri, 26 Aug 2005, CCL wrote: > > Sent to CCL by: Aaron Deskins [ndeskins:-:purdue.edu] > CCL wrote: > >> Sent to CCL by: Rick Venable [rvenable]|[pollux.cber.nih.gov] >> On Thu, 25 Aug 2005, CCL wrote: >> >> >> Since the question topic was "molecular dynamics" I was assuming a >> package such as CHARMM, AMBER, NAMD, GROMOS, TINKER, etc., most of which >> do fairly well at describing periodic structures, esp. for the 3D case. >> Details such as system height, slab thickess, etc. would need to be >> optimized, but it's a reasonable option, esp. if 2D PBC aren't readily >> available. OTOH, the water:gold interaction might be tricky to get >> right with a simple point charge based potential; a polarizable >> potential might be a better choice. >> >> > Thank you for the response. If it's not too much trouble, perhaps you (or any > CCL reader) could give a sample article(s)/review to look up on using some of > the more well-known empirical programs to model metal surfaces and especially > adsorbate/surface systems. > > Thank you again, > > Aaron Deskins > Purdue University> To send e-mail to subscribers of CCL put the string CCL: on your Subject: > line> > > > ============================= R. Kramer Campen Dept. of Geosciences Pennsylvania State University University Park, PA 16802 Phone (Office at PSU) = 814-865-1178 Borguet Group Department of Chemistry Temple University Philadelphia, PA Phone (at Temple) = 215-204-9704 ============================= From owner-chemistry@ccl.net Mon Aug 29 15:29:15 2005 From: "CCL" To: CCL Subject: CCL: W:clementti atomic functions tables Message-Id: <-29038-050829152350-8450-sY0f/B+VKit+lcn3g2/sLw!A!server.ccl.net> X-Original-From: "mamert ayao sossah" Sent to CCL by: "mamert ayao sossah" [msossah!A!yahoo.com] Where can I find the clementti atomic functions data tables on the internet. I need those data to build input data for the code civ3.Any ideas or suggestion is highly appreciated. Thanks, Mamert. From owner-chemistry@ccl.net Mon Aug 29 20:21:51 2005 From: "CCL" To: CCL Subject: CCL: Inaccurate quadrature in caldsu Message-Id: <-29039-050829201829-11601-sY0f/B+VKit+lcn3g2/sLw(a)server.ccl.net> X-Original-From: Kadir Diri Content-transfer-encoding: 7bit Content-type: text/plain; format=flowed; charset=us-ascii Date: Mon, 29 Aug 2005 11:47:12 -0400 MIME-version: 1.0 Sent to CCL by: Kadir Diri [kadir(a)visual1.chem.pitt.edu] Hi! I thought this was a problem with the default initial guess, but if other methods like indo fail too, you probabbly have a really bad guess. Since you are using ghost atoms, I tend to think that you maybe running into severe linear dependency problems. If that is the case, you should spend some time improving your basis set. kadir CCL wrote: >Sent to CCL by: Oluwakemi.Oloba|a|mail.uh.edu >Hello >Pls can anyone help me with this >i am runiung a a calculation on g03 with the Bq atoms but it keeps coming out with the error "inaccurate quadrature in caldsu" i have tried using guess=indo but it still does not work >Thanks a lot >Kemi Oloba> > > >