From chemistry-request@ccl.net Fri Mar 12 19:00:24 2004 Received: from web21505.mail.yahoo.com (web21505.mail.yahoo.com [66.163.169.16]) by server.ccl.net (8.12.8/8.12.8) with SMTP id i2D00Njs002241 for ; Fri, 12 Mar 2004 19:00:23 -0500 Message-ID: <20040313000221.82748.qmail/at/web21505.mail.yahoo.com> Received: from [130.74.167.139] by web21505.mail.yahoo.com via HTTP; Fri, 12 Mar 2004 16:02:21 PST Date: Fri, 12 Mar 2004 16:02:21 -0800 (PST) From: prashant desai Subject: GPCR Refinement To: chemistry/at/ccl.net MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="0-1268321628-1079136141=:81787" X-Spam-Status: No, hits=2.4 required=7.0 tests=FROM_ENDS_IN_NUMS,HTML_20_30, HTML_MESSAGE,MAILTO_TO_SPAM_ADDR autolearn=no version=2.61 X-Spam-Level: ** X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net --0-1268321628-1079136141=:81787 Content-Type: text/plain; charset=us-ascii Hi, I am Univ of Mississippi, Med Chem Grad Student. I am trying to do GPCR Homology Modeling. I have a crude GPCR model with which i am working which i have retrieved from internet. I mostly use Accelrys software and DISCOVER forcefield. I have done initial minimizations on the protein using DISCOVER Minimization module. This model still has some BUMPS at 0.3 angstrom. I need to know what is a good protocol to refine a GPCR Model, what kind of Minimization and Molecular Dynamics protocols can be used to effectively refine such GPCR models? and also What things in general shall we take care of during such refinement. I am new to Molecular Modeling and need ur opinions about the same. Looking forward to some good solutions. Akshay Patny (Graduate Student @ PhD) Department of Medicinal Chemistry School of Pharmacy, University of Mississippi 417, Faser Hall, University, MS - 38677 Tel: 662-915-1286(Off.), 662-236-3059(Res.), 662-801-7910(Cell) E-mail: akshay/at/patnys.com (Personal), akshay17/at/olemiss.edu (Office) Web: www.olemiss.edu (Office), www.patnys.com (Personal) --------------------------------- Do you Yahoo!? Yahoo! Search - Find what you re looking for faster. --0-1268321628-1079136141=:81787 Content-Type: text/html; charset=us-ascii
Hi,
 
I am Univ of Mississippi, Med Chem Grad Student. I am trying to do GPCR Homology Modeling. I have a crude GPCR model with which i am working which i have retrieved from internet. I mostly use Accelrys software and DISCOVER forcefield. I have done initial minimizations on the protein using DISCOVER Minimization module.
This model still has some BUMPS at 0.3 angstrom.
 
I need to know what is a good protocol to refine a GPCR Model, what kind of Minimization and Molecular Dynamics protocols can be used to effectively refine such GPCR models? and also What things in general shall we take care of during such refinement.
 
I am new to Molecular Modeling and need ur opinions about the same.
 
Looking forward to some good solutions.
 
Akshay Patny
(Graduate Student @ PhD)
 
Department of Medicinal Chemistry
School of Pharmacy, University of Mississippi
417, Faser Hall, University, MS - 38677
Tel: 662-915-1286(Off.), 662-236-3059(Res.),  662-801-7910(Cell)
E-mail: akshay/at/patnys.com (Personal), akshay17/at/olemiss.edu (Office)
Web: www.olemiss.edu (Office), www.patnys.com (Personal)
 

Do you Yahoo!?
Yahoo! Search - Find what you re looking for faster. --0-1268321628-1079136141=:81787-- From chemistry-request@ccl.net Sun Mar 14 11:00:10 2004 Received: from classic.chem.msu.su (classic.chem.msu.su [158.250.32.143]) by server.ccl.net (8.12.8/8.12.8) with SMTP id i2EG05js004453 for ; Sun, 14 Mar 2004 11:00:07 -0500 Received: from alexg (ras16.icp.rssi.ru [194.85.223.96] ) by classic.chem.msu.su (Hethmon Brothers Smtpd) ; Sun, 14 Mar 2004 19:03:33 +0000 Message-ID: <000701c409dc$79b3d420$60df55c2@alexg> Reply-To: "Alex. A. Granovsky" From: "Alex. A. Granovsky" To: "CCL" Subject: CCL: Parallel PC GAMESS v. 6.4 bugfix is available Date: Sun, 14 Mar 2004 18:32:54 +0300 Organization: MSU MIME-Version: 1.0 Content-Type: text/plain; charset="koi8-r" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.50.4522.1200 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4522.1200 X-Spam-Status: No, hits=0.7 required=7.0 tests=DATE_IN_PAST_03_06 autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Dear PC GAMESS users, After official public PC GAMESS version 6.4 build # 2606 had been released, we found a serious bug in all parallel PC GAMESS v. 6.4 binaries which can cause SOSCF routine to hang during parallel SCF calculations. The patch have been developed to fix this problem. At moment, this patch is available directly from me upon request and it will be available from the PC GAMESS download site at ISU within several days. The sequential PC GAMESS binaries are not affected by this bug. We are sorry for any inconvenience this can cause. Best regards, Alex Granovsky From chemistry-request@ccl.net Sat Mar 13 02:08:04 2004 Received: from mx1.ustc.edu.cn ([218.22.21.1]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i2D780js010890 for ; Sat, 13 Mar 2004 02:08:01 -0500 Received: from dxl ([210.45.66.65]) by mx1.ustc.edu.cn (8.8.7/8.8.6) with ESMTP id PAA02450 for ; Sat, 13 Mar 2004 15:06:43 +0800 Message-Id: <200403130706.PAA02450[at]mx1.ustc.edu.cn> Date: Sat, 13 Mar 2004 15:8:40 +0800 From: "6!Q8@W" Reply-To: dxl[at]mail.ustc.edu.cn To: CCL Subject: HOMO energy is higher than LUMO ! Organization: VP9z?F4sQ!<|;/Q'J5QiJR X-mailer: Foxmail 4.1 [cn] Mime-Version: 1.0 Content-Type: text/plain; charset="GB2312" X-Spam-Status: No, hits=4.7 required=7.0 tests=DATE_IN_PAST_12_24, HEAD_ILLEGAL_CHARS autolearn=no version=2.61 X-Spam-Level: **** X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id i2D784js010894 Dear CCLers#: !!!!One result in my calculation with Gaussian03 PW91PW91 surprised me. The energy of alfa HOMO is higher than the energy of beta LUMO. I have test to use stable=opt, guess=alter, guess=mix , and guess=read (read the correct result from B3LYP calculation), but all these test give the same wrong result. What else should I test to solve this problem ? Thank you for your help!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!Ding Xunlei !!!!!!!!!!!!!!!!!!!!!!!!!!!!2004-03-13 ______________________________________________ Ding Xunlei, Ph.D. Candidate Open Laboratory of Bond Selective Chemistry University of Science & Technology of China Hefei, Anhui 230026, P.R.China Tel.: 0086-551-3603418 Fax.: 0086-551-3602969 E-mail: dxl[at]mail.ustc.edu.cn Http://www.bsc.ustc.edu.cn/~dxl From chemistry-request@ccl.net Mon Mar 15 01:39:21 2004 Received: from ns1.scripps.edu (ns1.scripps.edu [192.42.82.59]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i2F6dHjs026038 for ; Mon, 15 Mar 2004 01:39:17 -0500 Received: from antigen.scripps.edu (antigen.scripps.edu [137.131.200.100]) by ns1.scripps.edu (8.11.7/TSRI-4.2rx) with SMTP id i2F6eoQ26467 for ; Sun, 14 Mar 2004 22:40:54 -0800 (PST) Received: from relay1.scripps.edu(137.131.200.29) by antigen.scripps.edu via csmap id ca821a84_764b_11d8_9ec2_00304811a0c8_24503; Mon, 15 Mar 2004 06:41:29 +0000 (UTC) Received: from gamow.scripps.edu (gamow [137.131.252.67]) by relay1.scripps.edu (8.11.7/TSRI-4.4.1rAVB) with ESMTP id i2F6fTb17628 for ; Sun, 14 Mar 2004 22:41:29 -0800 (PST) Received: from quine.scripps.edu (gamow [137.131.252.67]) by gamow.scripps.edu (8.9.2/TSRI-3.0.1) with SMTP id WAA1160734 for ; Sun, 14 Mar 2004 22:41:27 -0800 (PST) Received: by quine.scripps.edu (sSMTP sendmail emulation); Sun, 14 Mar 2004 22:41:28 -0800 Date: Sun, 14 Mar 2004 22:41:28 -0800 From: "David A. Case" To: chemistry..at..ccl.net Subject: CCL: Release announcement for Amber 8 Message-ID: <20040315064128.GA2468..at..scripps.edu> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline User-Agent: Mutt/1.4i X-Spam-Status: No, hits=0.0 required=7.0 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net The Amber development team is pleased to announce the release of version 8 of Amber package of biomolecular simulation programs. This represents a significant advance over version 7, which was released in March, 2002. Key features include new force fields and computational methods, faster execution, and better documentation. For details, please visit the Amber web site: http://amber.scripps.edu The Amber 8 authors are D.A. Case, T.A. Darden, T.E. Cheatham, III, C.L. Simmerling, J. Wang, R.E. Duke, R. Luo, K.M. Merz, B. Wang, D.A. Pearlman, M. Crowley, S. Brozell, V. Tsui, H. Gohlke, J. Mongan, V. Hornak, G. Cui, P. Beroza, C. Schafmeister, J.W. Caldwell, W.S. Ross, and P.A. Kollman. From chemistry-request@ccl.net Mon Mar 15 09:21:46 2004 Received: from post.it.helsinki.fi (post.it.helsinki.fi [128.214.205.132]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i2FELijs010993 for ; Mon, 15 Mar 2004 09:21:45 -0500 Received: from soul.it.helsinki.fi (soul.it.helsinki.fi [128.214.189.108]) by post.it.helsinki.fi (8.12.11/8.12.11) with ESMTP id i2FENwxR020182; Mon, 15 Mar 2004 16:23:59 +0200 (EET) Received: from soul.it.helsinki.fi (localhost [127.0.0.1]) by soul.it.helsinki.fi (8.12.10/8.12.10) with ESMTP id i2FENvaS044320; Mon, 15 Mar 2004 16:23:57 +0200 (EET) Received: from localhost (mpjohans@localhost) by soul.it.helsinki.fi (8.12.10/8.12.10/Submit) with ESMTP id i2FENv7f053652; Mon, 15 Mar 2004 16:23:57 +0200 (EET) X-Authentication-Warning: soul.it.helsinki.fi: mpjohans owned process doing -bs Date: Mon, 15 Mar 2004 16:23:57 +0200 (EET) From: Mikael Johansson X-X-Sender: mpjohans.-at-.soul.it.helsinki.fi To: "6!Q8@W" cc: CCL Subject: Re: CCL:HOMO energy is higher than LUMO ! In-Reply-To: <200403130706.PAA02450.-at-.mx1.ustc.edu.cn> Message-ID: References: <200403130706.PAA02450.-at-.mx1.ustc.edu.cn> MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Spam-Status: No, hits=0.0 required=7.0 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Hello! On Sat, 13 Mar 2004, 6!Q8@W wrote: > !!!!One result in my calculation with Gaussian03 PW91PW91 surprised me. > The energy of alfa HOMO is higher than the energy of beta LUMO. > I have test to use stable=opt, guess=alter, guess=mix , > and guess=read (read the correct result from B3LYP calculation), > but all these test give the same wrong result. (I assume that changing the occupation doesn't help.) With pure (non-hybrid) density functionals this can happen. The energy of the occupied orbitals are artificially raised. With a hybrid functional like B3LYP, the problem is partly remedied, and the HOMO-LUMO gap increases. If you really need the virtual orbitals to be higher in energy, then the quickest solution is to use a hybrid functional. Perhaps an electronic self-interaction correction could be applicable, also. I don't know if Gaussian does this, though. Have a nice day, Mikael J. http://www.helsinki.fi/~mpjohans/ From chemistry-request@ccl.net Mon Mar 15 12:13:49 2004 Received: from mxout1.cac.washington.edu (mxout1.cac.washington.edu [140.142.32.134]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i2FHDmjs016783 for ; Mon, 15 Mar 2004 12:13:49 -0500 Received: from smtp.washington.edu (smtp.washington.edu [140.142.33.9]) by mxout1.cac.washington.edu (8.12.11+UW04.02/8.12.11+UW04.02) with ESMTP id i2FHG6xK015588; Mon, 15 Mar 2004 09:16:06 -0800 Received: from u.washington.edu (D-128-95-235-225.dhcp4.washington.edu [128.95.235.225]) (authenticated bits=0) by smtp.washington.edu (8.12.11+UW04.02/8.12.11+UW04.02) with ESMTP id i2FHG6u2013985 (version=TLSv1/SSLv3 cipher=RC4-MD5 bits=128 verify=NOT); Mon, 15 Mar 2004 09:16:06 -0800 Message-ID: <4055E4DD.1000703*at*u.washington.edu> Date: Mon, 15 Mar 2004 09:16:13 -0800 From: Oliver Hucke User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.0.2) Gecko/20030208 Netscape/7.02 X-Accept-Language: en-us, en MIME-Version: 1.0 To: prashant desai , CCL Subject: Re: CCL:GPCR Refinement References: <20040313000221.82748.qmail*at*web21505.mail.yahoo.com> Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=1.1 required=7.0 tests=MAILTO_TO_SPAM_ADDR autolearn=no version=2.61 X-Spam-Level: * X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Hi Akshay, I do not know specifically about GPCR but the homology modelling program MODELLER has been used succesfully in numerous cases of modeling the structure of membrane proteins as a basis for subsequent molecular dynamics simulations. You might e.g. look in the literature for papers of the Sansom group in Oxford. From my own experience I can say that modeller generated structures look very reasonable with respect to the stereochemical quality unless you make serious errors with the alignment. Modeller is free (salilab.org). It might be part of your InsightII package but perhaps not in form of the most recent version. Hope this helps, Oliver prashant desai wrote: > Hi, > > I am Univ of Mississippi, Med Chem Grad Student. I am trying to do GPCR > Homology Modeling. I have a crude GPCR model with which i am working > which i have retrieved from internet. I mostly use Accelrys software and > DISCOVER forcefield. I have done initial minimizations on the protein > using DISCOVER Minimization module. > This model still has some BUMPS at 0.3 angstrom. > > I need to know what is a good protocol to refine a GPCR Model, what kind > of Minimization and Molecular Dynamics protocols can be used to > effectively refine such GPCR models? and also What things in general > shall we take care of during such refinement. > > I am new to Molecular Modeling and need ur opinions about the same. > > Looking forward to some good solutions. > > Akshay Patny > (Graduate Student @ PhD) > > Department of Medicinal Chemistry > School of Pharmacy, University of Mississippi > 417, Faser Hall, University, MS - 38677 > Tel: 662-915-1286(Off.), 662-236-3059(Res.), 662-801-7910(Cell) > E-mail: akshay*at*patnys.com (Personal), > akshay17*at*olemiss.edu (Office) > Web: www.olemiss.edu (Office), www.patnys.com > (Personal) > > > ------------------------------------------------------------------------ > Do you Yahoo!? > Yahoo! Search - Find what you re looking for faster. > -- _______________________________________________________________ Oliver Hucke, Dr. Health Sciences Building - K418C University of Washington 1959 NE Pacific St. Dept. of Biochemistry phone: (206) 685 7046 Box 357742 fax : (206) 685 7002 Seattle, WA 98195-7742 email: ohucke*at*u.washington.edu _______________________________________________________________ From chemistry-request@ccl.net Mon Mar 15 09:43:59 2004 Received: from caravelle.univ-lemans.fr (caravelle.univ-lemans.fr [195.221.244.4]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i2FEhwjs011935 for ; Mon, 15 Mar 2004 09:43:58 -0500 Received: from [193.52.30.144] (pascalgo-crihan.univ-lemans.fr [193.52.30.144]) by caravelle.univ-lemans.fr (8.12.10/8.12.10/(CeTIC - 18/09/03)) with ESMTP id i2FEjpR8022377 for ; Mon, 15 Mar 2004 15:45:59 +0100 (MET) Mime-Version: 1.0 (Apple Message framework v612) Message-Id: <565DAEDE-768F-11D8-A730-0003934391AA.-at-.univ-lemans.fr> Content-Type: text/plain; charset=ISO-8859-1; format=flowed To: chemistry.-at-.ccl.net From: Pascal Gosselin Subject: Spin Density vs SOMO surfaces Date: Mon, 15 Mar 2004 15:45:00 +0100 X-Mailer: Apple Mail (2.612) X-Spam-Status: No, hits=0.0 required=7.0 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id i2FEhxjs011939 Dear all, I wanted to visualize the localization of the unpaired electron in radical-cations whose structures were optimized at the UB3LYP/6-31G* level in Gaussian98. For that purpose, I asked Gaussview to compute both Spin Density and SOMO surfaces. In most cases, both pictures were very similar. However, in some cases, I was surprised to observe two very different pictures, i.e. the surfaces were located over completely different regions of the radical-cation. In some cases, alphaSomo, alphaSomo-1 and betaSomo were found very close in energy. I tried to obtain a "mean view" of the system by adding the alphaSomo and alphaSomo-1 then subtracting betaSomo (with the cubman utility within g98 package). The resulting picture remained different of the Spin Density surface. Has somebody an explanation? All the Best ********************************************** Dr Pascal Gosselin Laboratoire de Synthhse Organique/UMR-CNRS-6011 Faculti des Sciences & Techniques Universiti du Maine Avenue Olivier Messiaen F-72085 Le Mans Cedex 9 France Tel: + 33 (0)2 43 83 33 71 Fax: + 33 (0)2 43 83 39 02 Email: Pascal.Gosselin.-at-.univ-lemans.fr ********************************************** Soutenez le mouvement SAUVONS LA RECHERCHE : http://recherche-en-danger.apinc.org/ ********************************************** From chemistry-request@ccl.net Mon Mar 15 03:50:13 2004 Received: from irsun275.ifp.fr (ns2.ifp.fr [81.255.42.34]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i2F8oBjs000617 for ; Mon, 15 Mar 2004 03:50:12 -0500 Received: from smtp.ifp.fr by irsun275.ifp.fr (V35.12) with ESMTP Received: from irnts21.ifp.fr (irnts21 [156.118.15.51]) by irsun165.ifp.fr (8.8.5/8.8.5) with ESMTP id JAA09341 for ; Mon, 15 Mar 2004 09:52:28 +0100 (MET) Received: by irnts21.ifp.fr with Internet Mail Service (5.5.2657.72) id ; Mon, 15 Mar 2004 09:52:28 +0100 Message-ID: <3AA99E087354D61185E4002048403CFC02145B84.-at-.irnts23.ifp.fr> From: DE BRUIN theodorus To: "'chemistry.-at-.ccl.net'" Subject: compilation of G03 on Mac OS X Date: Mon, 15 Mar 2004 09:52:26 +0100 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2657.72) Content-Type: text/plain; charset="iso-8859-1" X-Spam-Status: No, hits=0.0 required=7.0 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id i2F8oDjs000621 Hello, Has anybody already successfully compiled Gaussian 03 for Mac OS X (G5 processor) from the source code. If so, could you share with me the necessary makefile ? Thanks in advance for your help. Kind regards, Theodorus de BRUIN -------- Theodorus de Bruin Institut Frangais du Pitrole Direction Chimie et Physico-Chimie Appliquies Dipartement Thermodynamique et Modilisation Moliculaire 1 & 4 Avenue de bois Preau 92852 Rueil-Malmaison Cedex Tel: +33 (0)1.47.52.54.38 Fax: +33 (0)1.47.52.70.58 Return-Path: Message-ID: <405053E0.5040301(at)cosmologic.de> Date: Thu, 11 Mar 2004 12:56:16 +0100 From: Andreas Klamt To: chemistry(at)ccl.net Subject: 04.04.21-22 COSMO-RS Symposium, Leverkusen, Germany Dear colleagues, I like to invite you to our COSMO-RS symposium on April 21/22 on the occasion of the 5th anniversary of our company COSMOlogic. By a mixture of presentation form industrial and academic users, collaboration partners, and COSMOlogic staff this symposium will give a good occasion to learn most about the COSMO-RS method for the calculation of thermodynamic fluid phase properties based on quantum chemical calculations. Application areas covered will come from - chemical engineering (activity coefficients, vapor pressures, etc.) - medicinal chemistry (solubility, physiological partition coefficients, pKa) - general physical and organic chemistry - and other areas of industrial application. Details about the venue are given below. Since the number of participants is limited, please first register by e-mail to me, and make your hotel reservation based on a confirmation. There are no conference fees apart from hotel and catering costs. Looking forward to see some of you on our symposium Andreas Klamt and the COSMOlogic Team -------- Final registration details of the COSMO-RS Symposium on April 21/22, 2004. The symposium will take place at the Armada Hotel Leverkusen. Am Buechelter Hof 11 Leverkusen, 51373 NRW Germany Phone: 49 214-3830 Fax: 49 214-383700 This hotel is close to the Leverkusen (Mitte) train station and thus well accessible by train and from the Duesseldorf (DUS) and Cologne (CGN) airports. Please note that there are several quite inexpensive European connections to CGN (see www.germanwings.com and www.hlx.com)! You can as well fly into Frankfurt (FRA) and use the high speed train to Cologne and connect to Leverkusen-Mitte from there. The travel time from the airport to Leverkusen will only be about 75 min. By car you can take the A1 or A3 to Leverkusen. For details about the hotel see: http://ramadainternational.com/ramada/dpp/propertyPage.mi?marshaCode=ZOALK Please make reservations by phone at best directly using the codeword "COSMOlogic" and inform us in parallel by e-mail. We made special arangements for the rate: - the night of April 21 can be booked at a rate of 95 EURO (single room) incl. full board srting from lunch on 21st and ending with lunch on 22nd. - additional nights before and after this can be booked at 75 EURO (incl. breakfast) for single and 86 EURO for double rooms. Participants not staying in the Ramada Hotel have to pay a catering fee (incl. lunch, cofee breaks) of 40 EURO if you stay the full time, or 20 EURO if you only participate on 21st or 22nd of April. Please pay this directly at the hotel reception. In the evening of the 21st April we cordially invite you to be our guest at the COSMOlogic Reception on the occasion of our 5th Anniversary. The plan for the symposium is: April 20: Optional training sessions for COSMOtherm, COSMOfrag, and TURBOMOLE (upon appointment) April 21: 10:00. - 12:00. : Software Demonstrations of COSMOtherm, COSMOfrag, and TURBOMOLE 12:00 : official symposium start at with a finger lunch 12:30 - 17:15: a more chemical engineering focussed session on COSMOtherm and COSMObase, covering the present state, future developments, and industrial needs. 19:30 - 21:30: Reception April 22: 08:00 - 12:30: a session focussing on life science applications of COSMOtherm and COSMOfrag. 12:30 - 13:00: finger lunch and official closure of the symposium 13:00. - 15:00. : Software Demonstrations of COSMOtherm, COSMOfrag, and TURBOMOLE April 23: Optional training sessions for COSMOtherm, COSMOfrag, and TURBOMOLE (upon appointment) Please register as soon as possible by e-mail to me. Please have the word "Symposium" in the Subject line. We have a limit of about 90 participants. I am grateful if you register as soon as possible, but there will be no deadline until we reach our capacity limit. Looking forward to see you in Leverkusen Andreas Klamt and the COSMOlogic team -------------------------------------------------------------------------------- Dr. Andreas Klamt COSMOlogic GmbH&CoKG Burscheider Str. 515 51381 Leverkusen, Germany Tel.: +49-2171-73168-1 Fax: +49-2171-73168-9 e-mail: klamt(at)cosmologic.de web: www.cosmologic.de ------------------------------------------------------------------------------- COSMOlogic Your Competent Partner for Computational Chemistry and Fluid Thermodynamics ------------------------------------------------------------------------------- Return-Path: Reply-To: From: "Mark Thompson" To: chemistry^at^ccl.net Subject: New ArgusLab beta installer available. Date: Mon, 15 Mar 2004 17:32:36 -0500 Message-ID: <000301c40141$f4432680$0200a8c0@planaria> ArgusLab 4.0 beta2 has expired. You will need to download a newer version of the installer from our website. The new expiration is 6 months from today. I apologize for the inconvenience of these beta-time-outs, but it is necessary to prevent bug reports and user feedback from older beta versions. I'm slowly addressing the bug fixes, stability issues, and the last new feature(s). Thanks for your patience and input. Cheers, Mark *************************** Mark Thompson Planaria Software LLC PO Box 55207 Seattle, WA 98155 mark^at^arguslab.com http://www.arguslab.com *************************** From chemistry-request@ccl.net Mon Mar 15 20:23:53 2004 Received: from mx1.ustc.edu.cn ([218.22.21.1]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i2G1Npjs031777 for ; Mon, 15 Mar 2004 20:23:51 -0500 Received: from dxl ([210.45.66.65]) by mx1.ustc.edu.cn (8.8.7/8.8.6) with ESMTP id JAA16021; Tue, 16 Mar 2004 09:13:40 +0800 Message-Id: <200403160113.JAA16021*at*mx1.ustc.edu.cn> Date: Tue, 16 Mar 2004 9:16:30 +0800 From: "6!Q8@W" Reply-To: dxl*at*mail.ustc.edu.cn To: "Shobe, David" , CCL Subject: Re: RE: HOMO energy is higher than LUMO ! Organization: VP9z?F4sQ!<|;/Q'J5QiJR X-mailer: Foxmail 4.1 [cn] Mime-Version: 1.0 Content-Type: text/plain; charset="GB2312" X-Spam-Status: No, hits=4.3 required=7.0 tests=HEAD_ILLEGAL_CHARS autolearn=no version=2.61 X-Spam-Level: **** X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id i2G1Nrjs031781 Dear Shobe, David#: !!!!I do a calculation on clusters with Au atoms. The problem(HOMO energy is higher than LUMO) is only for the PW91PW91 calculation for triplet state. The singlet state calculated by PW91PW91 is lower by 0.26eV than the triplet. On the contrary, the B3LYP result shows that the triplet is lower than the singlet, but only by 0.01eV. Can I get an conclustion that the singlet is the ground state ? Thank you for your help!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!Ding Xunlei !!!!!!!!!!!!!!!!!!!!!!!!!!!!2004-03-16 ______________________________________________ Ding Xunlei, Ph.D. Candidate Open Laboratory of Bond Selective Chemistry University of Science & Technology of China Hefei, Anhui 230026, P.R.China Tel.: 0086-551-3603418 Fax.: 0086-551-3602969 E-mail: dxl*at*mail.ustc.edu.cn Http://www.bsc.ustc.edu.cn/~dxl ======= 2004-03-15 10:07:00 You have written: ======= >What kind of molecule are you studying? Could it have a lower-spin ground state than your calculation assumes? > >--David Shobe, Ph.D., M.L.S. >Sud-Chemie, Inc. >phone (502) 634-7409 >fax (502) 634-7724 > >Don't bother flaming me: I'm behind a firewall. > > > >-----Original Message----- >From: Computational Chemistry List [mailto:chemistry-request*at*ccl.net]On Behalf Of 6!Q8@W >Sent: Saturday, March 13, 2004 2:09 AM >To: CCL >Subject: CCL:HOMO energy is higher than LUMO ! > > >Dear CCLers#: > > !!!!One result in my calculation with Gaussian03 PW91PW91 surprised me. >The energy of alfa HOMO is higher than the energy of beta LUMO. >I have test to use stable=opt, guess=alter, guess=mix , >and guess=read (read the correct result from B3LYP calculation), >but all these test give the same wrong result. > > What else should I test to solve this problem ? > > Thank you for your help!!!!!!!!!!!!!!!!! > >!!!!!!!!!!!!!!!!!!!!!!!!!!!!Ding Xunlei >!!!!!!!!!!!!!!!!!!!!!!!!!!!!2004-03-13 >______________________________________________ >Ding Xunlei, Ph.D. Candidate >Open Laboratory of Bond Selective Chemistry >University of Science & Technology of China >Hefei, Anhui 230026, P.R.China >Tel.: 0086-551-3603418 >Fax.: 0086-551-3602969 >E-mail: dxl*at*mail.ustc.edu.cn >Http://www.bsc.ustc.edu.cn/~dxl > > > > > > >-= 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 >and send your message to: CHEMISTRY*at*ccl.net > >Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST*at*ccl.net >HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs > >If your mail is bouncing from CCL.NET domain send it to the maintainer: >Jan Labanowski, jlabanow*at*nd.edu (read about it on CCL Home Page) >-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > > > >. = = = = = = = = = = = = = = = = = = = = From chemistry-request@ccl.net Mon Mar 15 16:17:10 2004 Received: from mail.uh.edu (SanJacinto.Mail.UH.EDU [129.7.235.116]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i2FLG7js025757 for ; Mon, 15 Mar 2004 16:16:38 -0500 Received: from conversion-daemon by mail.uh.edu (Sun Internet Mail Server sims.4.0.2001.07.26.11.50.p9) id <0HUM00E01Z5NKW[at]mail.uh.edu> for chemistry[at]ccl.net; Mon, 15 Mar 2004 15:17:51 -0600 (CST) Received: from localhost (Colorado.Mail.UH.EDU [129.7.235.114]) by mail.uh.edu (Sun Internet Mail Server sims.4.0.2001.07.26.11.50.p9) with ESMTP id <0HUM00DEKZ5MLY[at]mail.uh.edu> for chemistry[at]ccl.net; Mon, 15 Mar 2004 15:17:46 -0600 (CST) Date: Mon, 15 Mar 2004 15:17:46 -0600 (CST) From: Niharendu.Choudhury[at]mail.uh.edu Subject: Hydrogen bond calculation from MD trajectory To: chemistry[at]ccl.net Message-id: <482578373.1079385466421.JavaMail.root@localhost> MIME-version: 1.0 X-Mailer: Sun(TM) Web Access 1.2 Content-type: text/plain; charset=ISO-8859-1 Content-transfer-encoding: 7BIT X-Spam-Status: No, hits=0.3 required=7.0 tests=NO_REAL_NAME autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Hi everyone, Can anybody tell me about any available Fortran program for calculating average number of hydrogen-bond (say using geometric criteria) in water from the saved coordinate file from MD run? When I tried to calculate it by using following three gepmetric criteria for H-bond: (1)oxygen-oxygen distance less than 3.5 Angs. (2)oxygen of atom 1 and hydrogen of atom 2 diatance less than 2.5 Angs. (3)oxygen(1) oxygen(2) hydrogen bond angle less than 30 deg I found only around 3200 pairs (I have 1800 SPC/E water molecules) which fulfils simultaneously all the three criteria. Now, if I divide it by no of molecules (1800 in this case), no of hydrogen bonds per water molecules comes around 1.77 whereas reported value is around 3.5 in bulk water. I would appreciate any help. Niharendu Choudhury Univ. Houston Houston,TX From chemistry-request@ccl.net Mon Mar 15 15:48:13 2004 Received: from sentinel.ucr.edu (sentinel.ucr.edu [138.23.226.228]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i2FKmCjs024491 for ; Mon, 15 Mar 2004 15:48:13 -0500 Received: from dopetec (dunn4470.ucr.edu [138.23.156.82]) by sentinel.ucr.edu (Mirapoint Messaging Server MOS 3.3.8-GR) with ESMTP id AWJ95318 for ; Mon, 15 Mar 2004 12:50:31 -0800 (PST) Reply-To: From: "Donald Keidel" To: Subject: CCL: program to determine structurally important water molecules Date: Mon, 15 Mar 2004 12:50:16 -0800 Organization: UCR Message-ID: <000101c40acf$1ecdd350$529c178a@dopetec> MIME-Version: 1.0 Content-Type: text/plain; charset="us-ascii" X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook, Build 10.0.4510 Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1165 X-Spam-Status: No, hits=0.0 required=7.0 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id i2FKmDjs024499 Hello, I am looking for a program (free preferentially) that can find water molecules in a coordinate file (e.g. pdb) that are structurally important for the structure of the protein or macromolecule in question and find those that might not be that important. Does anyone know if such a program exists. I will summarize my results. Don ---------------------------------------------------------------------------- ----------------------------------- Donald J. Keidel University of California, Riverside Department of Biochemistry and Molecular Biology Riverside, CA 92521 phone: (909) 787-5493 fax: (909) 787-4434 dopetec[at]dslextreme.com webpage: www.biochemistry.ucr.edu/gru/gradstudents/don_keidel/index.htm From chemistry-request@ccl.net Mon Mar 15 20:25:55 2004 Received: from mx1.ustc.edu.cn ([218.22.21.1]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i2G1Prjs031832 for ; Mon, 15 Mar 2004 20:25:54 -0500 Received: from dxl ([210.45.66.65]) by mx1.ustc.edu.cn (8.8.7/8.8.6) with ESMTP id JAA16560; Tue, 16 Mar 2004 09:18:13 +0800 Message-Id: <200403160118.JAA16560|at|mx1.ustc.edu.cn> Date: Tue, 16 Mar 2004 9:21:6 +0800 From: "6!Q8@W" Reply-To: dxl|at|mail.ustc.edu.cn To: Mikael Johansson , CCL Subject: Re: Re: CCL:HOMO energy is higher than LUMO ! Organization: VP9z?F4sQ!<|;/Q'J5QiJR X-mailer: Foxmail 4.1 [cn] Mime-Version: 1.0 Content-Type: text/plain; charset="GB2312" X-Spam-Status: No, hits=4.9 required=7.0 tests=DATE_IN_PAST_06_12, HEAD_ILLEGAL_CHARS autolearn=no version=2.61 X-Spam-Level: **** X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id i2G1Ptjs031836 Dear Mikael#: !!!!But I need the result of PW91PW91, for this is only one part of a serial work. Thank you for your help!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!Ding Xunlei !!!!!!!!!!!!!!!!!!!!!!!!!!!!2004-03-16 ______________________________________________ Ding Xunlei, Ph.D. Candidate Open Laboratory of Bond Selective Chemistry University of Science & Technology of China Hefei, Anhui 230026, P.R.China Tel.: 0086-551-3603418 Fax.: 0086-551-3602969 E-mail: dxl|at|mail.ustc.edu.cn Http://www.bsc.ustc.edu.cn/~dxl ======= 2004-03-15 16:23:00 You have written: ======= >Hello! > >On Sat, 13 Mar 2004, 6!Q8@W wrote: > >> !!!!One result in my calculation with Gaussian03 PW91PW91 surprised me. >> The energy of alfa HOMO is higher than the energy of beta LUMO. >> I have test to use stable=opt, guess=alter, guess=mix , >> and guess=read (read the correct result from B3LYP calculation), >> but all these test give the same wrong result. > >(I assume that changing the occupation doesn't help.) With pure >(non-hybrid) density functionals this can happen. The energy of the >occupied orbitals are artificially raised. With a hybrid functional like >B3LYP, the problem is partly remedied, and the HOMO-LUMO gap increases. > >If you really need the virtual orbitals to be higher in energy, then the >quickest solution is to use a hybrid functional. Perhaps an electronic >self-interaction correction could be applicable, also. I don't know if >Gaussian does this, though. > >Have a nice day, > Mikael J. > http://www.helsinki.fi/~mpjohans/ > >. = = = = = = = = = = = = = = = = = = = = From chemistry-request@ccl.net Mon Mar 15 23:49:33 2004 Received: from mercury.ccmr.cornell.edu (mercury.ccmr.cornell.edu [128.84.231.97]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i2G4nVjs004403 for ; Mon, 15 Mar 2004 23:49:31 -0500 Received: from lock.ccmr.cornell.edu (lock.ccmr.cornell.edu [128.84.241.198]) by mercury.ccmr.cornell.edu (8.12.10/8.12.10) with ESMTP id i2G4poqj022742 for ; Mon, 15 Mar 2004 23:51:52 -0500 Received: from localhost (cc236@localhost) by lock.ccmr.cornell.edu (8.12.10/8.12.10) with ESMTP id i2G4pkUk026467 for ; Mon, 15 Mar 2004 23:51:50 -0500 Date: Mon, 15 Mar 2004 23:51:46 -0500 (EST) From: Connie Chang To: chemistry!at!ccl.net Subject: CCL:G03 and LINDA error Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Spam-Status: No, hits=0.9 required=7.0 tests=FROM_ENDS_IN_NUMS autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Hi CCLer's: Does anyone know what the following error is for a LINDA frequency in G03 job? PrismC: NFx= 2048 NFxT= 4 NFxU= 4. PrismC: NFx= 2048 NFxT= 4 NFxU= 4. There are 219 degrees of freedom in the 1st order CPHF. 219 vectors were produced by pass 0. AX will form 110 AO Fock derivatives at one time. PrismC: NFx= 2048 NFxT= 4 NFxU= 4. MaxFPS too small in GenRh1. Error termination via Lnk1e at Fri Mar 12 02:44:39 2004. THanks, Connie