From chemistry-request@server.ccl.net Thu Jul 1 04:01:10 1999 Received: from gwdu12.gwdg.de (gwdu42.gwdg.de [134.76.10.26]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id EAA31304 for ; Thu, 1 Jul 1999 04:01:09 -0400 Received: from taurus.uni-oc.gwdg.de ([134.76.66.164] helo=gwdg.de) by gwdu12.gwdg.de with esmtp (Exim 2.12 #1) id 10zbiY-0006zR-00 for chemistry@ccl.net; Thu, 1 Jul 1999 09:57:10 +0200 Sender: crinders@gwdg.de Message-ID: <377B3B5E.56C049B1@gwdg.de> Date: Thu, 01 Jul 1999 09:56:46 +0000 From: Christopher Rinderspacher Organization: Institut der Org. Chemie der =?iso-8859-1?Q?Universit=E4t=20G=F6ttingen?= X-Mailer: Mozilla 4.6 [en] (X11; I; SunOS 5.6 sun4u) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: Imaginary Components of wavefunctions Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi, I would like to get the imaginary component of a solution to the Schroedinger equation. I am working with Gaussian(98) and can't find any references anywhere. I would appreciate any help on how to obtain them (G98 or any other program). Thanks, Christopher -- Christopher Rinderspacher Institut fuer Organische Chemie Georg-August-Universitaet Goettingen Tammannstr. 2 37077 Goettingen crinder1@gwdg.de From chemistry-request@server.ccl.net Thu Jul 1 06:09:18 1999 Received: from mserv.rug.ac.be (mserv.rug.ac.be [157.193.40.37]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id GAA32654 for ; Thu, 1 Jul 1999 06:09:18 -0400 Received: from elptrs3.rug.ac.be (elptrs3.rug.ac.be [157.193.113.1]) by mserv.rug.ac.be (8.9.0/8.9.0) with SMTP id MAA16353 for ; Thu, 1 Jul 1999 12:05:30 +0200 (MET DST) Received: from lptpc66.rug.ac.be by elptrs3.rug.ac.be (AIX 4.1/UCB 5.64/4.03) id AA15094; Thu, 1 Jul 1999 12:08:32 +0100 Received: by localhost with Microsoft MAPI; Thu, 1 Jul 1999 12:08:20 +0200 Message-Id: <01BEC3BA.693AFF00.mark.saeys@rug.ac.be> From: Mark Saeys To: "'chemistry@ccl.net'" Subject: Hindered-rotor option and transition states in g98 Date: Thu, 1 Jul 1999 12:08:19 +0200 Organization: Universiteit Gent X-Mailer: Microsoft Internet-e-mail/MAPI - 8.0.0.4211 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit Dear all, When I tried using the Freq=HinderedRot keyword in Gaussian 98 for a transition state geometry, which I read from a checkpoint-file, g98 stopped and gave the following error: Low frequencies --- -374.5162 -20.3673 -12.8460 -0.0009 -0.0008 -0.0002 Low frequencies --- 4.0589 91.5939 216.9199 ****** 1 imaginary frequencies (negative Signs) ****** Hindered Internal Rotation Analysis Internal coordinate list checked Check for planar centers 1 2 4 5 359.873 Check reduced barrier height. Cut-off : V/RT = 33.7559 Check for ring deformation Number of internal rotation degrees of freedom = 1 NNew= 20 NTest= 1 NB= 5 IFrz= 0 IBar= 0 ICyc= 0 Problem with the number of degrees of freedom Error termination via Lnk1e in /usr/people/soft/g98/l716.exe. When I do a Freq calculation without HinderedRot the calculation terminates normally. Is it not possible to use Freq=HinderedRot for a transition state? Thanks, Mark Saeys Universiteit Gent From chemistry-request@server.ccl.net Thu Jul 1 10:53:38 1999 Received: from mail.chemie.fu-berlin.de (root@mail.chemie.fu-berlin.de [160.45.24.23]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id KAA03927 for ; Thu, 1 Jul 1999 10:53:35 -0400 Received: from ki1.chemie.fu-berlin.de([160.45.24.21]) (2028 bytes) by mail.chemie.fu-berlin.de via sendmail with P:smtp/R:bind_hosts/T:inet_zone_bind_smtp (sender: ) id for ; Thu, 1 Jul 1999 16:49:44 +0200 (CEST) (Smail-3.2.0.101 1997-Dec-17 #18 built 1999-Feb-17) Received: by ki1.chemie.fu-berlin.de (Smail3.2.0.98) from chemie.fu-berlin.de (160.45.24.178) with esmtp id ; Thu, 1 Jul 1999 16:49:39 +0200 (MEST) Sender: rabe@ccl.net Message-ID: <377B8002.4E4BEF39@chemie.fu-berlin.de> Date: Thu, 01 Jul 1999 16:49:38 +0200 From: Bjoern Rabenstein Organization: Freie Universitaet Berlin, Germany X-Mailer: Mozilla 4.51 [en] (X11; U; Linux 2.2.9 i686) X-Accept-Language: de MIME-Version: 1.0 To: Computational Chemistry Mailing List Subject: Compiling Rasmol for Linux Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi! Has anybody managed to compile rasmol on Linux 2.2.x with egcs? We have just tried to compile Rasmol26b2 (and also Rasmol26b1) and got the following error message: rasmol.c:46: sys/termio.h: No such file or directory We simply tried to link /usr/include/sys/termio.h to /usr/include/termio.h. Then we got the following error messages: rasmol.c: In function `OpenConnection': rasmol.c:329: invalid use of undefined type `struct fd_set' rasmol.c: In function `CloseConnection': rasmol.c:345: invalid use of undefined type `struct fd_set' rasmol.c: In function `InitTerminal': rasmol.c:392: invalid use of undefined type `struct fd_set' rasmol.c:392: invalid use of undefined type `struct fd_set' rasmol.c:393: invalid use of undefined type `struct fd_set' rasmol.c:399: invalid use of undefined type `struct fd_set' rasmol.c:409: invalid use of undefined type `struct fd_set' [...] What's the trick here? Thanks for any help! -- __ \__\__ \ Bjoern Rabenstein * PhD student * Freie Universitaet Berlin __\___\__\_\ Inst. f. Kristallographie * Takustrasse 6 * D-14195 Berlin \ \ \ \\ [email] rabe@chemie.fu-berlin.de [phone] +49-30-838-3484 [WWW] http://userpage.chemie.fu-berlin.de/~rabe/ [fax] +49-30-838-3464 From chemistry-request@server.ccl.net Thu Jul 1 11:08:18 1999 Received: from phare.univ-lille2.fr (root@phare.univ-lille2.fr [193.51.138.40]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA04102 for ; Thu, 1 Jul 1999 11:08:17 -0400 Received: from icpl6 (icpl6.univ-lille2.fr [193.51.138.127]) by phare.univ-lille2.fr (8.8.7/8.8.7) with SMTP id QAA14800 for ; Thu, 1 Jul 1999 16:01:35 +0200 Message-ID: <002301bec3d2$99d25740$7f8a33c1@icpl6.univ-lille2.fr> Reply-To: "Philippe CHAVATTE" From: "Philippe CHAVATTE" To: "CCL" Subject: Proteins comparison Date: Thu, 1 Jul 1999 17:01:29 +0200 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 4.72.2106.4 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.2106.4 Dear CCLers, What is the best methodology to compare two protein 3D structures (pdb format) ? What criteria permit to affirm their similarity ? Many thanks for your help. Philippe ----------------- Philippe CHAVATTE Institut de Chimie Pharmaceutique Albert Lespagnol BP 83 59006 LILLE CEDEX FRANCE E-Mail : pchavatt@phare.univ-lille2.fr From chemistry-request@server.ccl.net Thu Jul 1 12:27:45 1999 Received: from illinois.ncifcrf.gov (illinois.NCIFCRF.GOV [129.43.6.38]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id MAA04738 for ; Thu, 1 Jul 1999 12:27:45 -0400 Received: from localhost (huzj@localhost) by illinois.ncifcrf.gov (980427.SGI.8.8.8/970903.SGI.AUTOCF) via SMTP id MAA83987; Thu, 1 Jul 1999 12:23:43 -0400 (EDT) Date: Thu, 1 Jul 1999 12:23:43 -0400 (EDT) From: Zeng-Jian Hu To: Philippe CHAVATTE cc: CCL Subject: Re: CCL:Proteins comparison In-Reply-To: <002301bec3d2$99d25740$7f8a33c1@icpl6.univ-lille2.fr> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, Philippe, Just see: http://protein3d.ncifcrf.gov/tsai/ Hope it helpful to you. ----------------------------------------------------- Zengjian Hu Laboratory of Experimental and Computational Biology NCI-FCRDC, Building 469, Room 151 Frederick, MD 21702-1201, USA Ph# 301-846-5580 Fax# 301-846-5598 E-mail: huzj@illinois.ncifcrf.GOV ----------------------------------------------------- On Thu, 1 Jul 1999, Philippe CHAVATTE wrote: > Dear CCLers, > > What is the best methodology to compare two protein 3D structures (pdb > format) ? > What criteria permit to affirm their similarity ? > Many thanks for your help. > > Philippe > ----------------- > > Philippe CHAVATTE > Institut de Chimie Pharmaceutique Albert Lespagnol > BP 83 > 59006 LILLE CEDEX > FRANCE > > E-Mail : pchavatt@phare.univ-lille2.fr > > > > > -= 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 Thu Jul 1 13:42:33 1999 Received: from lucia.u.arizona.edu (mcafiero@lucia.U.Arizona.EDU [128.196.137.26]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id NAA05731 for ; Thu, 1 Jul 1999 13:42:31 -0400 Received: from localhost (mcafiero@localhost) by lucia.u.arizona.edu (8.8.8/8.8.8) with ESMTP id KAA48148; Thu, 1 Jul 1999 10:38:30 -0700 Date: Thu, 1 Jul 1999 10:38:30 -0700 (MST) From: Mauricio L Cafiero To: Christopher Rinderspacher cc: chemistry@ccl.net Subject: Re: CCL:Imaginary Components of wavefunctions In-Reply-To: <377B3B5E.56C049B1@gwdg.de> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello: Exactly what do you mean by the imaginary component? The wavefunctions given by Gaussian (approximate solutions of the Shrodinger equation) are defined in terms of real functions (that is, real basis sets). The angular dependence is given by powers of x, y and z in front of the cartesian gaussian basis functions. ======================================================================== Mauricio Cafiero University of Arizona Department of Chemistry On Thu, 1 Jul 1999, Christopher Rinderspacher wrote: > > Hi, > > I would like to get the imaginary component of a solution to the > Schroedinger equation. I am working with Gaussian(98) and can't find > any > references anywhere. I would appreciate any help on how to obtain them > (G98 or any other program). Thanks, > > Christopher > > -- > Christopher Rinderspacher > Institut fuer Organische Chemie > Georg-August-Universitaet Goettingen > Tammannstr. 2 > 37077 Goettingen > crinder1@gwdg.de > > -= 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 Thu Jul 1 14:27:03 1999 Received: from mailbox.syr.edu (root@mailbox.syr.edu [128.230.18.5]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id OAA06122 for ; Thu, 1 Jul 1999 14:27:03 -0400 Received: from syr.edu (curie.syr.edu [128.230.187.116]) by mailbox.syr.edu (8.9.2/8.9.2) with ESMTP id OAA24374 for ; Thu, 1 Jul 1999 14:23:11 -0400 (EDT) Sender: desingh@mailbox.syr.edu Message-ID: <377BB340.9633597A@syr.edu> Date: Thu, 01 Jul 1999 14:28:17 -0400 From: Deepak Singh Organization: Dept. of Chem & Biochem, Syracuse University X-Mailer: Mozilla 4.07C-SGI [en] (X11; I; IRIX64 6.5 IP30) MIME-Version: 1.0 To: Computational Chemistry List Subject: Heat of formation and stationary points Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hello again, I have been running MOPAC calculations on systems with 2 or more molecules (not bonded to each other). I have noticed something interesting. When I do not constrain anything, the SCF calculation goes along fine. However when I constrain 2 or more atoms, I almost always have my Heats of Formation eventually becoming self consistent, but not my gradiets and the arc file reports that although the SCF has been achieved, the geometry is not at a stationary point. What does this mean, especially in a physical sense? Regards Deepak. -- ********************************************************************** Deepak Singh Tel : (315)443 1739 (w) Graduate Student (315)472 9659 (h) Dept. of Chemistry Fax : (315)443 4070 Syracuse University email : desingh@syr.edu 1-014 CST, Syracuse URL : http://web.syr.edu/~desingh NY 13244 "Violence is the last refuge of the incompetent." --- Salvor Hardin ********************************************************************** From chemistry-request@server.ccl.net Thu Jul 1 14:44:50 1999 Received: from lucia.u.arizona.edu (mcafiero@lucia.U.Arizona.EDU [128.196.137.26]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id OAA06289 for ; Thu, 1 Jul 1999 14:44:50 -0400 Received: from localhost (mcafiero@localhost) by lucia.u.arizona.edu (8.8.8/8.8.8) with ESMTP id LAA37124; Thu, 1 Jul 1999 11:40:57 -0700 Date: Thu, 1 Jul 1999 11:40:56 -0700 (MST) From: Mauricio L Cafiero To: Deepak Singh cc: Computational Chemistry List Subject: Re: CCL:Heat of formation and stationary points In-Reply-To: <377BB340.9633597A@syr.edu> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello: A geometry optimization finds a minimum based on the gradients with respect to atomic coordinates. When you constrain any atoms, the optimization cannnot find a true minimum, and hence your total gradient will not become very small. So your gradients do not converge because you do not reach the minimum and you do not reach the minimum because you have constrained atoms. The SCF will work at any geometry, so you can find an energy at that non-optimum geometry. ======================================================================== Mauricio Cafiero University of Arizona Department of Chemistry On Thu, 1 Jul 1999, Deepak Singh wrote: > Hello again, > > I have been running MOPAC calculations on systems with 2 or more > molecules (not bonded to each other). I have noticed something > interesting. When I do not constrain anything, the SCF calculation goes > along fine. However when I constrain 2 or more atoms, I almost always > have my Heats of Formation eventually becoming self consistent, but not > my gradiets and the arc file reports that although the SCF has been > achieved, the geometry is not at a stationary point. What does this > mean, especially in a physical sense? > > Regards > > Deepak. > > > > -- > ********************************************************************** > Deepak Singh Tel : (315)443 1739 (w) > Graduate Student (315)472 9659 (h) > Dept. of Chemistry Fax : (315)443 4070 > Syracuse University email : desingh@syr.edu > 1-014 CST, Syracuse URL : http://web.syr.edu/~desingh > NY 13244 > > "Violence is the last refuge of the incompetent." --- Salvor Hardin > ********************************************************************** > > > > > -= 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 Thu Jul 1 18:38:32 1999 Received: from scriptgen.com (smtp.scriptgen.com [216.47.36.98]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id SAA08280 for ; Thu, 1 Jul 1999 18:38:31 -0400 Received: from scriptgen.com ([192.168.12.6]) by gateway.scriptgen.com with ESMTP id <115202>; Thu, 1 Jul 1999 18:36:04 -0400 Received: from diversity (192.168.12.152) by scriptgen.com with SMTP (Eudora Internet Mail Server 2.2.2); Thu, 1 Jul 1999 18:37:08 -0400 Message-Id: <3.0.6.32.19990701183712.009b6d10@pop.scriptgen.com> X-Sender: aarvanites@pop.scriptgen.com X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.6 (32) Date: Thu, 1 Jul 1999 18:37:12 -0400 To: CHEMISTRY@ccl.net From: Anthony Arvanites Subject: CCL: Natural Product Databases Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Hello CCL: I am very interested in finding out if there are any databases of natural products in an electronic format (SD file, etc.) that I could examine. I realize that some dictionaries of natural products do not exist as an SD file. I would like to perform advanced searches on a natural product database using for example MDL technology. Any information regarding this issue is greatly appreciated. I will summarize the answers received. Thank you Anthony Arvanites Anthony Arvanites Compound Distribution Manager Assistant Scientist SCRIPTGEN Pharmaceuticals, Inc. 610 Lincon St. Waltham, MA 02451 (781) 522-5082 fax: (781) 768-0040 e-mail: aarvanites@scriptgen.com