From lin@chu.Chem.nthu.edu.tw Fri Jul 10 00:34:08 1998 Received: from chu.Chem.nthu.edu.tw (Chu.Chem.nthu.edu.tw [140.114.45.233]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id AAA03769 Fri, 10 Jul 1998 00:33:56 -0400 (EDT) Received: by chu (AIX 3.2/UCB 5.64/4.03) id AA16553; Fri, 10 Jul 1998 12:10:17 +0800 From: lin@chu.Chem.nthu.edu.tw (Chiu-Ling Lin) Message-Id: <9807100410.AA16553@chu> Subject: 6-31G** Basis Set of I! To: CHEMISTRY@www.ccl.net Date: Fri, 10 Jul 1998 12:09:01 +0800 (TAIST) X-Mailer: ELM [version 2.4 PL25] Content-Type: text Hi, Does anyone have the 6-31G** basis set of atom I ? It will be better if it is for the G94 program. Any hits would be appreciated! ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Anne Lin Departament of Chemistry, NTHU, Hsin-Chu , Taiwan lin@chu.chem.nthu.edu.tw lin@chu1.chem.nthu.edu.tw ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ From Utz@apollo1.pharmazie.uni-erlangen.de Fri Jul 10 06:46:05 1998 Received: from max4.rrze.uni-erlangen.de (root@max4.rrze.uni-erlangen.de [131.188.71.16]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id GAA09759 Fri, 10 Jul 1998 06:45:58 -0400 (EDT) Received: from apollo1.pharmazie.uni-erlangen.de by max4.rrze.uni-erlangen.de; Fri, 10 Jul 1998 11:32:31 +0200 Received: from APOLLO1/SpoolDir by apollo1.pharmazie.uni-erlangen.de (Mercury 1.21); 10 Jul 98 11:30:23 +1 Received: from SpoolDir by APOLLO1 (Mercury 1.30); 10 Jul 98 11:30:17 +1 From: "Dr. Wolfgang Utz" Organization: LS fuer Pharmazie und LM-Chemie To: chemistry@www.ccl.net Date: Fri, 10 Jul 1998 11:30:16 MET MIME-Version: 1.0 Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7BIT Subject: Data for Titanium-compound Priority: normal Message-ID: Dear CCL'ers, does anybody have some optimized structures of the compound dichlorotitanocene (TiCl2Cyclopentadienyl2) or dimehtyltitanocene? Any format woud be accepted. Please sent files to my mail adress. Thank you in advance! Greetings from Erlangen, Germany Wolfgang *********************************************************************** Dr. Wolfgang Utz Institut fuer Pharmazie u. LM-Chemie Universitaet Erlangen-Nuernberg Schuhstr. 19 91052 Erlangen Tel. 09131/854100 Fax 09131/852585 E-mail:utz@pharmazie.uni-erlangen.de *********************************************************************** From jean.brion@univ-reims.fr Fri Jul 10 07:34:16 1998 Received: from cleo.univ-reims.fr (cleo.univ-reims.fr [193.50.208.4]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id HAA10717 Fri, 10 Jul 1998 07:34:15 -0400 (EDT) Received: from centre01.univ-reims.fr (centre01.univ-reims.fr [193.50.208.1]) by cleo.univ-reims.fr with SMTP (8.7.1/8.7.1) id NAA14504 for ; Fri, 10 Jul 1998 13:31:55 +0200 (METDST) Message-Id: <199807101131.NAA14504@cleo.univ-reims.fr> Received: by centre01.univ-reims.fr (1.38.193.4/16.2) id AA15299; Fri, 10 Jul 1998 12:25:55 +0100 From: BRION Jean Subject: summary: problem with g94 casscf77 under linux To: chemistry@www.ccl.net Date: Fri, 10 Jul 98 12:25:55 WETDST Mailer: Elm [revision: 70.85] Hello, I posted few days ago one question about a problem occuring with a g94 casscf(7,7) job under linux. ******************************************** * Hello, * *We have installed the Gaussian 94 package on a Linux machine *and we meet now one problem when trying a CASSCF(7,7) (generating *784 configurations)... *The problem is in link 510, *when the program begins "Generating Lanczos Guess". *At this moment, we establish that the running *does not create any output more... *(even with a long calculation time about 3000 minutes !). * *-We have a PII 400 machine, with 256Mo of memory and a 9Go hard disk. * *-Gaussian version is D.4 * *-Linux version is S.u.S.E 1998 5.2 Kernel 2.0.33 * *-the memory used for this calculation was 8MW * *-The previous CASSCF(5,5) has worked very well in 5 minutes for 75 *generated CONFIGURATIONS. * *-When adding the FULLDIAG keyword in *the CASSCF options list, the calculation *works ! (but takes a long time) * *- on a HP755 machine: * *The same CASSCF(5,5) calculations takes about 10 minutes * *The same CASSCF(7,7) works very well, and takes about 12 minutes * * *We have tried another thing to try to solve *our problem: i.e add the -malign-double in the *compilator options. * *=> Although other jobs (than the casscf(7,7) one) *run faster, our problem on the CASSCF(7,7) *remains the same (that means this job never stops *without output and without error). * ******************************************** I thank all the people who have answered. I thank particularly Darko Babic for giving us the solution. Under linux, the problem comes from the EPS variable (epsilon) which is evaluated in a "bad way" by the EPSETA subroutine in utilam.F in Gaussian 94 source (see the mail below). ******************************************** * *From: Darko Babic *Subject: Re: CCL:G:problem with g94 casscf77 under linux *In-Reply-To: <199807081545.RAA05980@cleo.univ-reims.fr> *Mime-Version: 1.0 *Content-Type: text/plain; charset="us-ascii" *Status: RO * * * * * * * Dear Prof. Henon, * * The problem you have with link 510 is related to the unusual result *of the variable EPS (epsilon) under Linux. This variable tells to Gaussian *what is the working precision in numerical computations. It is the minimum *positive floating number such that 1 + EPS = 1. EPS is computed in the sub- *routine EPSETA in utilam.F by successively halving EPS and adding the result *to ONE until EPS becomes so small that its addition to ONE does not affect *ONE. This value is used for numerical control of in Gaussian. * * It turns out that, under Linux, the value of EPS is calculated unrea- *listically SMALL and the requirements for convergence are therefore too to- *ugh. L510 gets into infinite loop at certain place (I don't remember now *where, but if you wish I'll find it). * * The value of EPS calculated in EPSETA is 1.084...E-19 under Linux. *On some other machines (Hewlett-Packard, SP2, ...) I got few orders of magni- *tude HIGHER value (by separately running the EPSETA subroutine from utilam.F). *There are built-in values of EPSILON and ETA in gcc-library (under Linux) *(DBL_EPSILON and DBL_MIN) as: 2.2204460492503131E-016 and 2.2250738585072014 *E-308, respectively, which are close to the values obtained on other machines. *So I concluded that the calculated value of EPS is unrealistically small and *I simply commented out the computation of EPS and ETA in SUBROUTINE EPSETA *(in utilam.F), inserted declaration of the above EPS and ETA values instead, *and recompiled Gaussian. * * In this way, the new values of EPS and ETA affect ALL the computation *of Gaussian. If you want be more selective, you can only replace calls to *EPSETA in l510.F (there are two, I think) by declarations of EPS and ETA as *above. * * Here is the modified SUBROUTINE EPSETA from utilam.F: SUBROUTINE EPSETA(EPS,ETA) Implicit Real*8(A-H,O-Z) C C COMPUTE AND RETURN ETA, THE SMALLEST REPRESENTABLE NUMBER, C AND EPS IS THE SMALLEST NUMBER FOR WHICH 1+EPS.NE.1. C Save ZERO, ONE, TWO DATA ZERO/0.0D0/, ONE/1.0D0/, TWO/2.0D0/ ETA=2.2250738585072014D-308 EPS=2.2204460492503131D-16 C ETA = ONE C 10 IF((ETA/TWO).EQ.ZERO) GOTO 20 C ETA = ETA / TWO C GOTO 10 C 20 EPS = ONE C 30 IF((ONE+(EPS/TWO)).EQ.ONE) GOTO 40 C EPS = EPS / TWO C GOTO 30 40 RETURN END Congratulations for the yesterday win! * Darko Babic *Institute "Rudjer Boskovic" *HR-10001 Zagreb, P.O.B. 1016 Croatia * * * ******************************************** Incidentally, I establish with pleasure that the result of the game "Croatie-France" in the world cup didn't affect the sympathy between chemical researchers ... ! ******************************************** *From: "Joseph W. Bausch" *Subject: Re: CCL:G:problem with g94 casscf77 under linux *Status: RO * *>Has someone already met this difficulty ? Is this *>a gaussian environement problem or a machine configuration problem ? * *I believe to get the most out of your compiling options, you should use the *following in your f2c.make file in place of the OPTFLAG = -02 line: * *OPTFLAG = -O3 -funroll-loops -fomit-frame-pointer -malign-double -m486 *-malign-loops=2 -malign-jumps=2 -malign-functions=2 * *Also, when running G94 jobs on a linux intel box, it appears you want to *give the job as little memory as it needs! I know this sounds strange, but *giving the job more memory than it needs results in a slowdown. I am sure *you'll get a response from M. Nicklaus that will explain this better than I *can. * Joe --------- * ******************************************** Sincerely. E. Henon From krys.radacki@ac.rwth-aachen.de Fri Jul 10 07:53:02 1998 Received: from mail.rwth-aachen.de (mail.RWTH-Aachen.DE [137.226.144.9]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id HAA11070 Fri, 10 Jul 1998 07:53:01 -0400 (EDT) Received: from ac.rwth-aachen.de (pae102.ac.RWTH-Aachen.DE) by mail.rwth-aachen.de (PMDF V5.1-10 #30440) with ESMTP id <01IZ8KLGAGSQ0009BX@mail.rwth-aachen.de> for CHEMISTRY@www.ccl.net; Fri, 10 Jul 1998 13:52:18 +0200 Date: Fri, 10 Jul 1998 11:50:55 +0000 From: Krzysztof Radacki Subject: basis functions in LaTeX Sender: root@mail.rwth-aachen.de To: CCL Message-id: <35A6001E.EC161BA9@ac.rwth-aachen.de> Organization: Inst.Inorg.Chem., RWTH Aachen, Germany MIME-version: 1.0 X-Mailer: Mozilla 4.05 [en] (X11; I; Linux 2.1.99 i586) Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7bit Dear CCL'ers, it's not quite computational chemistry question, but it's chemistry on computer with LaTeX (it makes also quite complicated calculatuions ;). I'm trying to formate table with some basis fuctions in first column. When I type: {\centering \begin{tabular}{|c|c|c|c|c|c|c|} \hline &$^1$H&$^{11}$B&$^{13}$C&$^{19}$F&$^{29}$Si &$^{31}$P\\ \hline \hline RHF/6$-$31G(d)&32.9017&106.750&201.7315&&450.1988&\\ \hline RHF/6$-$31G(d,p)&&&&&&\\ \hline RHF/6$-$31+G(d)&32.8172&106.3119&201.8511&&446.7210&\\ \hline B3LYP/6$-$311+G(d,p)&31.8976&84.0763&180.4099&&339.0217& \\ \hline \end{tabular}\par} I become something like (if one looks on first column and '/'): |----------------------------------------------... | | ... |----------------------------------------------... | RHF/6-31G(d) | ... |----------------------------------------------... | RHF/6-31G(d,p) | ... |----------------------------------------------... | RHF/6-31+G(d) | ... |----------------------------------------------... | B3LYP/6-311+G(d,p) | ... |----------------------------------------------... What should I write to obtain output with '/' in the same position in cell? regards Krzysztof Radacki _________________________---------------------------------------------------- ------------------------- e-mail: Krys.Radacki@ac.RWTH-Aachen.DE --- ----------------------------------------------------------------------------- From support@mathtrek.com Fri Jul 10 10:12:03 1998 Received: from granite.sentex.net (granite.sentex.ca [199.212.134.1]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id KAA13884 Fri, 10 Jul 1998 10:12:02 -0400 (EDT) Received: from pppuser.uoguelph.ca (p19a.radium.sentex.ca [207.245.212.84]) by granite.sentex.net (8.8.6/8.6.9) with SMTP id KAA05569 for ; Fri, 10 Jul 1998 10:11:20 -0400 (EDT) Message-Id: <3.0.5.32.19980710100347.009a4790@mathtrek.com> X-Sender: mathtrek@mathtrek.com X-Mailer: QUALCOMM Windows Eudora Pro Version 3.0.5 (32) Date: Fri, 10 Jul 1998 10:03:47 -0400 To: CHEMISTRY@www.ccl.net From: "W. R. Smith" Subject: Re: CCL:basis functions in LaTeX Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" At 11:50 AM 7/10/1998 +0000, you wrote: >Dear CCL'ers, >it's not quite computational chemistry question, but it's chemistry on >computer with LaTeX (it makes also quite complicated calculatuions ;). > >I'm trying to formate table with some basis fuctions in first column. >When I type: > >{\centering \begin{tabular}{|c|c|c|c|c|c|c|} >\hline >&$^1$H&$^{11}$B&$^{13}$C&$^{19}$F&$^{29}$Si &$^{31}$P\\ >\hline >\hline >RHF/6$-$31G(d)&32.9017&106.750&201.7315&&450.1988&\\ >\hline >RHF/6$-$31G(d,p)&&&&&&\\ >\hline >RHF/6$-$31+G(d)&32.8172&106.3119&201.8511&&446.7210&\\ >\hline >B3LYP/6$-$311+G(d,p)&31.8976&84.0763&180.4099&&339.0217& >\\ >\hline >\end{tabular}\par} > > >I become something like (if one looks on first column and '/'): > >|----------------------------------------------... >| | ... >|----------------------------------------------... >| RHF/6-31G(d) | ... >|----------------------------------------------... >| RHF/6-31G(d,p) | ... >|----------------------------------------------... >| RHF/6-31+G(d) | ... >|----------------------------------------------... >| B3LYP/6-311+G(d,p) | ... >|----------------------------------------------... > >What should I write to obtain output with '/' in the same position in >cell? Add an additional column to contain the '/', right-justify the column immediately before and left-justify the column immediately after? i.e. \begin{tabular}{|rcl|c|c|c|c|c|c|} and RHF & / & 6$-$31G(d) & 32.9017 & 106.750 & 201.7315 && 450.1988&\\ (but I haven't actually tested this) -- W. R. Smith, PhD, P. Eng., Senior Scientist, Mathtrek Systems -- 3-304 Stone Road West, Suite 165, Guelph, Ontario CANADA N1G 4W4 EMail: support@mathtrek.com Tel:519-763-1356,FAX:519-763-4525 --------------------- http://www.mathtrek.com --------------------- -Mathtrek Systems - Home of EQS4WIN Chemical Equilibrium Software - From workshop@sg1686.pharmazie.uni-marburg.de Fri Jul 10 13:27:56 1998 Received: from sg1686.pharmazie.uni-marburg.de (sg1686.Pharmazie.Uni-Marburg.DE [137.248.161.86]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id NAA17719 Fri, 10 Jul 1998 13:27:54 -0400 (EDT) Received: from sg1686.pharmazie.uni-marburg.de (sg1686.Pharmazie.Uni-Marburg.DE [137.248.161.86]) by sg1686.pharmazie.uni-marburg.de (950413.SGI.8.6.12/950213.SGI.AUTOCF) via ESMTP id TAA26119 for ; Fri, 10 Jul 1998 19:27:57 +0200 Sender: workshop@sg1686.pharmazie.uni-marburg.de Message-ID: <35A64F1C.86959859@sg1686.pharmazie.uni-marburg.de> Date: Fri, 10 Jul 1998 19:27:57 +0200 From: "Workshop: Virtual Screening" Organization: Dep. of Pharm. Chem., Univ. Marburg X-Mailer: Mozilla 4.04 [en] (X11; I; IRIX 6.3 IP32) MIME-Version: 1.0 To: chemistry@www.ccl.net Subject: Workshop: Virtual Screening Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear Colleagues, we want to announce a Workshop on Virtual Screening, Schloss Rauischholzhausen, March 15-18, 1999, Germany Virtual Screening has emerged as a prospective alternative to high-throughput screening. This computer method is by no means yet mature, however it is important to seriously develop and expand its scope and to learn about its limitations. Different techniques are involved. First of all, the handling and screening of large databases that involves clustering and similarity searching. Once a reduced selection has been obtained either docking or molecular superposition methods come into play. Alternatively, libraries based on combinatorial principles >from combinatorial chemistry or NMR evidence can be screened for complementarity with a given binding site or similarity with a set of given lead structures. Computational speed and reliable scoring functions either for docking or molecular superposition are essential in virtual screening. We think time is ripe to hold a workshop on this topic. The idea is to get leading experts (about 70) together at a pleasant place in a very informal atmosphere. We have reserved a castle near Marburg, about 80km from Frankfurt/M.at March 15th to 18th, 1999. If you want to know more about this meeting and you are interested to sign up please consider the web page http://pc1664.pharmazie.uni-marburg.de/workshop99/ for further information. Best regards, Hans-Joachim Boehm, Thomas Lengauer and Gerhard Klebe From robert@pauli.utmb.edu Fri Jul 10 17:27:53 1998 Received: from nmr.utmb.edu (dggin1.utmb.edu [129.109.73.3]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id RAA23473 Fri, 10 Jul 1998 17:27:51 -0400 (EDT) Received: from pauli.utmb.edu (pauli.utmb.edu [129.109.73.25]) by nmr.utmb.edu (950413.SGI.8.6.12/950213.SGI.AUTOCF) via ESMTP id QAA01199 for <@nmr.utmb.edu:CHEMISTRY@www.ccl.net>; Fri, 10 Jul 1998 16:50:06 -0500 Received: (from robert@localhost) by pauli.utmb.edu (980616/Sun/9.16./980616/Sun_Microsystems) id QAA08509; Fri, 10 Jul 1998 16:28:50 -0500 (CDT) From: "Robert Fraczkiewicz" Message-Id: <9807101628.ZM8507@pauli.utmb.edu> Date: Fri, 10 Jul 1998 16:28:50 -0500 X-Mailer: Z-Mail (3.2.3 08feb96 MediaMail) To: CHEMISTRY@www.ccl.net Subject: New Web Service: Solvent Accessible Surface Area Calculations Cc: werner@newton.utmb.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Dear Colleagues, We would like to announce the release of beta version of GETAREA 1.0, the new free WWW service for calculating the solvent accessible surface area of molecules. Users wanting to calculate SASA of proteins will merely supply the name of their local file containing atomic coordinates in PDB format. There is an otpion to calculate solvation energy and inclusion of molecules other than proteins. The relevant URL is: http://www.scsb.utmb.edu/getarea/area_form.html Note: the current release is for testing purposes only. Surely there are still some undiscovered bugs. Please help us disclose them by submitting test inputs. All remarks and suggestions should be directed to robert@nmr.utmb.edu or werner@newton.utmb.edu Thank you in advance, Robert Fraczkiewicz Sealy Center for Structural Biology University of Texas Medical Branch Galveston, TX 77555 From muggei@sanger.pprd.abbott.com Fri Jul 10 18:15:08 1998 Received: from kevlar.pprd.abbott.com (kevlar.pprd.abbott.com [192.103.72.5]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id SAA24339 Fri, 10 Jul 1998 18:15:07 -0400 (EDT) Received: from staple.pprd.abbott.com (mx1.pprd.abbott.com [10.250.91.76]) by kevlar.pprd.abbott.com (8.9.0/8.9.0) with ESMTP id RAA14695 for ; Fri, 10 Jul 1998 17:15:19 -0500 (CDT) Received: from sanger.pprd.abbott.com (sanger.pprd.abbott.com [10.250.254.223]) by staple.pprd.abbott.com (8.9.0/8.9.0) with ESMTP id RAA24449 for ; Fri, 10 Jul 1998 17:15:09 -0500 (CDT) Received: (from muggei@localhost) by sanger.pprd.abbott.com (8.8.5/8.8.3) id RAA08872 for chemistry@www.ccl.net; Fri, 10 Jul 1998 17:15:05 -0500 (CDT) From: Ingo Mugge Message-Id: <199807102215.RAA08872@sanger.pprd.abbott.com> Subject: assigning atom types To: chemistry@www.ccl.net Date: Fri, 10 Jul 1998 17:15:05 -0500 (CDT) X-Mailer: ELM [version 2.4 PL21] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Dear CCL'ers, I am looking for software that is able to automatically and reliably determine the number of hydrogen atoms attached to heavy atoms given in a reasonable conformation in a PDB file or any other format and assign atom types of some sophistication. Considering the pH and pKa dependence of protonation states I am asking only for potentially present hydrogens like in an imidazole ring where one, the other, or both nitrogens might be protonated in proteins, meaning that both imidazole nitrogens could be assigned the same atom type. On the other hand, however, if you have for instance pyrrol rings in a porphyrin the program should be able to distinguish between those nitrogens that have hydrogens attached and those that don't and assign different atom types to them. So, I guess I am more interested in a program that recognizes the right atom types of the heavy atoms (especially in heterocycles) leaving it open if they are really protonated or not. I realize that this question was asked before in CCL at least once about 4 years ago but I did not find a good answer (Sorry if I did not search the archives thoroughly enough). I know some programs that almost do it correctly but still ask for manual intervention at some point. Thank you very much for your help. Ingo Mugge ingo.mugge@abbott.com