From owner-chemistry@ccl.net Fri Sep 9 04:26:08 2005 From: "CCL" To: CCL Subject: CCL: W:GTO and STO Message-Id: <-29108-050909042243-25892-IkdSsI0o7bIbaeY2FfAFuw~!~server.ccl.net> X-Original-From: Marcel Swart Content-Type: multipart/alternative; boundary=Apple-Mail-5--229475054 Date: Fri, 9 Sep 2005 10:21:36 +0200 Mime-Version: 1.0 (Apple Message framework v622) Sent to CCL by: Marcel Swart [m.swart~!~few.vu.nl] --Apple-Mail-5--229475054 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=WINDOWS-1252; format=flowed I agree on the part of the functional, but disagree on the basis set: a STO-6G is not equivalent to a single-zeta Slater, nor can it provide the same accuracy. It might be better to compare with basis sets close to the basis set=20 limit; e.g. something like the QZ4P basis in ADF and the 6-311++G(3df,3pd)=20 basis, as was used by Scuseria/Perdew and co-workers for testing the TPSS and TPSSh functional. Note also that of course the speed depends on the accuracy of the=20 integration grid, so they should be chosen carefully. On Sep 9, 2005, at 12:50 AM, CCL wrote: > Sent to CCL by: John McKelvey [jmmckel-$-attglobal.net] > All, > > The test would be to compare two different programs using the same DFT=20= > functional and as similar basis sets as possible. In a Slater sense=20 > STO-6G _might_ be a near equivalent to a Slater; the question would be=20= > then what would be the flop count for a DZ Slater basis using two=20 > Slaters vs 2*STO-6G gaussian Slater mimics... > > Cheers, > > John McKelvey =96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96= =96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96 dr. Marcel Swart Theoretische Chemie Vrije Universiteit Amsterdam Faculteit der Exacte Wetenschappen De Boelelaan 1083 1081 HV Amsterdam The Netherlands Tel +31-(0)20-5987619 Fax +31-(0)20-5987629 E-mail m.swart~!~few.vu.nl Web http://www.few.vu.nl/~swart =96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96= =96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96 --Apple-Mail-5--229475054 Content-Transfer-Encoding: quoted-printable Content-Type: text/enriched; charset=WINDOWS-1252 I agree on the part of the functional, but disagree on the basis set: a STO-6G is not equivalent to a single-zeta Slater, nor can it provide the same accuracy. It might be better to compare with basis sets close to the basis set limit; e.g. something like the QZ4P basis in ADF and the 6-311++G(3df,3pd) basis, as was used by Scuseria/Perdew and co-workers for testing the TPSS and TPSSh functional. Note also that of course the speed depends on the accuracy of the integration grid, so they should be chosen carefully. On Sep 9, 2005, at 12:50 AM, CCL wrote: Sent to CCL by: John McKelvey [jmmckel-$-attglobal.net] All, The test would be to compare two different programs using the same DFT functional and as similar basis sets as possible. In a Slater sense STO-6G _might_ be a near equivalent to a Slater; the question would be then what would be the flop count for a DZ Slater basis using two Slaters vs 2*STO-6G gaussian Slater mimics... Cheers, John McKelvey = Helvetica=96=96=96=96=96= =96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96= =96=96=96=96=96=96=96=96=96=96=96=96=96=96 = Papyrusdr. Marcel Swart = Papyrus = OsakaTheoretische Chemie Vrije Universiteit Amsterdam Faculteit der Exacte Wetenschappen De Boelelaan 1083 1081 HV Amsterdam The Netherlands Tel +31-(0)20-5987619 Fax +31-(0)20-5987629 E-mail m.swart~!~few.vu.nl Web http://www.few.vu.nl/~swart = Helvetica=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96= =96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96 --Apple-Mail-5--229475054-- From owner-chemistry@ccl.net Fri Sep 9 07:36:19 2005 From: "CCL" To: CCL Subject: CCL: W:GTO and STO Message-Id: <-29109-050909061552-13868-IkdSsI0o7bIbaeY2FfAFuw|a|server.ccl.net> X-Original-From: John McKelvey Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=windows-1252; format=flowed Date: Fri, 09 Sep 2005 05:14:14 -0500 MIME-Version: 1.0 Sent to CCL by: John McKelvey [jmmckel|a|attglobal.net] Marcel, I agree that comparable high quality basis sets would perhaps give the best overall comparison. I do believe that I stated that STO-6G would not give the same result as a true Slater, and why. I was hoping to suggest a way a way to estimate the relative flop-count efficiencies of a Slater vs a gaussian based mimic, given the background of why current Hartree-Fock codes almost always avoid using Slaters. Cheers, John CCL wrote: > I agree on the part of the functional, but disagree on the basis set: > a STO-6G is not equivalent to a single-zeta Slater, > nor can it provide the same accuracy. > > It might be better to compare with basis sets close to the basis set > limit; > e.g. something like the QZ4P basis in ADF and the 6-311++G(3df,3pd) > basis, > as was used by Scuseria/Perdew and co-workers for testing the TPSS and > TPSSh functional. > > Note also that of course the speed depends on the accuracy of the > integration > grid, so they should be chosen carefully. > > On Sep 9, 2005, at 12:50 AM, CCL wrote: > > Sent to CCL by: John McKelvey [jmmckel-$-attglobal.net] > All, > > The test would be to compare two different programs using the same > DFT functional and as similar basis sets as possible. In a Slater > sense STO-6G _might_ be a near equivalent to a Slater; the > question would be then what would be the flop count for a DZ > Slater basis using two Slaters vs 2*STO-6G gaussian Slater mimics... > > Cheers, > > John McKelvey > > –––––––––––––––––––––––––––––––––––––––––––– > dr. Marcel Swart > > Theoretische Chemie > Vrije Universiteit Amsterdam > Faculteit der Exacte Wetenschappen > > De Boelelaan 1083 > 1081 HV Amsterdam > The Netherlands > > Tel +31-(0)20-5987619 > Fax +31-(0)20-5987629 > E-mail m.swart|a|few.vu.nl > Web http://www.few.vu.nl/~swart > –––––––––––––––––––––––––––––––––––––––––––– > > From owner-chemistry@ccl.net Fri Sep 9 08:54:10 2005 From: "CCL" To: CCL Subject: CCL: Molecular Modelling 2006 (MM2006) - Second Announcement and Call for Abstracts Message-Id: <-29110-050909043120-28879-DUcROUZqAAanpwYwt3FuqA(-)server.ccl.net> X-Original-From: "Ricardo Mancera" Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Fri, 9 Sep 2005 15:43:35 +0800 MIME-Version: 1.0 Sent to CCL by: "Ricardo Mancera" [r.mancera(-)wabri.org.au] MOLECULAR MODELLING 2006 (MM2006) - SECOND ANNOUNCEMENT AND CALL FOR ABSTRACTS PERTH, AUSTRALIA, 19-22 APRIL 2006 We are pleased to announce that Molecular Modelling 2006 (MM2006) will be held in Perth, Australia from Wednesday 19 until Saturday 22 of April 2006 at Curtin University of Technology. These series of meetings are held every 18-24 months and aim to bring together the modelling community in Australia, New Zealand, the Asia-Pacific region and other parts of the world. The members of the organising committee are Ricardo Mancera (chair), Julian Gale, Andrew Rohl, Mark Spackman and Sue Berners-Price. The Conference Secretary is Kate Wright. CALL FOR ABSTRACTS MM2006 will cover molecular modelling in the life and physical sciences. Abstracts are invited for both oral and poster contributions in the broad areas of biomolecular modelling (protein and macromolecular modelling, ligand- and structure-based drug design and general molecular modelling), computational chemistry (ab initio, DFT and QM/MM methods) and materials modelling (condensed matter and polymers). Abstracts should be no longer than one page long and submitted by e-mail as Word or RTF documents to the Conference Secretariat. Abstracts should include a title, names of authors and their affiliations, summary of the work presented and references. Figures may be included within the one-page limit, but reproduction will be done in black and white only. PROCEEDINGS The proceedings of the meeting will be published in a special issue of the journal Molecular Simulation. Participants of the meeting will be invited to submit papers, which will undergo peer review. LIST OF CONFIRMED SPEAKERS In keeping with previous conference formats, we will have a number of plenary speakers (mostly from overseas) as well as invited and contributed presentations. We will also hold a poster session. This is the list of confirmed speakers so far: Prof Alan Mark (University of Queensland) Dr Mark Smythe (University of Queensland) Prof Jill Gready (Australian National University) Dr Renate Griffith (University of Newcastle) Dr David Chalmers (Monash University) Dr Brian Smith (Walter and Eliza Hall Institute of Medical Research) Dr Bret Church (University of New South Wales) Dr Merridee Wouters (Victor Chang Cardiac Research Institute) Prof Peter Gill (Australian National University) Prof Sean Smith (University of Queensland) A/Prof Billy Todd (Swinburne University) Dr Ian Snook (RMIT) Dr Oliver Warschkow (University of Sydney) Dr Chandra Verma (Bioinformatics Institute, Singapore) Prof Kyoung Tai No (Yonsei University, Korea) Dr Jed Pitera (IBM Almaden Research Centre, USA) Prof Brian Shoichet (University of California, San Francisco, USA) Dr Jonathan Essex (University of Southampton, UK) Prof Alessandro Laio (ETH Zurich, Switzerland) Prof Simon Phillpot (University of Florida, USA) STUDENT BURSARIES We will be offering a number of student bursaries that will cover the registration fee and provide partial reimbursemente of travel expenses. Between 2 and 3 of these bursaries will be sponsored by Accelrys for work that is being carried out using any of their suites of molecular modelling softwares. REGISTRATION The organising committee would like to invite you to register for this meeting. The conference website has all appropriate forms for registration and application for student bursaries, as well as information about abstract submission. Please point your browsers to: http://www.nanochemistry.curtin.edu.au/conferences/mm_2006.cfm KEY DATES Abstract submission deadline: Friday 16 December 2005 Student bursary application deadline: Friday 16 December 2005 Earlybird registration deadline: Friday 18 February 2006 We would be delighted if you can join us next year here in Perth. Please circulate this announcement to others who might be interested in attending. We look forward to welcoming you to Perth next year! Ricardo Mancera (on behalf of the Organising Committee) ---------------------------------------------------- Ricardo L. Mancera, M.A., Ph.D. Senior Research Fellow / Senior Lecturer Western Australian Biomedical Research Institute & School of Pharmacy and School of Biomedical Sciences Curtin University of Technology GPO Box U1987 Perth WA 6845 Australia Tel: +61 8 9266 1017 Fax: +61 8 9266 7485 E-mail: R.Mancera(-)wabri.org.au R.Mancera(-)curtin.edu.au From owner-chemistry@ccl.net Fri Sep 9 10:09:23 2005 From: "CCL" To: CCL Subject: CCL: W:GTO and STO Message-Id: <-29111-050909060436-13311-DUcROUZqAAanpwYwt3FuqA#server.ccl.net> X-Original-From: Stephen D Williams Content-disposition: inline Content-language: en Content-Transfer-Encoding: 8bit Content-type: text/plain; charset=windows-1252 Date: Fri, 09 Sep 2005 04:59:23 -0400 MIME-version: 1.0 Sent to CCL by: Stephen D Williams [willsd#iplm2.appstate.edu] A couple of years ago we did a small comparison of several different scalar relativisitic methods. We compared their accuracy for prediction of the Rh-Rh bond length in rhodium acetate. ZORA in ADF did quite well, but the best was the C-E relativistic ECP (as implemented in DGAUSS, but now available (?) in G03). See Int. J. Molec. Sci. 2004, 5, 67-74. This is available as a pdf from the publisher at www.mdpi.org/ijms/papers/i5020067.pdf. Steve Williams ----- Original Message ----- > From: CCL Date: Thursday, September 8, 2005 10:53 am Subject: CCL: W:GTO and STO > > Sent to CCL by: "Dmitri G. Goussev" [dgoussev|*|wlu.ca] > I would be good if someone could make a brief critical comparative > evaluation of the Gaussian 03 and ADF packages. Some questions in > particular > can be raised about the choice of hybrid DFT (used mostly in > Gaussian 03) > and pure DFT functionals (used typically in ADF), and which give > better > reaction energies and barriers. I have heard that frequency > calculations are > so much longer in ADF that they are not practical for medium to > large > system, leaving the question open as to whether the optimized > geometries are > minimums or not. Relativistic effects are also treated differently > in the > two packages, with the use of ECP's in Gaussian and ZORA- > corrections in > ADF. It would be interesting to know what difference this could make. > Regards, > Dmitri > > Dmitri G. Goussev (Gusev) > Associate Professor of Chemistry > Wilfrid Laurier University > Department of Chemistry > Waterloo, Ontario > N2L 3C5 Canada > Tel.: (519) 884-1970, ext. 2736 > Fax: (519) 746-0677 > > > ----- Original Message ----- > > From: "CCL" > To: "Goussev, Dmitri " > Sent: Thursday, September 08, 2005 4:51 AM > Subject: CCL: W:GTO and STO > > > > > > Sent to CCL by: Stan van Gisbergen [vangisbergen~~scm.com] > > Dear Dr. McKelvey and others interested in STO code performance, > > > > Thank you for your compliments regarding ADF's capabilities. > > > > As there seems to be some doubt regarding the efficiency of STO- > based > > codes, > > such as ADF, I would like to give one timing example to make the > > discussion less theoretical. > > > > An 8-CPU job on a Linux cluster > > (http://www.sara.nl/userinfo/lisa/description/index.html) > > for a geometry step at the GGA level of a Pt-complex with 105 > atoms in a > > DZP basis set > > (1021 STO's) takes 17.5 minutes elapsed time. My conclusion is > that this > > is fast enough > > to do a lot of useful chemistry with ADF during one coffee break. > I can > > provide the input > > file upon request so you can check if other DFT codes are > similarly > > efficient. > > > > Further information on the efficiency of ADF is available in our > brochure> (http://www.scm.com/SCMForms/BrochureRequest.jsp) > > and can be tested through a free trial. > > > > Best regards, > > Stan van Gisbergen, > > Scientific Computing & Modelling (www.scm.com), provider of ADF > > > > On Sep 7, 2005, at 4:17 PM, CCL wrote: > > > >> > >> Sent to CCL by: John McKelvey [jmmckel;;attglobal.net] > >> All, > >> > >> I have not seen any timing benchmarks of ADF and Slater > functions versus > >> a gaussian based code. With intent to compare accuracy I > suppose one > >> could start by comparing a D-Z Slater calculation in ADF with > an > >> equivalent D-Z/STO-6G basis in a gaussian based code. The cusp > >> conditions and hence energies would be off some, but I would > guess that > >> geometries might be very similar.... Not sure of codes that > have STO-NG > >> for d functions.. > >> I have to say that after sitting through the ADF seminar at the > recent > >> ACS meeting I am quite impressed with it's capabilities. CPU > times may > >> not be the only issue; after all understanding chemistry is the > main > >> point. :-) > >> > >> Best regards, > >> > >> John McKelvey > >> > >> > >> CCL wrote: > >> > >>> Sent to CCL by: Laurence Cuffe [Laurence.Cuffe^ucd.ie] > >>> > >>> > >>> ----- Original Message ----- > >>> > >>>> From: CCL > >>>> > >>> Date: Tuesday, September 6, 2005 6:31 pm > >>> Subject: CCL: W:GTO and STO > >>> > >>> > >>>> Sent to CCL by: Serguei Patchkovskii [ps:+:ned.sims.nrc.ca] > >>>> > >>>>> Sent to CCL by: Laurence Cuffe [Laurence.Cuffe]*[ucd.ie] > >>>>> The short answer is that calculating the overlap between two > >>>>> Gaussiantype -Orbitals can be done in closed form. That is > given two > >>>>> GTO's A and B you can write an relatively simple algebraic > expression>>>>> for the size of the overlap between them. This is > not possible with > >>>>> Slater type orbitals. > >>>>> > >>>> This statement, of course, is false. Closed-form expressions for > >>>> overlap integrals in terms of exponential integral-type functions > >>>> are very well known. For example:…(cut) > >>>> Dr. Serguei Patchkovskii > >>>> > >>> A fair point Dr Patchkovskii. In hindsight I should, perhaps, > have put > >>> more emphasis on “relatively simple” As Ahmed. Bouferguene wrote: > >>> The "flip side of the coin" is, multi-center integrals (which > is the > >>> heart > >>> of ab initio calculations) over STOs is much much more > difficult than > >>> with > >>> GTOs. I think I’d trust his judgment in this area, as its one > where he’s > >>> published a number of papers e.g. > >>> Ahmed Bouferguene 2005 J. Phys. A: Math. Gen. 38 2899-2916 > “Addition>>> theorem of Slater type orbitals: a numerical > evaluation of > >>> Barnett–Coulson/Löwdin functions” > >>> Historically evaluating GTO’s was faster, and while there are > now > >>> claims > >>> that highly optimised STO codes can beat GTO codes, I remain to be > >>> convinced that highly optimised STO codes can beat highly > optimised GTO > >>> codes. > >>> In the wider sense original question was about the popularity of > >>> Gaussian type orbital codes over STO based ones. Here I think > the > >>> reason > >>> is also historical, and is based on the early popularity of the > >>> gaussian > >>> program as a collaborative venture among a number of > theoretical > >>> chemists. The use of GTO’s was, I think, first suggested by > S.F. Boys, > >>> in Proc. > >>> Roy. Soc. A200, 542 (1950) > >>> > >>> ADF (using STO’s) has been around for a long time, and I know > that the > >>> Zeigler group has made many substantial contributions to it. > It has > >>> not > >>> (yet) overtaken Gaussian in popularity, but maybe if( or when) > it does > >>> we’ll be wondering what the advantages of GTO’s are. I’m not > holding my > >>> breath. > >>> All the best > >>> Dr Laurence Cuffe> To send e-mail to subscribers of CCL put the > string > >>> CCL: on your > >> Subject: line> > >> Send your subscription/unsubscription requests to: > >> CHEMISTRY-REQUEST#ccl.net HOME Page: http://www.ccl.net | Jobs > Page: > >> http://www.ccl.net/jobs > >> If your is mail bouncing from ccl.net domain due to spam > filters, > >> please> -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+- > +-+-+-+-+-+- > >> +-+ > >> > >> > >> > >> > > Dr. S.J.A. van Gisbergen Scientific Computing & Modelling NV > > Theoretical Chemistry, Vrije Universiteit > > De Boelelaan 1083 > > 1081 HV Amsterdam > > The Netherlands vangisbergen#scm.com http://www.scm.com > > > > Please note NEW FAX AND TELEPHONE NUMBERS: > > T: +31-20-5987626 F: +31-20-5987629> To send e-mail to > subscribers of CCL put the string CCL: on your Subject: > > line> > > Send your subscription/unsubscription requests to: > > CHEMISTRY-REQUEST#ccl.net HOME Page: http://www.ccl.net | Jobs > Page: > > http://www.ccl.net/jobs> use the Web based form from CCL Home > > Page> > > > > > > > > -= This is automatically added to each message by the mailing > script =- > To send e-mail to subscribers of CCL put the string CCL: on your > Subject: line> > Send your subscription/unsubscription requests to: CHEMISTRY- > REQUEST#ccl.net > HOME Page: http://www.ccl.net | Jobs Page: > http://www.ccl.net/jobs > > If your is mail bouncing from ccl.net domain due to spam filters, > please> -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+- > +-+-+ > > > > From owner-chemistry@ccl.net Fri Sep 9 14:42:25 2005 From: "CCL" To: CCL Subject: CCL: CCL Ionic Interactions with active site Message-Id: <-29112-050909134917-16570-DUcROUZqAAanpwYwt3FuqA/a\server.ccl.net> X-Original-From: Yogesh Sabnis Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-1 Date: Fri, 9 Sep 2005 09:49:13 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Yogesh Sabnis [ysabnis/a\yahoo.com] Dear All, Ionization of specific functionalities in a compound depend on the pH of the surrounding environment. Examples: An aliphatic N having a pka more than the pH will get protonated and will bear a positive charge. The N in case of aryl sulfonamides which has a pka around 4.5 will be partially deprotonated and will bear a negative charge at physiological pH. My question is: When these molecules bind to the active site on a protein/receptor, should one always see ionic interactions with the charged species (N+ in case of quarternary nitogen or N- in case of aryl sulfonamides)? Can one have a case where the charge on a molecule does not interact with anything at all? If anyone knows any good reviews I would greatly appreciate mentioning them. Any help is appreciated. Thank you. Kind regards, Yogesh ######################## Yogesh Sabnis, PhD BMC, Box 574, Dept. Organic Pharmaceutical Chemistry Husargatan 3, Uppsala - 751 23 Sweden ______________________________________________________ Click here to donate to the Hurricane Katrina relief effort. http://store.yahoo.com/redcross-donate3/ From owner-chemistry@ccl.net Fri Sep 9 16:41:13 2005 From: "CCL" To: CCL Subject: CCL: Molpro and memory Message-Id: <-29113-050909163943-6850-DUcROUZqAAanpwYwt3FuqA---server.ccl.net> X-Original-From: Alexander Martins Silva Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Fri, 09 Sep 2005 17:44:05 -0300 MIME-Version: 1.0 Sent to CCL by: Alexander Martins Silva [alex.msilva---uol.com.br] Hi, This is my second message about the same issue: Molpro and memory. I've compiled the Molpro in a Xeon machine with 2 proc and 4 GB of memory. However, I couldn't use more than 1Gb of memory when executing jobs. I've already expanded the kernel.shmall and kernel.shmmax parameters up to 2Gb and nothing happens. The manual don't tell me nothing about this subject. Is it a problem related to the Intel Fotran Compiler? Anybody could help me? Thanks in advance, Alexander. From owner-chemistry@ccl.net Fri Sep 9 18:46:46 2005 From: "CCL" To: CCL Subject: CCL: Molpro and memory Message-Id: <-29114-050909184406-27557-DUcROUZqAAanpwYwt3FuqA[-]server.ccl.net> X-Original-From: Kirk Peterson Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Date: Fri, 9 Sep 2005 15:43:56 -0700 Mime-Version: 1.0 (Apple Message framework v622) Sent to CCL by: Kirk Peterson [kipeters[-]wsu.edu] Alexander, I would check the value in /proc/sys/kernel/shmmax, but I'm not sure if this is really the problem. This is really a Linux kernel issue and not anything specific to Molpro. Molpro just does a malloc call to reserve its memory. Can you allocate more than 1 GB with any other program? regards, Kirk On Sep 9, 2005, at 1:44 PM, CCL wrote: > > Sent to CCL by: Alexander Martins Silva [alex.msilva---uol.com.br] > > Hi, > > This is my second message about the same issue: Molpro and > memory. I've compiled the Molpro in a Xeon machine with 2 proc and 4 > GB of memory. However, I couldn't use more than 1Gb of memory when > executing jobs. I've already expanded the kernel.shmall and > kernel.shmmax parameters up to 2Gb and nothing happens. The manual > don't tell me nothing about this subject. Is it a problem related to > the Intel Fotran Compiler? Anybody could help me? > > > Thanks in advance, > > Alexander.> To send e-mail to subscribers of CCL put the string CCL: on your > Subject: line> > Send your subscription/unsubscription requests to: > CHEMISTRY-REQUEST[-]ccl.net HOME Page: http://www.ccl.net | Jobs Page: > http://www.ccl.net/jobs > If your is mail bouncing from ccl.net domain due to spam filters, > please> -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+- > +-+ > > > > From owner-chemistry@ccl.net Fri Sep 9 21:27:23 2005 From: "CCL" To: CCL Subject: CCL: CCL Ionic Interactions with active site Message-Id: <-29116-050909192606-11419-DUcROUZqAAanpwYwt3FuqA|a|server.ccl.net> X-Original-From: Steve Bowlus Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Fri, 09 Sep 2005 15:31:33 -0700 MIME-Version: 1.0 Sent to CCL by: Steve Bowlus [chezbowlus|a|goldrush.com] CCL wrote: > Sent to CCL by: Yogesh Sabnis [ysabnis/a\yahoo.com] > Dear All, > > Ionization of specific functionalities in a compound > depend on the pH of the surrounding environment. > > Examples: > An aliphatic N having a pka more than the pH will get > protonated and will bear a positive charge. > > The N in case of aryl sulfonamides which has a pka > around 4.5 will be partially deprotonated and will > bear a negative charge at physiological pH. > > My question is: When these molecules bind to the > active site on a protein/receptor, should one always > see ionic interactions with the charged species (N+ in > case of quarternary nitogen or N- in case of aryl > sulfonamides)? Can one have a case where the charge on > a molecule does not interact with anything at all? Ligands binding in relatively open sites (or sites which close upon ligand binding) _may_ have ionized groups directed toward bulk solvent. This seemingly non-specific interaction (not the same as no interaction!) may be very important in orienting the molecule during the binding process so that a more hydrophobic face/edge will be better disposed toward a relatively drier/greasier binding cleft. Remember too the fiction of formal charges: for sulfonamides (and sulfonylureas), the negative charge "on the nitrogen" is actually delocalized onto nitrogen and oxygen; similarly the charge of the "positive nitrogen" is really presented to the receptor via the protons attached to the nitrogen. So these groups look like blobs of charge (rather than points) which may (or may not) appear to have specific interactions, depending on how you view the situation. Steve From owner-chemistry@ccl.net Fri Sep 9 21:27:23 2005 From: "CCL" To: CCL Subject: CCL: Molpro and memory Message-Id: <-29115-050909195719-13636-DUcROUZqAAanpwYwt3FuqA/./server.ccl.net> X-Original-From: "Ben Swerts" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Sat, 10 Sep 2005 01:04:18 +0200 MIME-Version: 1.0 Sent to CCL by: "Ben Swerts" [ben.swerts/./ua.ac.be] Hi Alexander, I have absolutely no experience with Molpro but I can tell you this: When using GCC as the compiler in 32 bit mode, I noticed a limit of 1 GB for statically allocated memory when compiling fortran codes. I tried a lot of things to circumvent this problem but never succeeded. Now we have 64 bit machines and this 1 GB limit is finally a thing of the past. I guess the problem is related to Linux. Applications just crash when compiled with more than 1 GB. Greetz, Ben > -----Original Message----- > From: owner-chemistry/./ccl.net [mailto:owner-chemistry/./ccl.net] > Sent: Friday, September 09, 2005 10:44 PM > To: Swerts, Ben > Subject: CCL: Molpro and memory > > > Sent to CCL by: Alexander Martins Silva [alex.msilva---uol.com.br] > > Hi, > > This is my second message about the same issue: > Molpro and memory. I've compiled the Molpro in a Xeon > machine with 2 proc and 4 GB of memory. However, I couldn't > use more than 1Gb of memory when executing jobs. I've > already expanded the kernel.shmall and kernel.shmmax > parameters up to 2Gb and nothing happens. The manual don't > tell me nothing about this subject. Is it a problem related > to the Intel Fotran Compiler? Anybody could help me? > > > Thanks in advance, > > Alexander.