From owner-chemistry@ccl.net Mon Nov 7 04:01:00 2005 From: "Carsten Detering detering---biosolveit.de" To: CCL Subject: CCL: how to find active site? Message-Id: <-29888-051107034506-23765-0jtokRp/jbtQJvYadJjo0Q_._server.ccl.net> X-Original-From: Carsten Detering Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=GB2312 Date: Mon, 07 Nov 2005 08:48:44 +0100 MIME-Version: 1.0 Sent to CCL by: Carsten Detering [detering#%#biosolveit.de] Hi Yuan, In a protein-ligand structure, the active site is usually where the ligand sits. Should you have the protein structure only, you can perform a "blind" docking as a rough estimate. Take your entire protein structure and define it as the active site. Statistically you can then tell from how many ligand poses where genereated at the same spot where you will likely find your active site. Hope this helps, Carsten Zhao Yuan ccl%%mail.sioc.ac.cn wrote: > Hi, Everyone! > > I will very appreciate if somebody lets me know how to find an active site > from a protein-ligand structure? > Thank you! > > Steven > > From owner-chemistry@ccl.net Mon Nov 7 07:56:00 2005 From: "Gustavo Mercier gamercier ~~ yahoo.com" To: CCL Subject: CCL: whereabouts HESS2FF software Message-Id: <-29889-051107075413-31196-IyQ5G8YICWJHSAT//cVxTw : server.ccl.net> X-Original-From: "Gustavo Mercier" Sent to CCL by: "Gustavo Mercier" [gamercier/./yahoo.com] Hi! Does anyone know from where can I download the program HESS2FF? The following reference writes about the program, but there are only vague descriptions of the algorithm and no information as to where to request the program (if at all possible!) Acta Cryst. 2003, D59, 274-289. thanks for your help! GMercier BUMC gamercier- -yahoo.com gustavom- -baylorhealth.edu From owner-chemistry@ccl.net Mon Nov 7 09:49:00 2005 From: "Ian Hovell HOVELL|a|cetem.gov.br" To: CCL Subject: CCL:G: specifying solvent using IPCM Message-Id: <-29890-051107094723-25943-DhvkCYMZPYuc+pChcLNVDw{}server.ccl.net> X-Original-From: Ian Hovell Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01C5E3B2.441C0CE0" Date: Mon, 7 Nov 2005 12:45:23 -0300 MIME-Version: 1.0 Sent to CCL by: Ian Hovell [HOVELL^_^cetem.gov.br] This message is in MIME format. Since your mail reader does not understand this format, some or all of this message may not be legible. ------_=_NextPart_001_01C5E3B2.441C0CE0 Content-Type: text/plain; charset="iso-8859-1" Dear CCLers, I can specify a non standard solvent in a PCM calculation using G03W using the option "read" in the SCRF keyword. I would have thought the the same procedure holds for IPCM. Can someone enlighten me as to whether it is possible to define a non standard solvent using the IPCM method and if so how. TIA Ian Hovell - Ph.D. NUCLEO DE MODELAGEM MOLECULAR-NMM Centro de Tecnologia Mineral - CETEM Ministerio da Cincia e da Tecnologia- MCT Avenida Ip, No 900 - Cidade Universitaria Ilha do Fundo Rio de Janeiro RJ Brasil CEP 21941-590 tel 00 55 (xx) 3865 7344 ou 3865 - 7216 Fax 00 55 (xx) 22602837 ou 2290-4286 e-mail hovell]=[cetem.gov.br ------_=_NextPart_001_01C5E3B2.441C0CE0 Content-Type: text/html; charset="iso-8859-1"
Dear CCLers,
I can specify a non standard solvent in a PCM calculation using G03W using the option "read" in the SCRF keyword. I would have thought the the same procedure holds for IPCM. Can someone enlighten me as to whether it is possible to define a non standard solvent using the IPCM method and if so how.
 
TIA
Ian Hovell - Ph.D.
NUCLEO DE MODELAGEM MOLECULAR-NMM
Centro de Tecnologia Mineral - CETEM
Ministerio da Cincia e da Tecnologia- MCT
Avenida Ip, No 900 - Cidade Universitaria
Ilha do Fundo Rio de Janeiro RJ Brasil
CEP 21941-590
tel 00 55 (xx) 3865 7344 ou 3865 - 7216
Fax 00 55 (xx) 22602837 ou 2290-4286
e-mail hovell]=[cetem.gov.br
 
------_=_NextPart_001_01C5E3B2.441C0CE0-- From owner-chemistry@ccl.net Mon Nov 7 13:39:00 2005 From: "Monika Rella bmbmre(!)bmb.leeds.ac.uk" To: CCL Subject: CCL: how to find active site? Message-Id: <-29891-051107131733-25735-uQQQypgINDId3jiHpJLVUw;;server.ccl.net> X-Original-From: Monika Rella Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Mon, 7 Nov 2005 17:30:54 +0000 MIME-Version: 1.0 Sent to CCL by: Monika Rella [bmbmre],[bmb.leeds.ac.uk] Hi Steven, One of my colleagues wrote a piece of software (an energy based method) that helps you to quickly identify the active site on a protein in absence of a bound ligand. You just need to upload your protein structure at http://www.bioinformatics.leeds.ac.uk/qsitefinder/ Hope that may be useful! Monika From owner-chemistry@ccl.net Mon Nov 7 14:31:01 2005 From: "Ren AiMin aren;;uoguelph.ca" To: CCL Subject: CCL: how to set the overlap weighting factors in hyperchem software! Message-Id: <-29892-051107113851-31920-6RG2/F0mqxkP3LllHwuK1w:_:server.ccl.net> X-Original-From: Ren AiMin Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Mon, 7 Nov 2005 10:52:45 -0500 MIME-Version: 1.0 Sent to CCL by: Ren AiMin [aren*o*uoguelph.ca] Ren yanliang, 1.267, 0.585 is correct. Ai-Min REN Quoting "renyanliang yanliangren_2002{}yahoo.com.cn" : > Sent to CCL by: renyanliang [yanliangren_2002 : yahoo.com.cn] > Hi, everyone: > when I calculated the electronic spectrum by using > ZINDO/1 method in hyperchem, the result shows large > difference compared with the experimental spectrum. > And I found that the change of "overlap weighting > factors" have significant effects on the spectrum. The > default value for ZINDO/1 method in hyperchem is 1,1, > while that for ZINDO/S is 1.267, 0.585, I am wondering > which is correct. Who can give me some advice to get > the correct results. > Best Regard! > > > > ___________________________________________________________ > ÑÅ»¢Ãâ·ÑGÓÊÏ䣭No.1µÄ·À¶¾·ÀÀ¬»ø³¬´óÓÊÏä > http://cn.mail.yahoo.com> > > > From owner-chemistry@ccl.net Mon Nov 7 15:06:00 2005 From: "Jens Spanget-Larsen spanget^^^virgil.ruc.dk" To: CCL Subject: CCL:G: transition moments Message-Id: <-29893-051107130143-17269-nZe0AcuCcnkNnvDr8n0JNQ..server.ccl.net> X-Original-From: "Jens Spanget-Larsen" Content-description: Mail message body Content-transfer-encoding: 7BIT Content-type: text/plain; charset=US-ASCII Date: Mon, 7 Nov 2005 18:02:08 +0100 MIME-Version: 1.0 Sent to CCL by: "Jens Spanget-Larsen" [spanget#,#virgil.ruc.dk] Dear Orlin, in the Gaussian FREQ job, include IOP(7/33=1). The output will contain the dipole derivatives dMx/Q, dMy/dQ, and dMz/dQ with respect to the normal modes Q (x, y, and z in the 'standard orientation'): Dipole derivatives wrt mode 1: -3.69200D-01 -1.19305D+00 -1.99521D-07 Dipole derivatives wrt mode 2: -1.75385D-07 2.40980D-07 3.56555D-01 Dipole derivatives wrt mode 3: -5.71819D-07 -3.58901D-07 3.70369D-01 Dipole derivatives wrt mode 4: -2.44104D-01 1.06179D+00 -3.25447D-07 etc. Jens >--< On 4 Nov 2005 at 7:26, Orlin Blajiev blajiev^_^vub.a wrote: > > Sent to CCL by: "Orlin Blajiev" [blajiev~~vub.ac.be] > Hi everybody, > > I will very appreciate if somebody lets me know how to get the direction of the vibrational transition dipole moments out of the Gaussian or Gamess output. They can be visualized by Gaussview, but I do not know how to relate them to the molecular coordination system. > > Thank you in advance. > > Orlin > > blajiev|vub ac be >---------------------------------------------------------< JENS SPANGET-LARSEN Office: +45 4674 2710 Department of Chemistry Fax: +45 4674 3011 Roskilde University (RUC) Mobile: +45 2320 6246 P.O.Box 260 E-Mail: spanget++ruc.dk DK-4000 Roskilde, Denmark http://virgil.ruc.dk/~spanget >---------------------------------------------------------< From owner-chemistry@ccl.net Mon Nov 7 20:44:00 2005 From: "Renxiao Wang renxiao:_:med.umich.edu" To: CCL Subject: CCL: The PDBbind database version 2004 is being released Message-Id: <-29894-051107204135-23957-sVf7SkGw2sT8ozDhdV32+w(0)server.ccl.net> X-Original-From: "Renxiao Wang" Sent to CCL by: "Renxiao Wang" [renxiao : med.umich.edu] Dear researchers, We are glad to announce a new release of the PDBbind database, i.e. v.2004. The PDBbind database, publicly accessible at http://www.pdbbind.org/, is constructed to provide a collection of binding affinity data for the protein-ligand complexes in the Protein Data Bank (PDB). This updated version has binding affinity data (Kd, Ki, & IC50) for over 2,200 protein-ligand complexes released by PDB before 01/01/2005. The PDBbind database is developed in Dr. Shaomeng Wang's group at the University of Michigan. All of the current registered users may still access this database through their existing accounts. Other researchers who are interested are welcome to explore it through a demo account set on our web site. Best regards, Renxiao Wang, Ph.D. Research Investigator University of Michigan Medical School From owner-chemistry@ccl.net Mon Nov 7 22:04:00 2005 From: "Eric Scerri scerri%a%chem.ucla.edu" To: CCL Subject: CCL: Message-Id: <-29895-051107215551-13554-M2hcsbV1OYEEwgFvnY747Q_+_server.ccl.net> X-Original-From: Eric Scerri Content-Type: multipart/alternative; boundary=Apple-Mail-27-639855915 Date: Mon, 7 Nov 2005 18:53:14 -0800 Mime-Version: 1.0 (Apple Message framework v734) Sent to CCL by: Eric Scerri [scerri ~~ chem.ucla.edu] --Apple-Mail-27-639855915 Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed > > > Foundations of Chemistry > > > > Philosophical, Historical, Educational and Interdisciplinary > Studies of Chemistry > Editor-in-Chief: E.R. Scerri > > > ISSN: 1386-4238 (print version) > ISSN: 1572-8463 (electronic version) > Journal no. 10698 > Springer Netherlands > > > > > > Most viewed articles > > > > Most viewed articles are the full-text articles from this journal > that have been accessed most frequently within the last 90 days. > The collection of most viewed articles below is updated weekly. > > > > 1. The Ontological Autonomy Of The Chemical World > Lombardi, O., Labarca, M. > Published Print: January 2005 > > 2. Book Review: Jaap van Brakel: Philosophy of Chemistry: Between > the Manifest and the Scientific Image Leuven University Press, > Leuven, 2000, xiv + 246 pp., ISBN 90-5867-063-5 > Hendry, R.F. > Published Print: January 2005 > > > 3. Chemistry and a Theoretical Model of Science: On the Occasion of > a Recent Debate with the Christies > Vihalemm, R. > Published Print: January 2005 > > > 4. Explaining Models: Theoretical and Phenomenological Models and > Their Role for the First Explanation of the Hydrogen Spectrum > Wilholt, T. > Published Print: January 2005 > > > 5. Editorial 19 Special Issue on Philosophical Problems of Chemical > Kinds > Scerri, E. > Published Print: January 2005 > > > > Dr. Eric Scerri, Department of Chemistry & Biochemistry, UCLA, Los Angeles, CA 90095-1569 E-mail scerri===chem.ucla.edu Tel: 310 206 7443 Web Page http://www.chem.ucla.edu/dept/Faculty/scerri/ Editor of Foundations of Chemistry, http://www.springer.com/sgw/cda/frontpage/0,11855,5-0-70-35545882-0,00.h Also see International Society for the Philosophy of Chemistry http://ispc.sas.upenn.edu/ --Apple-Mail-27-639855915 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=ISO-8859-1




Foundations of = Chemistry
<= BR>

Philosophical, Historical, = Educational and Interdisciplinary Studies of = Chemistry
Editor-in-Chief: E.R. = Scerri

ISSN: 1386-4238 (print = version)
ISSN: 1572-8463 (electronic = version)
Journal no. = 10698
Springer = Netherlands




Most viewed = articles


Most viewed articles are = the full-text articles from this journal that have been accessed most = frequently within the last 90 days. The collection of most viewed = articles below is updated weekly.


1. The Ontological = Autonomy Of The Chemical WorldLombardi, O., Labarca, = M.Published Print: January = 2005

Published Print: January = 2005

Vihalemm, R.Published Print: January = 2005


Scerri, E.Published Print: January = 2005




=
Dr. Eric = Scerri,
Department of Chemistry & = Biochemistry,
UCLA,
Los Angeles,
CA = 90095-1569

Te= l: 310 206 7443

Web Page

Editor of Foundations of = Chemistry,=A0


Also see International Society for = the Philosophy of Chemistry

=A0

=
= --Apple-Mail-27-639855915-- From owner-chemistry@ccl.net Mon Nov 7 23:42:00 2005 From: "janl||speakeasy.net" To: CCL Subject: CCL: Now you can filter your CCL mail and new services from CCL Message-Id: <-29896-051107233715-29824-buP2tiyDcTYim3lp9OSojw#%#server.ccl.net> X-Original-From: janl.#%#.speakeasy.net Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="iso-8859-1" Date: Tue, 08 Nov 2005 04:37:09 +0000 MIME-Version: 1.0 Sent to CCL by: janl~~speakeasy.net Dear CCL Members, I would like to announce the availability of the CCL mail filter gizmo. http://www.ccl.net/chemistry/resources/tips/filter.shtml Now you can filter out CCL messages that you do not want to receive. Use of the filter is optional. If you do not set up the filter you will get all CCL messages. While this is not an easy tool to use, you have a lot of flexibility. You will need to learn the basics of Perl regular expressions (flexible text matches). Check: http://server.ccl.net/chemistry/resources/tips/regular_expressions.shtml if you are not familiar with them. Perl is a very powerful language for text processing (among others) and time spent on learning Perl will be returned manifold through your increased productivity that will free you from boring, and repetitive editing tasks. The filter requires you to specify a number of regular expressions and their "score". The scores of the expressions that matched the message are added and if the sum is not negative, the message is delivered to you. Report bugs to me, since it not tested well. I use also this occasion to appeal to your good will and ask for you support for CCL. I really need it. The new support options are available. Check: http://www.ccl.net/chemistry/aboutccl/supporting Beside the Job Advertising (got several kudos lately -- it really works!) you can now: 1) announce your workshops and conferences 2) place advertising banner of your organization on CCL Web pages 3) buy DVD with CCL archives Please do not look at it as a charity. CCL site is a well visited and indexed by all major Search Engine robots. Placing your ad on CCL will enhance your score on Google and bring good publicity and visibility. Let your boss and/or friends know about these opportunities. The fresh copy of the CCL archives will allow you to search 2.5 Gigabytes of CCL accumulated content on your local computer. Your support is essential for keeping CCL running and my work on its improvement. Your CCL Unmoderator Jan Labanowski jkl . ccl.net