From chemistry-request@server.ccl.net Fri Dec 10 00:26:47 1999 Received: from donkeykong.gpcc.itd.umich.edu (smtp@donkeykong.gpcc.itd.umich.edu [141.211.2.163]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id AAA12867 for ; Fri, 10 Dec 1999 00:26:47 -0500 Received: from tempest.gpcc.itd.umich.edu (smtp@tempest.gpcc.itd.umich.edu [141.211.2.155]) by donkeykong.gpcc.itd.umich.edu (8.8.8/4.3-mailhub) with ESMTP id XAA07038 for ; Thu, 9 Dec 1999 23:17:26 -0500 (EST) Received: from localhost (brupalf@localhost) by tempest.gpcc.itd.umich.edu (8.8.8/5.1-client) with ESMTP id XAA16298 for ; Thu, 9 Dec 1999 23:17:26 -0500 (EST) Precedence: first-class Date: Thu, 9 Dec 1999 23:17:26 -0500 (EST) From: Bruce Allan Palfey X-Sender: brupalf@tempest.gpcc.itd.umich.edu To: chemistry@ccl.net Subject: hydrodynamic properties from structures? Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Thank you Rick Venable and Mike Gilson for providing answers (included below) to my recent question. Bruce Original Question: In the "old" days of biophysics, when 3-D structures were still fairly hard to come by, people would get very rough ideas of the shape of proteins from hydrodynamic experiments like analytical ultracentrifugation or viscosity measurements. I was wondering if things have now come full circle: Given a protein structure from crystallography or NMR, are there any programs that will calculate the frictional coefficient or shape parameters used in hydrodynamic analyses? ********************************************************************** There are several programs; we've developed one named HI in our own lab based on bead models published years ago by Bloomfield and Garcia de la Torre. Another is HYDRO from Garcia de la Torre's lab. While original work was done using a small number of beads, e.g. 8 beads for a protein subunit, computer power advances allowed us to move to atomic detail. We've found that a solvation shell is needed to reproduce experimental data at that level of detail. We've applied our program to NMR studies of proteins. I'm aware of at least one other approach as well. Refs, program pointers available on request. -- Rick Venable =====\ |=| "Eschew Obfuscation" FDA/CBER Biophysics Lab |____/ |=| Bethesda, MD U.S.A. | \ / |=| ( Not an official statement or Rick_Venable@nih.gov | \ / |=| position of the FDA; for that, http://www.erols.com/rvenable \/ |=| see http://www.fda.gov ) *********************************************************************** Yes, there are such programs. See references from J. Antosiewicz and also Garcia-Torres. Best regards, Mike Gilson ************************************************************************ From chemistry-request@server.ccl.net Fri Dec 10 02:50:51 1999 Received: from sc2a.unige.ch (sc2a.unige.ch [129.194.48.4]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id CAA13635 for ; Fri, 10 Dec 1999 02:50:48 -0500 From: David.DeVito@chiphy.unige.ch Received: from sc2a.unige.ch by sc2a.unige.ch (PMDF V5.2-32 #37940) id <01JJBUI5AKU8000LHV@sc2a.unige.ch> for CHEMISTRY@CCL.NET; Fri, 10 Dec 1999 07:41:21 MET-DST Date: Fri, 10 Dec 1999 07:41:21 +0200 (MET-DST) Subject: Problem with DFT To: CHEMISTRY@CCL.NET Message-id: <01JJBUI5ANO2000LHV@sc2a.unige.ch> X-VMS-To: CHEMISTRY@CCL.NET MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Hello ! I'm performing optimisation on a hexaaquaion of rhodium (III) complex and I would like to know which kind of functional are the best ones to make this kind of calculations. The next step should be optimisations with solvent environment and using (if possible) relativistic effects. Thanks in advance for the preciously help !! Best regards, D. De Vito, University of Geneva, Switzerland. From chemistry-request@server.ccl.net Fri Dec 10 05:55:23 1999 Received: from jivdhan.unipune.ernet.in (jivdhan.unipune.ernet.in [196.1.114.31]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id FAA14484 for ; Fri, 10 Dec 1999 05:55:20 -0500 Received: from chem.unipune.ernet.in (chem.unipune.ernet.in [196.1.114.10]) by jivdhan.unipune.ernet.in (8.9.0/UnipuneMailhubV1.3) with ESMTP id PAA08110 for ; Fri, 10 Dec 1999 15:07:39 +0530 Received: from localhost (tcg@localhost) by chem.unipune.ernet.in (8.8.7/8.8.7) with SMTP id PAA20277 for ; Fri, 10 Dec 1999 15:35:50 +0530 Date: Fri, 10 Dec 1999 15:35:49 +0530 (IST) From: "Students of Dr. S.R. Gadre" Reply-To: "Students of Dr. S.R. Gadre" To: CHEMISTRY@server.ccl.net Subject: Anyone interested in ab initio quality MESP? Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Sirs and Madams : We have developed a nice algorithm for molecular fragmentation. This enables us to obtain ab initio quality molecular electron densities and electrostatic potentials of large molecules (with 100 or more atoms) without much effort. If you are interested in applying it to ANY REAL MOLECULAR SYSTEM containing 100 to 200 atoms, please let me know! Thanks....................................K. Babu From chemistry-request@server.ccl.net Thu Dec 9 14:30:31 1999 Received: from igor.wag.caltech.edu (igor.wag.caltech.edu [131.215.33.3]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id OAA09138 for ; Thu, 9 Dec 1999 14:30:31 -0500 Received: from wag.caltech.edu (octane2 [131.215.33.125]) by igor.wag.caltech.edu (8.9.3/8.9.3) with ESMTP id KAA69713; Thu, 9 Dec 1999 10:21:16 -0800 (PST) Sender: rpm@wag.caltech.edu Message-ID: <384FF31C.2494A33C@wag.caltech.edu> Date: Thu, 09 Dec 1999 10:21:16 -0800 From: "Richard P. Muller" X-Mailer: Mozilla 4.6 [en] (X11; U; IRIX64 6.4 IP30) X-Accept-Language: en MIME-Version: 1.0 To: "Gantasala N. Srinivas" CC: CHEMISTRY@ccl.net Subject: Re: CCL:ECP on transition metals References: <384FD9B0.41C6@picasso.chem.uab.edu> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit "Gantasala N. Srinivas" wrote: > > Dear CCL, > > Can some one please suggest me the recent > review articles on ECPs for transition metals. > Thank you > -Srinivas Well, it isn't exactly recent, but Hamann's papers are excellent: @article{Bachelet82, author = {G. B. Bachelet and D. R. Hamann and M. Schl\"{u}tter}, title = {Pseudopotentials that work: From H to Pu}, journal = PRB, volume = 26, pages = 4199, year = 1982} @article{Hamann79, author = {D. R. Hamann and M. Schl\"{u}tter and C. Chiang}, title = {Norm-Conserving Pseudopotentials}, journal = PRL, volume = 43, pages = 1494, year = 1979} @article{Hamann89, author = {D. R. Hamann}, title = {Generalized Norm-Conserving Pseudopotentials}, journal = PRB, volume = 40, pages = 2980, year = 1989} Rick -- Richard P. Muller, Ph.D. rpm@wag.caltech.edu http://www.wag.caltech.edu/home/rpm From chemistry-request@server.ccl.net Thu Dec 9 15:46:16 1999 Received: from lauca.usach.cl (lauca.usach.cl [158.170.64.28]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id PAA09449 for ; Thu, 9 Dec 1999 15:46:11 -0500 Received: from localhost (fgonzale@localhost) by lauca.usach.cl (8.9.1b+Sun/8.9.2) with ESMTP id QAA25218 for ; Thu, 9 Dec 1999 16:36:47 -0300 (CDT) Date: Thu, 9 Dec 1999 16:36:47 -0300 (CDT) From: Fdo Danilo Gonzalez Nilo To: Computational Chemistry List Subject: InsightII View ARG+ Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi all! Anybody know how can I see only the ARG (+)?, using Molecule/Display (InsightII V97.0) I Tried with : Molecule/Display Molecule Spec TEST:ARG+ or Molecule/Display Molecule Spec TEST:ARG* Thanks a lot! Danilo/// ************************************************************************* Fernando Danilo Gonzalez N. University of Santiago de Chile Faculty of Chemistry and Biology, Computational Chemistry Lab. Casilla 40, Correo 33, Santiago, Chile Fono: (562) 681 1542 Anexo:799 E-mail : fgonzale@lauca.usach.cl Fax : (562) 681 2108 URL : ************************************************************************** From chemistry-request@server.ccl.net Fri Dec 10 05:44:52 1999 Received: from jivdhan.unipune.ernet.in (jivdhan.unipune.ernet.in [196.1.114.31]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id FAA14422 for ; Fri, 10 Dec 1999 05:44:43 -0500 Received: from chem.unipune.ernet.in (chem.unipune.ernet.in [196.1.114.10]) by jivdhan.unipune.ernet.in (8.9.0/UnipuneMailhubV1.3) with ESMTP id OAA08013 for ; Fri, 10 Dec 1999 14:56:42 +0530 Received: (from gadre@localhost) by chem.unipune.ernet.in (8.8.7/8.8.7) id PAA20204 for CHEMISTRY@www.ccl.net; Fri, 10 Dec 1999 15:24:44 +0530 Date: Fri, 10 Dec 1999 15:24:44 +0530 From: "Prof. Shridhar R. Gadre" Message-Id: <199912100954.PAA20204@chem.unipune.ernet.in> To: CHEMISTRY@server.ccl.net Subject: ab initio quality (H2O)n clusters Dear Friends : We will appreciate receiving the geometries and energies of ab initio optimized (H2O)n clusters (n lying between 6 to 20). Can anyone help? Thanks in anticipation........................Shridhar gadre From chemistry-request@server.ccl.net Fri Dec 10 09:23:16 1999 Received: from igor.wag.caltech.edu (igor.wag.caltech.edu [131.215.33.3]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id JAA16510 for ; Fri, 10 Dec 1999 09:23:15 -0500 Received: from wag.caltech.edu (charter-185-227.caltech.edu [131.215.185.227]) by igor.wag.caltech.edu (8.9.3/8.9.3) with ESMTP id FAA85182; Fri, 10 Dec 1999 05:13:45 -0800 (PST) Sender: rpm@wag.caltech.edu Message-ID: <3850FC87.D510C8B2@wag.caltech.edu> Date: Fri, 10 Dec 1999 05:13:43 -0800 From: "Richard P. Muller" X-Mailer: Mozilla 4.6 [en] (X11; I; Linux 2.2.6-15apmac ppc) X-Accept-Language: en MIME-Version: 1.0 To: David.DeVito@chiphy.unige.ch CC: CHEMISTRY@ccl.net Subject: Re: CCL:Problem with DFT References: <01JJBUI5ANO2000LHV@sc2a.unige.ch> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit David.DeVito@chiphy.unige.ch wrote: > > Hello ! > I'm performing optimisation on a hexaaquaion of rhodium (III) complex and > I would like to know which kind of functional are the best ones to make this > kind of calculations. > The next step should be optimisations with solvent environment and using > (if possible) relativistic effects. > > Thanks in advance for the preciously help !! Most people believe that a little bit of exact exchange makes calculations more reliable. Our group, which does a fair amount of transition metal clusters and organometallic systems, has found the B3LYP functional to work well in most cases. There has also been a great deal of recent excitement surrounding the PBE functional -- the rumors that I have heard claim that it has the accuracy of B3LYP without having to resort to exact exchange (which is a bit of a pain to program in an otherwise pure DFT code) -- and we'll probably start exploring PBE for transition metal species shortly. I'd be interested in hearing yours or other peoples experiences in this area. Rick Muller rpm@wag.caltech.edu http://www.wag.caltech.edu/home/rpm From chemistry-request@server.ccl.net Fri Dec 10 10:26:44 1999 Received: from theo1.theochem.tu-muenchen.de (theo2.theochem.tu-muenchen.de [129.187.191.1]) by server.ccl.net (8.8.7/8.8.7) with SMTP id KAA16875 for ; Fri, 10 Dec 1999 10:26:42 -0500 Received: from theo3.theochem.tu-muenchen.de (theo3.theochem.tu-muenchen.de [129.187.157.6]) by theo1.theochem.tu-muenchen.de (950413.SGI.8.6.12/950213.SGI.AUTOCF) via ESMTP id PAA04256 for ; Fri, 10 Dec 1999 15:17:14 +0100 Received: from theochem.tu-muenchen.de by theo3.theochem.tu-muenchen.de (SMI-8.6/SMI-SVR4) id PAA03441; Fri, 10 Dec 1999 15:18:07 +0100 Sender: matveev@theochem.tu-muenchen.de Message-ID: <38510B46.48E3EBA8@theochem.tu-muenchen.de> Date: Fri, 10 Dec 1999 15:16:38 +0100 From: Alexei Matveev Organization: TUM X-Mailer: Mozilla 4.51 [en] (X11; I; Linux 2.2.10 i586) X-Accept-Language: en, de, ru MIME-Version: 1.0 To: "CHEMISTRY@ccl.net" Subject: BLAS bugs? Content-Type: text/plain; charset=koi8-r Content-Transfer-Encoding: 7bit Hello world! Has anybody ever had problems with runnig optimized for Intel processors BLAS routines (dgemm). We get segmentation fault for some particular sizes of matrices and nothing helps. f90 = Absoft 6.2 compiler Platform = Pentimu III running Linux Any comments wanted! Alexei Matveev From chemistry-request@server.ccl.net Fri Dec 10 12:00:33 1999 Received: from [194.162.211.36] ([194.162.211.36]) by server.ccl.net (8.8.7/8.8.7) with SMTP id MAA17317 for ; Fri, 10 Dec 1999 12:00:32 -0500 From: Thomas.Fox@bc.boehringer-ingelheim.com Received: from gscinghub2.ing.de.bic by [194.162.211.36] via smtpd (for server.ccl.net [192.153.40.39]) with SMTP; 10 Dec 1999 15:50:48 UT Received: by gscinghub2.ing.de.bic with Internet Mail Service (5.5.2650.21) id ; Fri, 10 Dec 1999 16:51:04 +0100 Message-ID: <6183A835796ED211801A00005A4243B104F8BC@bc0exch7.bc.de.bic> To: CHEMISTRY@ccl.net Subject: G: PM3 ESP charges (Summary) Date: Fri, 10 Dec 1999 16:51:02 +0100 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2650.21) Content-Type: text/plain A while ago I posted a question concerning the calculation of ESP derived charges in G98; for the semiempirical AM1 and PM3 calculations, these ESP charges looked pretty weird. I have received a couple of responses which I (finally, finally) want to summarize. At the end, Ive added the original query. - George Ford from the SMU in Dallas was very helpful in first confirming my G98 results with G94 (i.e. getting the same rubbish numbers that I got), and then running the same input geometry in his MOPAC or Spartan copy (mopac93 v.2) and getting reasonable numbers back. - Richard Dixon (BASF) suspected that " most semi-empirical ESP charge routines first deorthogonalize the basis by fitting to some sort of gaussian approximation (STO-6G in mopac for example) The electrostatic potential is then calculated with respect to this basis. My first guess is that you are using the orthogonal PM3 basis for your charge calculation. If so, and if G98 does not have the "correct" algorithm available, you may want to check out some other program." - Don Boyd pointed me to a chapter by Francl and Chirlian in Vol. 14 of Reviews in Compuational Chemistry. The chapter supposedly (unfortunately I dont have this issue yet) gives an review of the problem and what can be done to try to fix it. Well, bottom line is that if you want ESP derived charges from a semiempricial wavefunction, Gaussian is not the method of choice. Thanks again to all who helped me with this problem. Th. --- ORIGINAL QUESTION-- I am investigating some small molecule inhibitors of thrombin (20-30 heavy atoms) and try to extract some atomic charges with different methods and at various levels of theory with G98 Rev A7. While the Mulliken charges at all levels, and the HF-ESP charges (POP=MK, or POP=CHELP) look pretty reasonable, I have problems with the ESP charges generated by a AM1 or PM3 calculation. For some atoms I get charges of the order of +-10 ! I do know that the fitting procedure simply tries to reproduce the electrostatic potential of the wavefunction as accurately as possible and does not take into account chemical intuition or my prejudices about how big partial charges should be, and I also know the discussion of the underdetermined buried atoms, but still, 'partial' charges of this magnitude seem a little excessive to me...especially as the same molecules treated at HF level give atomic charges that very well agree with what I would have expected. So...my questions are: 1) has anybody experienced a similar behavior (which would make me much more confident that I didnt goof at some point, or that there is a bug in the new semiempirical routine) or has it been described before? 2) if my results are correct, can one rationalize why the semiempirical ESP charges are so different from the HF ones? My first guess would be that a 6-31G generated ESP is 'smoother' than a minimal basis one from the semiempirical calculations, and therefore easier to fit with atom centered monopoles, but is this really the reason? -- Dr. Thomas Fox Dept. Chemical Reseach / Structural Research Boehringer Ingelheim Pharma KG 88397 Biberach/Germany Thomas.Fox@bc.boehringer-ingelheim.com From chemistry-request@server.ccl.net Fri Dec 10 15:44:17 1999 Received: from mail.ceniai.inf.cu (ceniai.net.cu [169.158.128.142]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id PAA18259 for ; Fri, 10 Dec 1999 15:44:11 -0500 Received: from int.ceniai.inf.cu (ceniai.inf.cu [169.158.128.138]) by mail.ceniai.inf.cu (8.9.3/8.9.3) with ESMTP id OAA27994 for ; Fri, 10 Dec 1999 14:32:22 GMT Received: (from uucp@localhost) by int.ceniai.inf.cu (8.9.3/8.9.3) with UUCP id OAA22736 for chemistry@ccl.net; Fri, 10 Dec 1999 14:35:34 -0500 (CST) Received: from ceinpet.inf.cu ([192.168.1.188]) by hermes.ceinpet.inf.cu (8.8.7/8.8.7) with ESMTP id MAA01157 for ; Fri, 10 Dec 1999 12:26:49 -0500 Sender: rgrau@hermes.ceinpet.inf.cu Message-ID: <385125AF.8C5BFDE@ceinpet.inf.cu> Date: Fri, 10 Dec 1999 11:09:19 -0500 From: Ricardo Grau Crespo Organization: CEINPET X-Mailer: Mozilla 4.51 [en] (X11; I; Linux 2.2.5-15 i686) X-Accept-Language: en MIME-Version: 1.0 To: "chemistry@ccl.net" Subject: column editor Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi CCL, Could you please tell if there is any editor for Linux that allows working (inserting, deleting, moving, etc) with data columns. And, if yes, where can I find it? Excuse me if this is not strictly a computational chemistry question, but I need to know that for working with input and output files of my calculations. Thank you very much in advance, Ricardo. -- ************************************************************** * Ricardo Grau Crespo * * Catalysis Department, Center for Petroleum Research. * * Washington # 169. Cerro, Havana, CUBA * ************************************************************** From chemistry-request@server.ccl.net Fri Dec 10 16:26:47 1999 Received: from nucleus.harvard.edu (nucleus.harvard.edu [140.247.90.196]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id QAA18599 for ; Fri, 10 Dec 1999 16:26:47 -0500 Received: from localhost (daizadeh@localhost) by nucleus.harvard.edu (8.9.3/8.9.3) with ESMTP id PAA08099; Fri, 10 Dec 1999 15:19:37 -0500 (EST) Date: Fri, 10 Dec 1999 15:19:36 -0500 (EST) From: Iraj Daizadeh To: Ricardo Grau Crespo cc: "chemistry@ccl.net" Subject: Re: CCL:column editor In-Reply-To: <385125AF.8C5BFDE@ceinpet.inf.cu> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Interesting query... For multiple alignments editors require in a most direct way your interests...please check the following--for example... http://www.ibcp.fr/mpsa First transform your data into the following form: > 150109492812 > 10328283823 > 39183923023043 or > agtctgtctttct > agcttttcttctc I am only guessing that it can perform the same column functions with numbers as well...--doubt it in retrospect....this is not excel.... please summarize--ricardo..... iraj. Iraj Daizadeh, Ph.D. Harvard University Department of Cellular and Molecular Biology The Biological Laboratories 16 Divinity Avenue Cambridge, MA 02138 Phone: (617) 495-0783 (617) 495-0560 Fax: (617) 496-4313 Email: daizadeh@nucleus.harvard.edu WebPage: http://mcb.harvard.edu/gilbert/daizadeh On Fri, 10 Dec 1999, Ricardo Grau Crespo wrote: > Hi CCL, > Could you please tell if there is any editor for Linux that allows > working (inserting, deleting, moving, etc) with data columns. And, if > yes, where can I find it? > Excuse me if this is not strictly a computational chemistry question, > but I need to know that for working with input and output files of my > calculations. > Thank you very much in advance, > Ricardo. > > -- > ************************************************************** > * Ricardo Grau Crespo * > * Catalysis Department, Center for Petroleum Research. * > * Washington # 169. Cerro, Havana, CUBA * > ************************************************************** > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > > From chemistry-request@server.ccl.net Fri Dec 10 18:48:34 1999 Received: from smurf.chem.usu.edu (smurf.chem.usu.edu [129.123.3.85]) by server.ccl.net (8.8.7/8.8.7) with SMTP id SAA19363 for ; Fri, 10 Dec 1999 18:48:34 -0500 Received: from localhost (pczyryca@localhost) by smurf.chem.usu.edu (950413.SGI.8.6.12/950213.SGI.AUTOCF) via ESMTP id PAA18556 for ; Fri, 10 Dec 1999 15:29:47 -0800 Date: Fri, 10 Dec 1999 15:29:47 -0800 From: "Przemyslaw G. Czyryca" To: chemistry@ccl.net Subject: Re: CCL:column editor In-Reply-To: <385125AF.8C5BFDE@ceinpet.inf.cu> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Fri, 10 Dec 1999, Ricardo Grau Crespo wrote: > Could you please tell if there is any editor for Linux that allows > working (inserting, deleting, moving, etc) with data columns. And, if > yes, where can I find it? In your linux distribution :-). Linux's vi is in fact a link to vim - an improved version of vi. In vim selecting of a column may be done with cursor arrows after ctrl-v combination. Then deleting with 'd' and so on (as always - man vi). Przemek G. Czyryca Utah State University