From chemistry-request@ccl.net Tue Oct 28 01:20:21 2003 Received: from ns0.scripps.edu (ns0.scripps.edu [192.42.82.58]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h9S6Jmch022155 for ; Tue, 28 Oct 2003 01:19:49 -0500 Received: from antigen.scripps.edu (antigen.scripps.edu [137.131.200.100]) by ns0.scripps.edu (8.11.7/TSRI-4.2rx) with SMTP id h9S6Jmh28377 for ; Mon, 27 Oct 2003 22:19:48 -0800 (PST) Received: from relay1.scripps.edu(137.131.200.29) by antigen.scripps.edu via csmap id 9838; Mon, 27 Oct 2003 22:21:37 -0800 (PST) Received: from gamow.scripps.edu (gamow [137.131.252.67]) by relay1.scripps.edu (8.11.7/TSRI-4.4.1rAVB) with ESMTP id h9S6IPI20876; Mon, 27 Oct 2003 22:18:25 -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 WAA542601; Mon, 27 Oct 2003 22:18:24 -0800 (PST) Received: by quine.scripps.edu (sSMTP sendmail emulation); Mon, 27 Oct 2003 22:21:17 -0800 Date: Mon, 27 Oct 2003 22:21:17 -0800 From: "David A. Case" To: Joey Harriman Cc: chemistry)at(ccl.net Subject: Re: CCL:Implicit MD simulations in AMBER Message-ID: <20031028062117.GA3848)at(scripps.edu> References: <1067004617.3f9932c9668c8)at(webmail.unb.ca> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline In-Reply-To: <1067004617.3f9932c9668c8)at(webmail.unb.ca> User-Agent: Mutt/1.4i X-Spam-Status: No, hits=-5.2 required=7.0 tests=EMAIL_ATTRIBUTION,IN_REP_TO,QUOTED_EMAIL_TEXT,REFERENCES, REPLY_WITH_QUOTES,SIGNATURE_LONG_DENSE,USER_AGENT_MUTT version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) On Fri, Oct 24, 2003, Joey Harriman wrote: > > I am currently in the process of running some implicit MD simulations in > Amber7. As far > as I can tell the only flags that need to be included in the MD input file are: > gbsa=1 > igb=1 > extdiel=*** > > Can anyone confirm this? In addition, I am trying to do a MD simulation on > a ligand in Toluene (extdiel=2.4)...are there any suggestions to make this > calculation faster? I am currently usine SHAKE 2 for the calculations. You also need to set ntb=0 to get a non-periodic simulation. Of course, any other options you want are required as well. Note that the GB model has not been characterized very well for non-aqueous solvents, so you should proceed with caution. ..good luck...dac -- ================================================================== David A. Case | e-mail: case)at(scripps.edu Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896 The Scripps Research Institute | phone: +1-858-784-9768 10550 N. Torrey Pines Rd. | home page: La Jolla CA 92037 USA | http://www.scripps.edu/case ================================================================== From chemistry-request@ccl.net Mon Oct 27 18:58:41 2003 Received: from home.delsci.net (adsl-64-166-142-98.dsl.snfc21.pacbell.net [64.166.142.98]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h9RNw9ch012008 for ; Mon, 27 Oct 2003 18:58:09 -0500 Received: from Ultra2 (router.delsci.net [192.168.0.1]) by home.delsci.net (8.11.6/8.11.6) with ESMTP id h9S07ka13203; Mon, 27 Oct 2003 16:07:46 -0800 From: "Warren L. DeLano" To: Cc: "'Phil Hultin'" Subject: PyMOL 0.92 Released (plus RE:Advertising) Date: Mon, 27 Oct 2003 15:58:09 -0800 Message-ID: <000001c39ce6$2c88f490$0c00a8c0@Ultra2> MIME-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook, Build 10.0.2627 Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1165 X-Spam-Status: No, hits=-0.5 required=7.0 tests=QUOTED_EMAIL_TEXT version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) PyMOL 0.92 is available for download from http://pymol.sf.net at your convenience. This new release will be more useful to students, educators, and scientists for the following reasons: 1) PyMOL can now assign secondary structure rapidly. 2) PyMOL now renders faster and generates sharper images. 3) PyMOL can now be used more effectively as a Python module. 4) PyMOL now supports new map file formats (AVS/MEAD, O/BRIX, Biosym GRID). 5) Numerous bugs and user requests have been addressed. End Announcement. Begin Comment on CCL:Advertising. From: Phil Hultin Sent: Friday, October 24, 2003 8:37 AM To: Computational Chemistry List Subject: CCL:Advertising ... >I have observed an increase in the number of commercial advertisements (as distinct from >comments suggesting that one program/product does a particular task better or worse than > another, coming from persons with no direct connection to the products in question) over > the last year or so, and I think this has no place on this discussion list. ... Hopefully Dr. Hultin won't construe this post as inappropriate "commercial" advertising given that PyMOL is Open-Source and freely available, even though we exist as a business in order to maintain, develop, and support the package. It is also worth pointing out that most academic scientists aren't even able to create unrestricted Open-Source tools like PyMOL due to University technology transfer and software licensing policies. Thus, a blanket prejudice against all commercial entities is un-"warren"-ted, given present conditions. Ironically, I had to form a private commercial entity because that was the only way we could be free to make truly open-ended, Open-Source contributions to Science as a lasting career pursuit. Eventually academia and the funding agencies will recognize the potential of Open-Source software to enable fundamental, ubiquitous, and cumulative advances. But until then, we have to operate by whatever means are available. Of course, many commercial entities do tend to behave as if making money is the sole purpose of their existence, and that *is* indeed the purpose for companies owned by dispassionate shareholders whose sole demand is maximed return on investment (i.e. most big businesses). But the same does not apply to small, private, scientist-owned companies (truly OWNED, not just scientist-managed), and there are many such companies who post to CCL (from Santa Fe, Montreal, or California -- just to hint at a few examples). Most scientist-owned companies are simply trying to create and disseminate great tools capable of enabling great science. As scientists, we share your love of progress and discovery at a personal level. That is what drives us -- not the bottom line. We are not in the same league as the scientific software "giants", and that is by choice. We play a different game and do it for different reasons. DeLano Scientific demonstrates this most explicitly by sharing source code, and thereby permanently slaying the nefarious License Daemon, but that is just one of many ways in which companies can show a commitment to science and progress over profit maximization. Please just keep this in mind when evaluating CCL posts from commercial entities, since there are important distinctions to be made. Yes, some companies act like extortive tyrants, but others behave like friendly academic labs. Look to company ownership and past conduct for guidance on future behavior. If CCL is not enriched by certain commerical posts, then by all means take up the issue with that particular company, but please don't uniformly discourage commercial entities from participating in the community. Some companies are more like you than you may realize, and most would appreciate advice on how to become better net citizens, if provided discretely. Cheers, Warren -- mailto:warren:at:delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 From chemistry-request@ccl.net Mon Oct 27 21:02:54 2003 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 h9S22Nch015349 for ; Mon, 27 Oct 2003 21:02:23 -0500 Received: from dopetec (dunn4470.ucr.edu [138.23.156.82]) by sentinel.ucr.edu (Mirapoint Messaging Server MOS 3.2.1-GA) with ESMTP id ASJ24873 for ; Mon, 27 Oct 2003 18:02:22 -0800 (PST) Reply-To: From: "Donald Keidel" To: Subject: Program to search SD/MDL formatted files from chemical companies Date: Mon, 27 Oct 2003 18:02:14 -0800 Organization: UCR Message-ID: <000101c39cf7$81cc2240$529c178a@dopetec> MIME-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook, Build 10.0.3416 Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1165 X-Spam-Status: No, hits=0.0 required=7.0 tests=none version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Hello, I am looking for a program to search SD/MDL formatted files (chemical company libraries of compounds). I have found ISIS/Base and 3DFS, but I was wondering if anyone knows of others that might be cheaper than ISIS/Base (hopefully free), but commercial examples would be of great help also. Thank you in advance to anyone who reads and responds to this request. Have a great day. 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 Tue Oct 28 03:00:13 2003 Received: from ozone.cs.vu.nl (ozone.cs.vu.nl [130.37.24.158]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h9S7xgch025052 for ; Tue, 28 Oct 2003 02:59:42 -0500 Received: from chem.vu.nl (far27.chem.vu.nl [130.37.148.106]) by ozone.cs.vu.nl with esmtp (Smail #87) id m1AEOlR-000NHMC; Tue, 28 Oct 2003 08:59 +0100 Message-ID: <3F9D4CD8.2010405/at/chem.vu.nl> Date: Mon, 27 Oct 2003 17:50:32 +0100 From: Anton Feenstra Organization: Vrije Universiteit Amsterdam - Pharmaceutical Chemistry User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.0; en-US; rv:1.4.1) Gecko/20031008 X-Accept-Language: en-us, en MIME-Version: 1.0 To: chemistry/at/ccl.net Subject: Re: CCL:a question about g(r) for heteroatoms References: <3f96fdb5.1796.17301/at/mail.rochester.edu> In-Reply-To: <3f96fdb5.1796.17301/at/mail.rochester.edu> Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=0.5 required=7.0 tests=DEAR_SOMETHING,IN_REP_TO,QUOTED_EMAIL_TEXT,REFERENCES, REPLY_WITH_QUOTES,USER_AGENT_MOZILLA_UA,X_ACCEPT_LANG version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) weiz wrote: > Dear Sir: > I have a problem to calculate the g(r) for heteroatoms. the system that I > am studying is a peptide in DMSO system.now I want to calculate the g(r) > for the polar H of peptide (which are [...] I'm sorry for not having read all of your question in detail, but I thought I might refer you to existing analysis tools in the Gromacs package. These are g_rdf for calculating g(r) of arbitrary selections of atoms in your system, and g_hbond for calculating hydrogen bonds and related properties. The tools will read concatenated pdb files as trajectory, which should cover possible output for almost any simulation package you might (wish to) use. Gromacs if available free of charge (and without registration) at www.gromacs.org, available in various pre-compiled binary packages but also as (usually easy to compile) source-code. -- Groetjes, Anton _____________ _______________________________________________________ | | | | _ _ ___,| K. Anton Feenstra | | / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam | |( | )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands | | \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610 | | | Feenstra/at/chem.vu.nl - www.chem.vu.nl/~feenstra/ | | | "If You See Me Getting High, Knock Me Down" | | | (Red Hot Chili Peppers) | |_____________|_______________________________________________________| From chemistry-request@ccl.net Mon Oct 27 17:35:48 2003 Received: from mail.ciq.uchile.cl (mail.ciq.uchile.cl [146.83.36.3]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h9RMZFch009617 for ; Mon, 27 Oct 2003 17:35:16 -0500 Received: from localhost (localhost [127.0.0.1]) by mail.ciq.uchile.cl (Postfix) with ESMTP id 5B6345404832; Mon, 27 Oct 2003 19:35:23 -0500 (EST) Received: from udft (unknown [172.16.92.143]) by mail.ciq.uchile.cl (Postfix) with SMTP id 3CC015403C36; Mon, 27 Oct 2003 19:34:05 -0500 (EST) Message-ID: <004001c39cda$99f8aa40$8f5c10ac@udft> Reply-To: "Diego Venegas Yazigi" From: "Diego Venegas Yazigi" To: "Computational Chemistry List" Subject: UDFT versus RODFT Date: Mon, 27 Oct 2003 19:31:24 -0300 Organization: CIMAT MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_002E_01C39CC0.E8B51020" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2800.1106 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1106 X-Virus-Scanned: by AMaViS perl-11 X-Spam-Status: No, hits=2.4 required=7.0 tests=ASCII_FORM_ENTRY,HTML_20_30,HTML_MESSAGE version=2.55 X-Spam-Level: ** X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) This is a multi-part message in MIME format. ------=_NextPart_000_002E_01C39CC0.E8B51020 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Dear CCLers I am performing calculations to a crystal structure of a dicopper = macrocycle. I did the UDFT and RODFT calculations using B3LYP and = LANL2DZ. The MO composition under UDFT theory level show a very low = metal character in the frontier orbitals, however the RODFT calculations = give a MO composition with the frontier orbitals with a large metal = character, being these results a more expectable description of a Werner = type complex. Does anybody have an experience in getting so different = results under both theory levels? Thanks a lot in advance Diego _________________________________________________ Dr. Diego Venegas-Yazigi Postdoctoral Researcher New Magnetic Materials Laboratory Centre for the Advanced and Interdisciplinary=20 Research in Material Science (CIMAT) Olivos 1007, Of. 313, Independencia, 8380492 Santiago, CHILE ----- W Ph. : 56 (2) 678-2801 Mobile : 56 (9) 841-8497 _________________________________________________ ------=_NextPart_000_002E_01C39CC0.E8B51020 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Dear CCLers
    I am performing calculations to a = crystal=20 structure of a dicopper macrocycle. I did the UDFT and RODFT = calculations using=20 B3LYP and LANL2DZ. The MO composition under UDFT theory level show = a very=20 low metal character in the frontier orbitals, however the RODFT = calculations=20 give a MO composition with the frontier orbitals with a large metal = character,=20 being these results a more expectable description of a Werner type = complex. Does=20 anybody have an experience in getting so different results under both = theory=20 levels?
Thanks a lot in advance
 
Diego
 
_________________________________________________
  = ;  =20 Dr. Diego Venegas-Yazigi
Postdoctoral Researcher
New Magnetic = Materials=20 Laboratory
Centre for the Advanced and Interdisciplinary
Research = in=20 Material Science (CIMAT)
Olivos 1007, Of. 313, Independencia,=20 8380492
Santiago, CHILE
-----
W Ph.  : 56 (2) = 678-2801
Mobile :=20 56 (9)=20 841-8497
_________________________________________________
<= /DIV>

------=_NextPart_000_002E_01C39CC0.E8B51020-- From chemistry-request@ccl.net Mon Oct 27 21:16:26 2003 Received: from adenine.cgl.ucsf.edu (socrates.cgl.ucsf.edu [169.230.27.3]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h9S2Fsch015607 for ; Mon, 27 Oct 2003 21:15:55 -0500 Received: from localhost (socrates.cgl.ucsf.edu [169.230.27.3]) by adenine.cgl.ucsf.edu (8.12.10/8.12.10/GSC1.16) with ESMTP id h9S2FqhH920864 for ; Mon, 27 Oct 2003 18:15:52 -0800 (PST) Date: Mon, 27 Oct 2003 18:15:52 -0800 (PST) From: Pradipta Bandyopadhyay To: chemistry~at~ccl.net Subject: ewald parameters for ST2 model of water!! Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Spam-Status: No, hits=0.0 required=7.0 tests=USER_AGENT_PINE version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Hi, My simulation with ST2 model of water shows large fluctuations of k-space energy with little change in geometry. Can anyone suggest me the optimum ewald parameters for ST2 model (separation parameter alpha and k-space vector threshold, Kmax)? thanks. Pradipta From chemistry-request@ccl.net Tue Oct 28 07:54:41 2003 Received: from mail1.rrz.Uni-Koeln.DE (mail1.rrz.Uni-Koeln.DE [134.95.100.208]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h9SCs9ch003046 for ; Tue, 28 Oct 2003 07:54:09 -0500 Received: from uni-koeln.de (relax.cubic.Uni-Koeln.DE [134.95.151.118]) by mail1.rrz.Uni-Koeln.DE (8.12.10/8.12.10) with ESMTP id h9SCs4r8005198 (version=TLSv1/SSLv3 cipher=RC4-MD5 bits=128 verify=NOT); Tue, 28 Oct 2003 13:54:07 +0100 (MET) Message-ID: <3F9E6672.7050609_at_uni-koeln.de> Date: Tue, 28 Oct 2003 13:52:02 +0100 From: Christoph Steinbeck Reply-To: c.steinbeck_at_uni-koeln.de Organization: Cologne University Bioinformatics Center User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.5) Gecko/20031013 Thunderbird/0.3 X-Accept-Language: en-us, en MIME-Version: 1.0 To: Donald Keidel CC: chemistry_at_ccl.net Subject: Re: CCL:Program to search SD/MDL formatted files from chemical companies References: <000101c39cf7$81cc2240$529c178a@dopetec> In-Reply-To: <000101c39cf7$81cc2240$529c178a@dopetec> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 8bit X-Virus-Scanned: by amavisd-new X-Spam-Status: No, hits=-2.6 required=7.0 tests=EMAIL_ATTRIBUTION,IN_REP_TO,QUOTED_EMAIL_TEXT,REFERENCES, REPLY_WITH_QUOTES,USER_AGENT_MOZILLA_UA,X_ACCEPT_LANG version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Donald Keidel wrote: > Hello, > > I am looking for a program to search SD/MDL formatted files (chemical > company libraries of compounds). I have found ISIS/Base and 3DFS, but I > was wondering if anyone knows of others that might be cheaper than > ISIS/Base (hopefully free), but commercial examples would be of great > help also. Thank you in advance to anyone who reads and responds to > this request. Have a great day. > > Don Don, not sure what exactly you mean by "to search SD/MDL formatted files". Our open source java library for structural chemo- and bioinformatics, The Chemistry Development Kit (CDK) [1] can read SD/MDL files and perform a number of operations on it, like searching for a particular substructure, etc. Other operations, like calculating certain descriptors, can be quickly implemented. The CDK lives on http://cdk.sourceforge.net. Feel free to contact the CDK development team on the cdk-devel_at_lists.sourceforge.net mailing list to discuss whatever CDK-related question you have. Cheers, Chris [1] Steinbeck, C.; Han, Y. Q.; Kuhn, S.; Horlacher, O.; Luttmann, E., Willighagen, E.; The Chemistry Development Kit (CDK): An open-source Java library for chemo- and bioinformatics. Journal of Chemical Information and Computer Sciences 2003, 43, 493-500. -- Dr. Christoph Steinbeck (e-mail: c.steinbeck_at_uni-koeln.de) Groupleader Junior Research Group for Applied Bioinformatics Cologne University BioInformatics Center (http://www.cubic.uni-koeln.de) Z|lpicher Str. 47, 50674 Cologne Tel: +49(0)221-470-7426 Fax: +49 (0) 221-470-7786 What is man but that lofty spirit - that sense of enterprise. ... Kirk, "I, Mudd," stardate 4513.3.. From chemistry-request@ccl.net Tue Oct 28 09:00:23 2003 Received: from fornells.imim.es (fornells.imim.es [193.147.240.141]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h9SDxpch005628 for ; Tue, 28 Oct 2003 08:59:52 -0500 Received: by fornells.imim.es with Internet Mail Service (5.5.2657.72) id ; Tue, 28 Oct 2003 14:59:05 +0100 Received: from imim.es (homer.imim.es [193.146.190.141]) by hpserv.imim.es with SMTP (Microsoft Exchange Internet Mail Service Version 5.5.2657.72) id VC28XT4J; Tue, 28 Oct 2003 15:04:30 +0100 From: Fabien Fontaine To: Donald Keidel Cc: chemistry~at~ccl.net Message-ID: <3F9E76D1.2040401~at~imim.es> Date: Tue, 28 Oct 2003 15:01:53 +0100 Organization: IMIM/UPF User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.0.2) Gecko/20030208 Netscape/7.02 X-Accept-Language: en-us, en MIME-Version: 1.0 Subject: Re: CCL:Program to search SD/MDL formatted files from chemical companies References: <000101c39cf7$81cc2240$529c178a@dopetec> Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=-2.1 required=7.0 tests=EMAIL_ATTRIBUTION,QUOTED_EMAIL_TEXT,REFERENCES, REPLY_WITH_QUOTES,USER_AGENT_MOZILLA_UA,X_ACCEPT_LANG version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) If you look for a free substructure search program, try obgrep which is a tool available at the open babel sourceforge web site http://sourceforge.net/projects/openbabel/ The program uses daylight SMART chemical language to perform the query (http://www.daylight.com/dayhtml/doc/theory/theory.smarts.html) Unfortunately, the program is not in the current release (1.100.1) for the moment, but you can get it by anonymous access to the CVS repository. Regards, Fabien Donald Keidel wrote: > Hello, > > I am looking for a program to search SD/MDL formatted files (chemical > company libraries of compounds). I have found ISIS/Base and 3DFS, but I > was wondering if anyone knows of others that might be cheaper than > ISIS/Base (hopefully free), but commercial examples would be of great > help also. Thank you in advance to anyone who reads and responds to > this request. Have a great day. > > 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 > > > > > > > -= 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, jkl~at~ccl.net (read about it on CCL Home Page) > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > > -- Fabien Fontaine Engineer in Biotechnology Computer-Assisted Drug Design Laboratory Research Group on Biomedical Informatics (GRIB) - IMIM/UPF Passeig Maritim de la Barceloneta, 37-49 Tel: +34 93 224 08 94 E-08003 Barcelona (Spain) Fax: +34 93 224 08 75 e-mail: ffontaine~at~imim.es http://www.imim.es/grib From chemistry-request@ccl.net Tue Oct 28 11:47:55 2003 Received: from aquarius.ime.eb.br (aquarius.ime.eb.br [200.20.120.44]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h9SGlNch012425 for ; Tue, 28 Oct 2003 11:47:23 -0500 Received: from epq.ime.eb.br (epq.ime.eb.br [200.20.120.217]) by aquarius.ime.eb.br (8.12.8/8.12.8) with ESMTP id h9SGlHKG014853 for ; Tue, 28 Oct 2003 14:47:21 -0200 Received: from EPQ/SpoolDir by epq.ime.eb.br (Mercury 1.48); 28 Oct 03 14:49:52 -0300 Received: from SpoolDir by EPQ (Mercury 1.48); 28 Oct 03 14:49:33 -0300 Received: from epq.ime.eb.br (200.20.123.218) by epq.ime.eb.br (Mercury 1.48) with ESMTP; 28 Oct 03 14:49:28 -0300 Message-ID: <3F9E8156.8000107_at_epq.ime.eb.br> Date: Tue, 28 Oct 2003 14:46:46 +0000 From: Teodorico Ramalho User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.3) Gecko/20030313 X-Accept-Language: en-us, en MIME-Version: 1.0 To: chemistry_at_ccl.net Subject: Gibbs and Helmontz Free Energy Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=-0.1 required=7.0 tests=USER_AGENT_MOZILLA_UA,X_ACCEPT_LANG version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Dear CCl 's I Have used the SCAAS (Surface Constraint All-Atom Solvent) model to calculate the Free energy of solvation through FDTI model in InsightII program. This mean that I use an ensemble (NVT). The values obtained are either Helmotz or Gibbs free energy ? I guess, the values should be of Helmontz free energy. Could I to compare my results with experimental data (free energy of Gibbs). In other way, which would it be correction factor? Could anyone help me about this? Thanks very much, Teodorico From chemistry-request@ccl.net Tue Oct 28 20:31:48 2003 Received: from ns.ciac.jl.cn ([202.98.16.1]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h9T1V7ch003497 for ; Tue, 28 Oct 2003 20:31:12 -0500 Received: from dell (localhost [127.0.0.1]) by ns.ciac.jl.cn (8.9.1/8.9.1) with SMTP id JAA02359 for ; Wed, 29 Oct 2003 09:36:56 +0800 (CST) Message-Id: <200310290136.JAA02359-.at.-ns.ciac.jl.cn> Date: Wed, 29 Oct 2003 9:35:37 +0800 From: zhijian WU Reply-To: zjwu-.at.-ns.ciac.jl.cn To: "chemistry-.at.-ccl.net" Subject: CCL: TDDFT problem Organization: ciac X-mailer: FoxMail 4.0 beta 1 [cn] Mime-Version: 1.0 Content-Type: text/plain; charset="GB2312" X-Spam-Status: No, hits=4.1 required=7.0 tests=BASE64_ENC_TEXT,INVALID_DATE,RCVD_IN_NJABL, RCVD_IN_UNCONFIRMED_DSBL,X_NJABL_OPEN_PROXY version=2.55 X-Spam-Level: **** X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from base64 to 8bit by server.ccl.net id h9T1Vmch003525 Hi, CCLers, I am trying to calculate the vertical excited states of AuCl2 cluster, but my calculation fails with the error message "Cannot mix post-SCF and DFT". Does anybody tell me how to solve the problem? My second question is: is it now possible to optimize the structure using TDDFT? input file: ----------------------------- %mem=512mb %chk=os2_tddft.chk # b3lyp/lanl2dz opt scf=(maxcycle=1024) Title Card Required 0 2 Au Cl 1 R Cl 1 R 2 180.0 R 1.8 --Link1-- %mem=512mb %chk=os2_tddft.chk #b3lyp/lanl2dz td=(nstates=5) scf=(direct,maxcycle=1024) density geom=check guess=read Title Card Required 0 2 ------------------- error message: ------------------ Excited state symmetry could not be determined. Excited State 5: ?Spin -?Sym 1.6080 eV 771.04 nm f=0.0000 11B -> 17B 0.99359 Cannot mix post-SCF and DFT. Error termination via Lnk1e in d:\G98W\l1002.exe. Job cpu time: 0 days 0 hours 1 minutes 12.0 seconds. ------------------ Thank you very much in advance for your help. Best wishes, Zhijian WU