From chemistry-request@server.ccl.net Wed Jan 26 05:46:26 2000 Received: from gwdu42.gwdg.de (root@gwdu42.gwdg.de [134.76.10.26]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id FAA21513 for ; Wed, 26 Jan 2000 05:46:26 -0500 Received: from gwdu20.gwdg.de ([134.76.98.2] ident=awittko) by gwdu42.gwdg.de with smtp (Exim 3.12 #1) id 12DOvw-0007Wm-00 for CHEMISTRY@ccl.net; Wed, 26 Jan 2000 10:40:16 +0100 Received: from localhost by gwdu20.gwdg.de (5.65v4.0/1.1.10.5/11Feb98-0154PM) id AA16755; Wed, 26 Jan 2000 10:40:14 +0100 Date: Wed, 26 Jan 2000 10:40:14 +0100 (MET) From: Alexander Wittkopp To: "'CHEMISTRY@ccl.net'" Subject: B96 functional in G98 Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear all, we tried to utilize the B96 DFT functional offered by Gaussian98, but found for all combinations with the implemented correlation functionals (even for the hybrid B1B96, mentioned in the manual) the following error message: ********************************************* Gaussian 98: x86-Linux-G98RevA.5 21-Sep-1998 26-Jan-2000 ********************************************* %chk=XXXXX ---------------------------------------------------- # B1B96/6-31G* Opt Freq=NoRaman Pop=None ---------------------------------------------------- QPERR --- A SYNTAX ERROR WAS DETECTED IN THE INPUT LINE. # B1B96/6-31G* OPT FREQ=NORAMAN POP=NONE ' Did anyone use that functional in Gaussian98? We would be grateful for any advice! Ciao, Alexander ******************************************************************************* ("`-/")_.-'"``-._ Alexander Wittkopp (. . `) -._ )-;-,_() Institut fuer Organische Chemie (v_,)' _ )`-.\ ``- Georg-August Universitaet _;- _,-_/ / ((,' Tammannstrasse 2 ((,.-' ((,/ 37077 Goettingen Email: awittko@gwdg.de URL: http://www.gwdg.de/~awittko Germany Phone: +49-(0)551-393290 Fax: +49-(0)551-399475 "eine ungerade Zahl, am besten prim hat immer guenstige Auswirkungen auf cache-trashing." T. Nau ******************************************************************************* From chemistry-request@server.ccl.net Wed Jan 26 06:51:02 2000 Received: from matavnet.hu (matavnet.hu [145.236.224.246]) by server.ccl.net (8.8.7/8.8.7) with SMTP id GAA22592 for ; Wed, 26 Jan 2000 06:51:00 -0500 Received: (qmail 3793 invoked from network); 26 Jan 2000 11:44:46 +0100 Received: from line-213-52.dial.matav.net (HELO chemaxon.com) (145.236.213.52) by matavnet.hu with SMTP; 26 Jan 2000 11:44:46 +0100 Message-ID: <388ECD42.32076C5F@chemaxon.com> Date: Wed, 26 Jan 2000 11:32:34 +0100 From: Ferenc Csizmadia Organization: ChemAxon X-Mailer: Mozilla 4.61 [en] (WinNT; I) X-Accept-Language: en MIME-Version: 1.0 To: CHEMISTRY@ccl.net, CHMINF-L@LISTSERV.INDIANA.EDU, MOL-DIVERSITY@LISTSERV.ARIZONA.EDU, chemweb@ic.ac.uk Subject: Marvin 2.2 released Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Please excuse multiple postings. Version 2.2 of the Marvin for drawing and displaying chemical structures has been released and can be downloaded at http://www.chemaxon.com/marvin. Marvin contains: - Marvin Applets. Entering and viewing structures in web browsers. - NEW: Marvin Beans. Java beans for chemical software development. Now MarvinSketch and MarvinView can be inserted into forms visually. - NEW: MarvinSketch application. Structure drawing program created using the MarvinSketch bean. NEW FEATURES, CHANGES: - Keyboard shortcuts: all elements, 8 bond types, templates, erase mode, undo, redo, etc. - Pop-up menus at right-clicks - Recent structures: speeding up the creation of similar molecules. - New query bond and atom types - Fixes - etc. ALSO AVAILABLE JChem is our new Java based system for searching and handling chemical structures in relational databases (http://www.jchem.com). Regards, Ferenc -- Dr. Ferenc Csizmadia Managing Director ChemAxon Ltd. Valyog u. 7, H-1032 Budapest, Hungary http://www.chemaxon.com T: +3620 9570988 mailto:fcsiz@chemaxon.com From chemistry-request@server.ccl.net Wed Jan 26 06:51:05 2000 Received: from matavnet.hu (matavnet.hu [145.236.224.246]) by server.ccl.net (8.8.7/8.8.7) with SMTP id GAA22598 for ; Wed, 26 Jan 2000 06:51:03 -0500 Received: (qmail 3920 invoked from network); 26 Jan 2000 11:44:50 +0100 Received: from line-213-52.dial.matav.net (HELO chemaxon.com) (145.236.213.52) by matavnet.hu with SMTP; 26 Jan 2000 11:44:50 +0100 Message-ID: <388ED023.4F42862E@chemaxon.com> Date: Wed, 26 Jan 2000 11:44:51 +0100 From: Ferenc Csizmadia Organization: ChemAxon X-Mailer: Mozilla 4.61 [en] (WinNT; I) X-Accept-Language: en MIME-Version: 1.0 To: CHEMISTRY@ccl.net, CHMINF-L@LISTSERV.INDIANA.EDU, MOL-DIVERSITY@LISTSERV.ARIZONA.EDU, chemweb@ic.ac.uk Subject: Marvin 2.2 released Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Please excuse multiple postings. Version 2.2 of the Marvin Applets and Beans for drawing and displaying chemical structures has been released and can be downloaded at http://www.chemaxon.com/marvin. Free for free internet sites and scientific/technical publications in HTML format. Marvin contains: - Marvin Applets. Entering and viewing structures in web browsers. - NEW: Marvin Beans. Java beans for chemical software development. Now MarvinSketch and MarvinView can be inserted into forms visually. - NEW: MarvinSketch application. Structure drawing program created using the MarvinSketch bean. NEW FEATURES, CHANGES: - Keyboard shortcuts: all elements, 8 bond types, templates, erase mode, undo, redo, etc. - Pop-up menus at right-clicks - Recent structures: speeding up the creation of similar molecules. - New query bond and atom types - Fixes - etc. ALSO AVAILABLE JChem is our new Java based system for searching and handling chemical structures in relational databases (http://www.jchem.com). Regards, Ferenc -- Dr. Ferenc Csizmadia Managing Director ChemAxon Ltd. Valyog u. 7, H-1032 Budapest, Hungary http://www.chemaxon.com T: +3620 9570988 mailto:fcsiz@chemaxon.com From chemistry-request@server.ccl.net Wed Jan 26 12:02:24 2000 Received: from relay.unizar.es (tozal.unizar.es [155.210.3.20]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id MAA23972 for ; Wed, 26 Jan 2000 12:02:13 -0500 Received: from posta.unizar.es (posta.unizar.es [155.210.11.16]) by relay.unizar.es (8.9.3/8.9.1) with ESMTP id QAA18889 for ; Wed, 26 Jan 2000 16:55:43 +0100 (MET) Received: from qo_jigl ([155.210.88.191]) by posta.unizar.es (8.9.1/8.9.1) with SMTP id QAA09017 for ; Wed, 26 Jan 2000 16:55:07 +0100 (MET) Message-Id: <3.0.6.32.20000126165324.007d83a0@posta.unizar.es> X-Sender: jig@posta.unizar.es X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.6 (32) Date: Wed, 26 Jan 2000 16:53:24 +0100 To: chemistry@ccl.net From: Jose Ignacio Garcia Subject: Problem with IPCM calculations Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Dear CCL netters, I am trying to do some IPCM calculations using both g94 and g98, and I have obtained the following surprising results: 1. When I use the following keyword list: > # B3LYP/3-21G* SCRF=(IPCM) SCF=TIGHT test the calculation does not converge at all. In the first cycle, I get the following results: > Total "Solvent Accessible Surface Area" of Solute = 1.304706E+03 > Volume of Solute Cavity = 2.330747E+03 > SCF Done: E(RB+HF-LYP) = -2578.41449028 A.U. after 15 cycles 2. Next, with the same molecular geometry, I use the following keywords: > # B3LYP/3-21G* Nosymm SCRF=(IPCM) SCF=TIGHT test and then the calculation does converge without problems. Furthermore, in the first cycle I get the followint results: > Total "Solvent Accessible Surface Area" of Solute = 6.992377E+02 > Volume of Solute Cavity = 1.869951E+03 > SCF Done: E(RB+HF-LYP) = -2578.39952991 A.U. after 14 cycles As you can see, the solvent accesible surface area, the volume of solute cavity and the total energy are dramatically different, only by imposing the initial molecular orientation by means of NoSymm (btw, the molecule belongs to the C1 symmetry group). Any explanation for this behavior will be welcomed. Of course, any recipe to "stabilize" this kind of calculations would be great. I'll summarize the responses. Regards, Jose I. Garcia ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Dr. Jose Ignacio Garcia-Laureiro Depto. Quimica Organica. Instituto de Ciencia de Materiales de Aragon Facultad de Ciencias (edificio D). Universidad de Zaragoza-CSIC c/ Pedro Cerbuna, 12. E-50009 Zaragoza (Spain) Phone: +34 976762271 e-mail: jig@posta.unizar.es Fax: +34 976762077 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From chemistry-request@server.ccl.net Wed Jan 26 06:06:18 2000 Received: from kasei.materials.ox.ac.uk (kasei.materials.ox.ac.uk [163.1.64.46]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id GAA21657 for ; Wed, 26 Jan 2000 06:06:17 -0500 Received: from localhost (hfield@localhost) by kasei.materials.ox.ac.uk (8.9.3/8.9.3) with ESMTP id KAA06166 for ; Wed, 26 Jan 2000 10:02:17 GMT X-Authentication-Warning: kasei.materials.ox.ac.uk: hfield owned process doing -bs Date: Wed, 26 Jan 2000 10:02:17 +0000 (GMT) From: Andrew Horsfield X-Sender: hfield@kasei.materials.ox.ac.uk Reply-To: Andrew Horsfield To: Computational Chemistry List Subject: Beowulf meeting in London Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII There will be a one day Beowulf Computing meeting on February 10th at the Institute of Physics in London (UK). This meeting is open to all. Please see http://harvey.phy.cam.ac.uk/meeting.html for the program and registration details. Cheers, Andrew +----------------------------------------------------+ Andrew Horsfield e-mail: horsfield@fecit.co.uk FECIT, 2 Longwalk Road, Stockley Park, Uxbridge, Middlesex UB11 1AB, United Kingdom. phone: +44-(0)181-606-4653 FAX: +44-(0)181-606-4422 +----------------------------------------------------+ From chemistry-request@server.ccl.net Wed Jan 26 10:06:08 2000 Received: from grapevine2.com (grapevine2.com [192.41.12.99]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id KAA23539 for ; Wed, 26 Jan 2000 10:06:06 -0500 Received: from CC911078A (cc911078-a.abdn1.md.home.com [24.9.150.137]) by grapevine2.com (8.8.5) id GAA21057 for ; Wed, 26 Jan 2000 06:59:46 -0700 (MST) X-Authentication-Warning: grapevine2.com: Host cc911078-a.abdn1.md.home.com [24.9.150.137] claimed to be CC911078A Reply-To: From: "Dr. Guillermo A. Morales" To: "CCL" Subject: Announcing CombiChem Lab: A new website dedicated to Combinatorial Chemistry and High-Throughput Screening. Date: Wed, 26 Jan 2000 08:58:23 -0500 Message-ID: <000901bf6805$68e00420$0300a8c0@abdn1.md.home.com> MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook 8.5, Build 4.71.2173.0 Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2919.6600 My apologies if you receive this message multiple times. I would like to announce the opening of CombiChem Lab. This site is intended to provide free online information in the areas of Combinatorial Chemistry, High-Throughput Screening, and other related topics. This site is academic oriented. There are no specials, offers or ads of any kind and I intend to keep it that way. The site is still under construction. The combinatorial chemistry section is half way finished. As soon as this section is complete I will work on the High-Throughput Screening section. Since this is a one-person effort, it is taking time to build the site. Please come and visit the site at www.combichemlab.com Any suggestions to improve the site are always welcome. Thanks. Guillermo A. Morales, Ph.D. ----- "We can't solve problems by using the same kind of thinking we used when we created them." -- Albert Einstein -- ---- Guillermo A. Morales E-mail: morales@combichemlab.com From chemistry-request@server.ccl.net Wed Jan 26 14:25:54 2000 Received: from ccshst04.cs.uoguelph.ca (ccshst04.cs.uoguelph.ca [131.104.96.17]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id OAA25084 for ; Wed, 26 Jan 2000 14:25:52 -0500 Received: from ccshst01 (ccshst01.cs.uoguelph.ca [131.104.96.81]) by ccshst04.cs.uoguelph.ca (8.9.3/8.9.3) with SMTP id NAA09106; Wed, 26 Jan 2000 13:19:26 -0500 (EST) Date: Wed, 26 Jan 2000 13:19:26 -0500 (EST) From: WeiQuan Tian X-Sender: wtian@ccshst01 To: Alexander Wittkopp cc: "'CHEMISTRY@ccl.net'" Subject: Re: CCL:B96 functional in G98 In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Gaussian Inc. told us that some of the functionals specified in the manula are not available for the present version, one is B1. Wei Quan Tian On Wed, 26 Jan 2000, Alexander Wittkopp wrote: > Dear all, > > we tried to utilize the B96 DFT functional offered by Gaussian98, but > found for all combinations with the implemented correlation functionals > (even for the hybrid B1B96, mentioned in the manual) the following error > message: > > ********************************************* > Gaussian 98: x86-Linux-G98RevA.5 21-Sep-1998 > 26-Jan-2000 > ********************************************* > %chk=XXXXX > ---------------------------------------------------- > # B1B96/6-31G* Opt Freq=NoRaman Pop=None > ---------------------------------------------------- > QPERR --- A SYNTAX ERROR WAS DETECTED IN THE INPUT LINE. > # B1B96/6-31G* OPT FREQ=NORAMAN POP=NONE > ' > > Did anyone use that functional in Gaussian98? > > We would be grateful for any advice! > > Ciao, > Alexander > > ******************************************************************************* > ("`-/")_.-'"``-._ > Alexander Wittkopp (. . `) -._ )-;-,_() > Institut fuer Organische Chemie (v_,)' _ )`-.\ ``- > Georg-August Universitaet _;- _,-_/ / ((,' > Tammannstrasse 2 ((,.-' ((,/ > 37077 Goettingen Email: awittko@gwdg.de URL: http://www.gwdg.de/~awittko > Germany Phone: +49-(0)551-393290 Fax: +49-(0)551-399475 > > "eine ungerade Zahl, am besten prim hat immer guenstige Auswirkungen auf > cache-trashing." > T. Nau > ******************************************************************************* > > > > -= 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 Wed Jan 26 17:39:45 2000 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 RAA26006 for ; Wed, 26 Jan 2000 17:39:45 -0500 Received: from syr.edu (curie.syr.edu [128.230.187.116]) by mailbox.syr.edu (8.9.2/8.9.2) with ESMTP id QAA29783 for ; Wed, 26 Jan 2000 16:33:26 -0500 (EST) Sender: desingh@mailbox.syr.edu Message-ID: <388F6949.64893FB8@syr.edu> Date: Wed, 26 Jan 2000 16:38:17 -0500 From: Deepak Singh Organization: Birge Group, Dept. Of Chemistry, Syracuse Univ. X-Mailer: Mozilla 4.61C-SGI [en] (X11; I; IRIX64 6.5 IP30) X-Accept-Language: en MIME-Version: 1.0 To: Computational Chemistry List Subject: GENERAL QUESTION Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi CCLer's I have been reading up some papers on this subject and would like a second opinion. Caves, Evanseck and Karplus , Protein Sci. (1998), 7:649-666 argue for multiple (100-120 ps) md simulations of a protein as opposed to long nanosecond scale simulations. The Karplus approach seems to be yielding fairly good results for me, but what I have not seen that many examples of this approach in literature (it was published just under two years ago). Do you think that such an approach is valid for homology models where there is no real "reference structure"? Any input is much appreciated. If there is sufficient interest, I will post a summary. Thanks and 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 Wed Jan 26 18:46:13 2000 Received: from mail1.panix.com (mail1.panix.com [166.84.0.212]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id SAA26419 for ; Wed, 26 Jan 2000 18:46:11 -0500 From: kynn@panix.com Received: from panix3.panix.com (panix3.panix.com [166.84.0.228]) by mail1.panix.com (Postfix) with ESMTP id F124B30F1D; Wed, 26 Jan 2000 17:39:10 -0500 (EST) Received: (from kynn@localhost) by panix3.panix.com (8.8.8/8.7.1/PanixN1.0) id RAA00586; Wed, 26 Jan 2000 17:39:10 -0500 (EST) Date: Wed, 26 Jan 2000 17:39:10 -0500 (EST) Message-Id: <200001262239.RAA00586@panix3.panix.com> X-Authentication-Warning: panix3.panix.com: kynn set sender to kynn@panix.com using -f To: CHEMISTRY@ccl.net Subject: Why WHAM? I've read Kumar's paper [1] on the WHAM method for combining multiple histograms, but it's still not clear to me what's exactly the advantage of this method over the original umbrella sampling method proposed by Torrie and Valleau? In Chandler's textbook [2] (for example) he describes a way of using umbrella potentials to construct a curve of density of states as a function of a reaction coordinate (I think this is basically Torrie and Valleau's method). The approach is very straightforward: the curves obtained with the different window potentials are spliced by shifting them around vertically to produce a smooth curve (p. 172). This may be a bit crude compared to WHAM, but at least it is completely transparent. It is true that this "naive splicing" procedure would be difficult to carry out if one wanted to produce a density of states *surface* (in contrast to a curve) as a function of two reaction coordinates, and altogether impossible when the number of reaction coordinates is greater than 2. But, at any rate, naively it seems to me that if one has a single reaction coordinate, then the simple procedure that Chandler describes should suffice. My concern is that, in such relatively simple cases, the additional complexity of WHAM may not be justified by its advantages. Am I missing something? I would very much like to read your opinions. Regards, Kynn Jones [1] Kumar, S. et al., J. Comp. Chem. 13(8):1011-1021, 1992 [2] Chandler, D. "Introduction to Modern Statistical Mechanics", (1987) pp. 169-175