From owner-chemistry@ccl.net Fri Feb 23 00:30:00 2007 From: "Seth Olsen s.olsen1,,uq.edu.au" To: CCL Subject: CCL: calculating titration state distributions for multiprotic acids with coupled sites Message-Id: <-33685-070222221126-10053-6VaKNjO+mBvtKqrvAnBakA*_*server.ccl.net> X-Original-From: Seth Olsen Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Fri, 23 Feb 2007 12:39:03 +1000 MIME-Version: 1.0 Sent to CCL by: Seth Olsen [s.olsen1(~)uq.edu.au] Hi CCLers, I have been trying to find references or algorithms which can estimate equilibrium distributions of different protonation states of a multiprotic acid where the sites may be coupled. Can anyone point me in the right direction? Cheers, Seth From owner-chemistry@ccl.net Fri Feb 23 01:05:01 2007 From: "Ben Vastine vastinator=gmail.com" To: CCL Subject: CCL: decontracting the Well Tempered Basis Set of Huzinaga and Miguel. Message-Id: <-33686-070223002852-15079-5c75bLucz3YvDPJO1fT9qA%%server.ccl.net> X-Original-From: "Ben Vastine" Content-Type: multipart/alternative; boundary="----=_Part_48139_17686105.1172204551638" Date: Thu, 22 Feb 2007 22:22:31 -0600 MIME-Version: 1.0 Sent to CCL by: "Ben Vastine" [vastinator[A]gmail.com] ------=_Part_48139_17686105.1172204551638 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Content-Disposition: inline All: I would like to improve the flexibility of the well tempered basis set (WTBS) of Huzinaga and Miguel. Does anyone know if there is a particular way to decontract these basis sets? For what I'm doing, I've seen some improvement through decontracting the valence shells of, for example, scandium, but I'm not sure of how to systematically improve the performance. Thanks. Ben ------=_Part_48139_17686105.1172204551638 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline All:

I would like to improve the flexibility of the well tempered basis set (WTBS) of Huzinaga and Miguel.  Does anyone know if there is a particular way to decontract these basis sets?  For what I'm doing, I've seen some improvement through decontracting the valence shells of, for example, scandium, but I'm not sure of how to systematically improve the performance.  Thanks.

Ben
------=_Part_48139_17686105.1172204551638-- From owner-chemistry@ccl.net Fri Feb 23 01:49:00 2007 From: "Andreas Klamt klamt .. cosmologic.de" To: CCL Subject: CCL: calculating titration state distributions for multiprotic acids with coupled sites Message-Id: <-33687-070223011315-6804-eu1NsLLR5OVtozQ9HU8dmg-.-server.ccl.net> X-Original-From: Andreas Klamt Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Fri, 23 Feb 2007 07:13:12 +0100 MIME-Version: 1.0 Sent to CCL by: Andreas Klamt [klamt : cosmologic.de] Dear Seth, depending on the expected accuracy, basically COSMOtherm can do that. With our DFT/COSMO-RS based pKa method we can calculate the pKa of the different species. Andreas Seth Olsen s.olsen1,,uq.edu.au schrieb: > > Sent to CCL by: Seth Olsen [s.olsen1(~)uq.edu.au] > > Hi CCLers, > > I have been trying to find references or algorithms which can estimate > equilibrium distributions of different protonation states of a > multiprotic acid where the sites may be coupled. Can anyone point me > in the right direction? > > Cheers, > > Sethhttp://www.ccl.net/chemistry/sub_unsub.shtmlConferences: > http://server.ccl.net/chemistry/announcements/conferences/> > > > > -- ----------------------------------------------------------------------------- Dr. habil. Andreas Klamt COSMOlogic GmbH&CoKG Burscheider Str. 515 51381 Leverkusen, Germany Tel.: +49-2171-73168-1 Fax: +49-2171-73168-9 e-mail: klamt..cosmologic.de web: www.cosmologic.de ----------------------------------------------------------------------------- COSMOlogic Your Competent Partner for Computational Chemistry and Fluid Thermodynamics ----------------------------------------------------------------------------- From owner-chemistry@ccl.net Fri Feb 23 02:23:00 2007 From: "Patrick Pang skpang::ctimail.com" To: CCL Subject: CCL:G: Increase no. of steps for geometry optimization using UFF in G03 Message-Id: <-33688-070223021812-11627-l3qT1mT3l0zAqT4B8+J9Pw|server.ccl.net> X-Original-From: "Patrick Pang" Date: Fri, 23 Feb 2007 02:18:09 -0500 Sent to CCL by: "Patrick Pang" [skpang:-:ctimail.com] Dear all, I try to optimize DNA (12 base pairs) geometry using UFF implemented in Gaussian 03 but it is terminated at 5000 step. Do you know how to increase the number of steps for geometry optimization when UFF implemented in Gaussian 03 is employed? Thank you for your attention! Patrick Pang My e-mail address is: skpang() ctimail.com From owner-chemistry@ccl.net Fri Feb 23 04:14:00 2007 From: "CRYSTAL crystal(_)unito.it" To: CCL Subject: CCL: MSSC2007 - Modeling in Solid State Chemistry Message-Id: <-33689-070223031745-14829-fCXFnLaGUOcxVY3OwlqzjQ[*]server.ccl.net> X-Original-From: CRYSTAL Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii Date: Fri, 23 Feb 2007 08:23:29 +0100 MIME-Version: 1.0 Sent to CCL by: CRYSTAL [crystal ~ unito.it] The Theoretical Chemistry Group of the University of Torino is organizing a new edition of the Summer School: Ab initio Modelling in Solid State Chemistry MSSC2007 http://www.crystal.unito.it/mssc2007 September 2-7, 2007 - Torino, Italy Directors: B. Civalleri - R. Orlando The School is addressed to PhD students, Post-Docs and researchers with interests in solid state chemistry, physics, materials science, surface science and catalysis. It provides an overview of the possibilities offered by ab initio quantum mechanical techniques when applied to the characterization of crystalline materials. The capabilities of CRYSTAL06 (http://www.crystal.unito.it/) will be illustrated, with hands-on tutorials organized in the afternoon sessions. Basic tutorials are reserved to beginners. More advanced sessions will be available for groups of experienced CRYSTAL users. Application will be open from March 15th, 2007 From owner-chemistry@ccl.net Fri Feb 23 08:47:00 2007 From: "chupvl chupvl!A!gmail.com" To: CCL Subject: CCL: Docking programs Message-Id: <-33690-070223035752-18235-PcTPJrlzvequagDd2H6MuQ]*[server.ccl.net> X-Original-From: chupvl Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Fri, 23 Feb 2007 11:03:19 +0300 MIME-Version: 1.0 Sent to CCL by: chupvl [chupvl:gmail.com] Hello, I think it's interesting problem - there are a lot of methods to replace natural amino acids woth various linkers, rigid or not. Thou yuo can go from the opposite point of view compiling the library of such kind of linkers. Chupakhin Vladimir Ronald L Cook cookrl===tda.com wrote: > Sent to CCL by: "Ronald L Cook" [cookrl###tda.com] > Dear CCLers > > Many of the docking programs available calculate a fit between a host (e.g. an enzyme, etc) and a small molecule to look for small molecule drugs. My interest/need lies in the opposite direction. Does anyone know of a program that takes a guest and (using for example a genetic algorithm or other equivalent stochastic optimization method) builds a small peptide (or other molecular backbone) chain that provides a good fit to the small molecule? > > Thanks > Ronald Cook > Principal Scientist > TDA Research, Inc.> > > > > From owner-chemistry@ccl.net Fri Feb 23 10:15:01 2007 From: "Michel Petitjean ptitjean-.-itodys.jussieu.fr" To: CCL Subject: CCL: cavity determination Message-Id: <-33691-070223101006-26889-JjU6Jq1y6KP6D0u2BCVKlg*server.ccl.net> X-Original-From: Michel Petitjean Date: Fri, 23 Feb 2007 16:09:46 +0100 (MET) Sent to CCL by: Michel Petitjean [ptitjean%x%itodys.jussieu.fr] To: chemistry{}ccl.net Subject: CCL: Re: cavity determination Hi Victor, I do not know how widely alpha-shapes are used, but it seems to me that it is actually the best way to define and compute cavities of a rigid conformer (in fact, if you know other ones please tell me). The calculated cavities are parametrized by the radius of the probe sphere. This radius may be set to 1.4 A when the probe sphere modelizes a water molecule. However, in the case of a macrocycle, I would look for the greatest radius allowing to indeed retrieve the torus topology of the macrocycle. Remark: For a given conformer, this calculation of cavities depends on only 1 parameter (the probe radius). It is a major interest of the mathod. Furthermore you are lucky because in the case of a macrocycle there is a way to fix this parameter in a non arbitrary manner. Most modeling softwares contain numerous parameters of crucial importance, which are generally set to arbitrary default values because the user has no time to test the stability of the result for various sets of parameter values. But of course the reliability of the result is low if nothing is known about its stability. It often happens that the user has little help to fix optimally parameter values. So, less a method has such parameters, more I like it. Michel Petitjean, Email: petitjean{}itodys.jussieu.fr ITODYS (CNRS, UMR 7086) ptitjean{}ccr.jussieu.fr 1 rue Guy de la Brosse Phone: +33 (0)1 44 27 48 57 75005 Paris, France. FAX : +33 (0)1 44 27 68 14 http://petitjeanmichel.free.fr/itoweb.petitjean.shape.html http://petitjeanmichel.free.fr/itoweb.petitjean.spheres.html Sent to CCL by: "Victor Rosas-Garcia" [quimico69 _ yahoo.com]: > Hello everybody, > > I am trying to calculate the size of the molecular cavity for a series of macrocycles, and someone suggested the use of alpha shapes. I am not very familiar with these. I have located some (highly mathematical) literature and web pages about alpha shapes. In addition, I am trying to get a copy of Edelbrunner's papers on its application to chemical species (don't have them yet). So my questions are: > > a) How widely used are alpha shapes in working with molecular cavities? (my library search has turned up very little) > > b) Can anyone recommend software to calculate alpha shapes of molecules? > > So far I have found Hull by Ken Clarkson, and Alpha Shapes at Duke, but I'm still trying to get them to compile with gcc. > > thank you for you attention > > Victor M. Rosas Garca, PhD > Facultad de Ciencias Quimicas, UANL > e-mail: quimico69.:.yahoo.com From owner-chemistry@ccl.net Fri Feb 23 10:51:01 2007 From: "Xunlei Ding ding],[sissa.it" To: CCL Subject: CCL: G03- full of hard disk Message-Id: <-33692-070223100940-26829-xbItW1+VDHdwJx0tg2R2Lg^^server.ccl.net> X-Original-From: Xunlei Ding Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Fri, 23 Feb 2007 14:47:08 +0100 MIME-Version: 1.0 Sent to CCL by: Xunlei Ding [ding{}sissa.it] Dear Sir, I did a CCSD calculation, with 10 rwf files (each is 2GB) and the output says: --------------------------------- Estimate disk for full transformation -296817082 words. Semi-Direct transformation. ModeAB= 4 MOrb= 270 LenV= 57414934 LASXX= 172588842 LTotXX= 172588842 LenRXX= 507473515 LTotAB= 334884673 MaxLAS= 485629290 LenRXY= 0 NonZer= 680062357 LenScr= 1030487040 LnRSAI= 967674600 LnScr1= 1470303744 LExtra= 0 Total= -319028397 MaxDsk= -1 SrtSym= T ITran= 5 No file to extend for IUnit= 1 -- out of disk space. Error termination in NtrErr: NtrErr called from NtrExt. ------------------------------------------- I think the calculation need much more hard disk than 20GB. Is it ? Thank you! Best regards! Ding From owner-chemistry@ccl.net Fri Feb 23 11:25:01 2007 From: "Green Power powergreen,+,gmail.com" To: CCL Subject: CCL:G: How to print two-electron integral in g03 Message-Id: <-33693-070223020956-7626-ht0dyurEnJR2VyPJHQunJw() server.ccl.net> X-Original-From: "Green Power" Content-Type: multipart/alternative; boundary="----=_Part_48796_21544050.1172205572589" Date: Thu, 22 Feb 2007 23:39:32 -0500 MIME-Version: 1.0 Sent to CCL by: "Green Power" [powergreen/a\gmail.com] ------=_Part_48796_21544050.1172205572589 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Content-Disposition: inline Hi, CCLer's, Anybody can tell me how to print out two-electron integrals in gaussian03? Also, I would like to exclude interactions between the some atom pairs within a molecule using gaussian calculation. Is there any way to do that? Thank you in advance. Tian ------=_Part_48796_21544050.1172205572589 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Hi, CCLer's,

Anybody can tell me how to print out two-electron integrals in gaussian03? Also, I would like to exclude interactions between the some atom pairs within a molecule using gaussian calculation. Is there any way to do that? Thank you in advance.

Tian
------=_Part_48796_21544050.1172205572589-- From owner-chemistry@ccl.net Fri Feb 23 16:17:01 2007 From: "Axel Mathieu AMathieu**tranzyme.com" To: CCL Subject: CCL: Docking programs Message-Id: <-33694-070223160510-22546-ZwLwkEEX84pIn/wNYsdY1A_._server.ccl.net> X-Original-From: "Axel Mathieu" Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Fri, 23 Feb 2007 15:29:57 -0500 MIME-Version: 1.0 Sent to CCL by: "Axel Mathieu" [AMathieu|*|tranzyme.com] Hello Ronald, There's a group of computational chemists headed by Ghislain Deslongchamps at the University of New Brunswick working on "reverse docking" for the design of catalysts. The have been using MOE to do this. Maybe you'll find what you need in their publications - you may be able to find their presentation on the Chemical Computing Group User group meeting site (ca 2 years ago) http://www.compchem.com. Hope this is what you're looking for, Axel --------------------------- Axel Mathieu, Ph.D. Scientist, Structural Studies and NMR Support Tranzyme Pharma Inc. Phone: 819.820.6840 Fax: 819.820.6841 http://www.tranzyme.com   NOTICE: The information transmitted by this email is private and confidential and is intended solely for the exclusive use of the intended recipients specified therein. If you are neither an intended recipient nor an employee or agent responsible for delivery to an intended recipient, you should be aware that any dissemination, distribution or copying of this communication is strictly prohibited. If you received this communication in error, please notify us immediately. -----Original Message----- > From: owner-chemistry]-[ccl.net [mailto:owner-chemistry]-[ccl.net] Sent: 23 février, 2007 03:03 To: Axel Mathieu Subject: CCL: Docking programs Sent to CCL by: chupvl [chupvl:gmail.com] Hello, I think it's interesting problem - there are a lot of methods to replace natural amino acids woth various linkers, rigid or not. Thou yuo can go from the opposite point of view compiling the library of such kind of linkers. Chupakhin Vladimir Ronald L Cook cookrl===tda.com wrote: > Sent to CCL by: "Ronald L Cook" [cookrl###tda.com] > Dear CCLers > > Many of the docking programs available calculate a fit between a host (e.g. an enzyme, etc) and a small molecule to look for small molecule drugs. My interest/need lies in the opposite direction. Does anyone know of a program that takes a guest and (using for example a genetic algorithm or other equivalent stochastic optimization method) builds a small peptide (or other molecular backbone) chain that provides a good fit to the small molecule? > > Thanks > Ronald Cook > Principal Scientist > TDA Research, Inc.http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Fri Feb 23 23:56:00 2007 From: "Vincent Xianlong Wang xloongw=yahoo.com" To: CCL Subject: CCL: calculating titration state distributions for multiprotic acids with coupled sites Message-Id: <-33695-070223235239-11240-jJCu1/Z9yuXjR/b1m2LMug~~server.ccl.net> X-Original-From: Vincent Xianlong Wang Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-1 Date: Fri, 23 Feb 2007 20:52:26 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: Vincent Xianlong Wang [xloongw*yahoo.com] Dear Dr. Olsen, I am not sure if the following reference is what you want.It talks about the equilibrium distribution of different protonation species for multiprotic acids. Martell, A. E. and Motekaitis, R. J. (ed.) Determination and Use of Stability Constants, 1992, VCH Publishers Inc., New York, 37. The book includes the source code written in Fortran. Best regards, Vincent --- "Seth Olsen s.olsen1,,uq.edu.au" wrote: > > Sent to CCL by: Seth Olsen [s.olsen1(~)uq.edu.au] > > Hi CCLers, > > I have been trying to find references or algorithms > which can estimate > equilibrium distributions of different protonation > states of a > multiprotic acid where the sites may be coupled. > Can anyone point me in > the right direction? > > Cheers, > > Seth > > > > -= This is automatically added to each message by > the mailing script =- > To recover the email address of the author of the > message, please change > the strange characters on the top line to the (~) > sign. You can also > look up the X-Original-From: line in the mail > header.> > E-mail to administrators: CHEMISTRY-REQUEST(~)ccl.net > or use> > Before posting, check wait time at: > http://www.ccl.net> Conferences: > http://server.ccl.net/chemistry/announcements/conferences/ > > Search Messages: http://www.ccl.net/htdig (login: > ccl, Password: search) > > If your mail bounces from CCL with 5.7.1 error, > check:> > RTFI: > http://www.ccl.net/chemistry/aboutccl/instructions/> > > > ____________________________________________________________________________________ Don't get soaked. Take a quick peak at the forecast with the Yahoo! Search weather shortcut. http://tools.search.yahoo.com/shortcuts/#loc_weather