From owner-chemistry@ccl.net Wed Sep 6 05:08:00 2006 From: "Bruce Palfey brupalf\a/umich.edu" To: CCL Subject: CCL: program for disulfide design Message-Id: <-32491-060906002953-14233-eTV4VU/pEWHPZfJVxI97+A/./server.ccl.net> X-Original-From: Bruce Palfey Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Date: Tue, 5 Sep 2006 23:18:30 -0400 Mime-Version: 1.0 (Apple Message framework v752.2) Sent to CCL by: Bruce Palfey [brupalf[]umich.edu] Does anyone know of a program that can scan through a protein structure and suggest residue pairs to mutate to create plausible cystine disulfides? ciao, Bruce From owner-chemistry@ccl.net Wed Sep 6 08:27:00 2006 From: "Antje Wolf antje.wolf^^scai.fraunhofer.de" To: CCL Subject: CCL: program for disulfide design Message-Id: <-32492-060906073049-10480-j7cOgrO9jvniDVVet6Fa8A.:.server.ccl.net> X-Original-From: Antje Wolf Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 06 Sep 2006 12:42:51 +0200 MIME-Version: 1.0 Sent to CCL by: Antje Wolf [antje.wolf]~[scai.fraunhofer.de] Dear Bruce, I have heard of a program called "Disulfide by Design". Have a look at: http://www.ehscenter.org/dbd/ Hope, this helps. Cheers, Antje Bruce Palfey brupalfa/umich.edu wrote: >Sent to CCL by: Bruce Palfey [brupalf[]umich.edu] >Does anyone know of a program that can scan through a protein >structure and suggest residue pairs to mutate to create plausible >cystine disulfides? > >ciao, >Bruce> > > > > > > -- Antje Wolf Fraunhofer-Institute for Algorithms and Scientific Computing (SCAI) Schloss Birlinghoven 53754 Sankt Augustin Tel.: +49 2241 14 2537 E-mail: Antje.Wolf^-^scai.fraunhofer.de Internet: http://www.scai.fraunhofer.de From owner-chemistry@ccl.net Wed Sep 6 09:02:00 2006 From: "Thammarat Aree thammarat.aree,gmail.com" To: CCL Subject: CCL: Force field of Si Message-Id: <-32493-060906034025-2274-RwpEagErFwFbICpQH7r4ng]|[server.ccl.net> X-Original-From: "Thammarat Aree" Date: Wed, 6 Sep 2006 03:40:25 -0400 Sent to CCL by: "Thammarat Aree" [thammarat.aree(~)gmail.com] Could you please suggest where to look for force fields of Si. I would like to use Lennard-Jones 12-6 parameters of Si-C, Si-H, Si-O, Si-N for docking. Thanks. Thammarat Aree thammarat.aree::gmail.com From owner-chemistry@ccl.net Wed Sep 6 11:11:00 2006 From: "Tom Sundius Tom.Sundius!^!helsinki.fi" To: CCL Subject: CCL: Fermi resonance & Vib spectroscopy Message-Id: <-32494-060906093944-20505-ViCaxYXM4LFX82dyMxm6RA~~server.ccl.net> X-Original-From: Tom Sundius Content-Type: MULTIPART/MIXED; BOUNDARY="1824380544-2092798488-1157547780=:238658" Date: Wed, 6 Sep 2006 16:03:00 +0300 (EEST) MIME-Version: 1.0 Sent to CCL by: Tom Sundius [Tom.Sundius,,helsinki.fi] This message is in MIME format. The first part should be readable text, while the remaining parts are likely unreadable without MIME-aware tools. --1824380544-2092798488-1157547780=:238658 Content-Type: TEXT/PLAIN; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: QUOTED-PRINTABLE Dear Aron, I would suggest to you to study some books on vibrational spectroscopy. A good introduction to start with would be Daniel C. Harris and Michael D. Bertolucci, "Symmetry and Spectroscopy", Dover Publ. 1989 (originally published by Oxford University Press 1978). A good theoretical textbook is S. Califano: "Vibrational States", J. Wiley & Sons, London (1976) These books should be available in good chemistry libraries. Best regards, Tom On Tue, 5 Sep 2006, Anil Aron anisamron . yahoo.com wrote: > Sent to CCL by: Anil Aron [anisamron|a|yahoo.com] > > --0-1943192406-1157406899=3D:47768 > Content-Type: text/plain; charset=3Diso-8859-1 > Content-Transfer-Encoding: 8bit > > Hello There, > I am basically from biology student and doing my Masters. I am not well = versed with spectroscopy & theory and in the process of learning. > > I am doing some vibrational calculations and I have couple of fundamenta= l doubts. > > 1) I would like to know how to assign the vibrations to the frequency fr= om theoretical data. I mean, how do I give the n1, n2, n3, =85. correspon= ding each frequency? (neu1, neu2, etc,) > > 2) About Fermi resonances. How do I select the bands/modes which form th= e Fermi resonance. > > Also could you any one of you suggest some online materials to read/ OR = > From where (books) to get some information related to these? I would really= appreciate any feedback from you. > > I guess some one in this list has asked questions similar to what I like= =2E > > > > Thanks, > Regards, > Aron Tom Sundius University of Helsinki, Dept of Physical Sciences phone +358-9-191 50672 P.O.Box 64, FIN-00014 Helsinki, Finland fax +358-9-191 50610 +++ for we know in part, and we prophesy in part +++ --1824380544-2092798488-1157547780=:238658-- From owner-chemistry@ccl.net Wed Sep 6 14:07:01 2006 From: "Juvenal Yosa Reyes jyosa#,#javeriana.edu.co" To: CCL Subject: CCL: path of reaction Message-Id: <-32495-060906133601-19487-bAxbLDssIDRZca5nF5VRVA*server.ccl.net> X-Original-From: Juvenal Yosa Reyes Content-disposition: inline Content-Transfer-Encoding: 8bit Content-type: text/plain; charset=iso-8859-1 Date: Wed, 06 Sep 2006 11:20:03 -0500 MIME-version: 1.0 Sent to CCL by: Juvenal Yosa Reyes [jyosa . javeriana.edu.co] Hi everyone I'm new in this business, I try to learn how I do to generated the calculations for a path of reaction, I search help with this, someone knows a tutorial that it can helpme, for any help thank you -- Juvenal Yosa Reyes MSc Bioquímica Computacional y Estructural y Bioinformática Departamento de Nutrición y Bioquímica Facultad de Ciencias Pontificia Universidad Javeriana Bogota-Colombia Carrera 7 No. 40 - 62 Tel: (571) 3208320 ext 4136 jyosa=javeriana.edu.co juvenal.yosa=gmail.com ___________________________________ AVISO LEGAL: El presente correo electronico no representa la opinion o el consentimiento oficial de la PONTIFICIA UNIVERSIDAD JAVERIANA. Este mensaje es confidencial y puede contener informacion privilegiada la cual no puede ser usada ni divulgada a personas distintas de su destinatario. Esta prohibida la retencion, grabacion, utilizacion, aprovechamiento o divulgacion con cualquier proposito. Si por error recibe este mensaje, por favor destruya su contenido y avise a su remitente. En este aviso legal se omiten intencionalmente las tildes. Este mensaje ha sido revisado por un sistema antivirus, por lo que su contenido esta libre de virus. This e-mail has been scanned by an antivirus system, so its contents is free of viruses. From owner-chemistry@ccl.net Wed Sep 6 16:03:01 2006 From: "=?ISO-8859-1?Q?Carlos_Javier_Nu=F1ez_Aguero?= carlosjn(~)ce.fis.unam.mx" To: CCL Subject: CCL: Force field of Si Message-Id: <-32496-060906150738-7829-YEkwq8kAyWsiojjstlR87A-.-server.ccl.net> X-Original-From: =?ISO-8859-1?Q?Carlos_Javier_Nu=F1ez_Aguero?= Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 06 Sep 2006 13:22:07 -0500 Mime-Version: 1.0 Sent to CCL by: =?ISO-8859-1?Q?Carlos_Javier_Nu=F1ez_Aguero?= [carlosjn^_^ce.fis.unam.mx] Hi, Thammarat Aree thammarat.aree,gmail.com wrote: >Could you please suggest where to look for force fields of Si. I would like to use Lennard-Jones 12-6 parameters of Si-C, Si-H, Si-O, Si-N for docking. Thanks. > > > maybe you can find this set of parameters in papers from Dr. Stephen H. Garofalini. See for example: o Litton & Garofalini, 2001. Modeling of hydrophobic wafer bonding by molecular dynamics simulations. Journal of Applied Physics 89 (11): 6013-6023 o Webb & Garofalini, 1998. Relaxation of silica glass surfaces before and after stress modification in a wet and dry atmosphere: molecular dynamics simulations. Journal of Non-Crystalline Solids 226: 47-57 and others. Hasta la proxima vez, Carlos N. -- No virus found in this outgoing message. Checked by AVG Free Edition. Version: 7.1.405 / Virus Database: 268.11.7/438 - Release Date: 9/5/2006 From owner-chemistry@ccl.net Wed Sep 6 17:24:00 2006 From: "Sengen Sun sengensun,,yahoo.com" To: CCL Subject: CCL: Help needed from Dr. Eric Scerri Message-Id: <-32497-060906172004-19667-O2JaOrffflujykOLamF5fw-.-server.ccl.net> X-Original-From: Sengen Sun Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-1 Date: Wed, 6 Sep 2006 14:20:02 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Sengen Sun [sengensun . yahoo.com] . Dear Dr. Scerri, . I noticed on the CCL that you advertised your FOCH journal/your book(s) over, and over, and over, ......, and over again. I hope that you and your organization have made a good profit from it. . I do recognize that your motivation for the advertisements is not only to make money, but also to stimulate scientific and philosophical discussions on theoretical chemistry. I greatly appreciate what you did as we have something in common in this regard. As a university Professor, a journal Editor, and a philosopher as you claimed, you must know well what you posted, you will take care of what you posted, and you are responsible to address some issues that other CCLers may have. . I read seriously and very carefully two FOCH papers. One is the recent one by Shahbazian & Zahedi, Published Print: February 2006. And the other is titled THEORETICAL CHEMISTRY by Roald Hoffmann (Foundations of Chemistry 2004, Volume 6: Page 11). . I have unresolvable conflicts in my mind on these two papers. Therefore, I have to consult you. Please kindly help me. And I will greatly appreciate it. . Here are some questions I have: . 1. In the statement "The sp3 hybridization of the carbon atom in methane causes its tetrahedral geometry", do you think the word "cause" is mis-used? If so, do you think the "mis-use" is justified? In the other words, do you think that correct use of words should be banned occassionally in science and philosophy? . 2. In my opinion, logic - the key element of philosophy of science is messed up everywhere in the paper by Shahbazian and Zahedi. If neccessary, I can compile a list of examples of anti-logic statements in that paper. As the journal Editor, are you aware of these problems? . 3. What made you recommend the paper by Shahbazian and Zahedi to the CCL? "The most viewed" is misleading and cannot justify its merit simply because many people like me were allured by its title. To me, it is time- and life-wasting to read its content. . 4. How does the paper by Hoffmann contribute to science and philosophy in a FOCH journal? Is it a poem, philosophy, or science? . 5. Hoffmann mentioned a friend he met in his paper. Do you know who is the friend and what his friend did in science? . 6. Wasn't it an accident that a section of References was missing in Hoffmann's paper? At least, there should be a section of Notes. Without these sections, many people like me will never ever understand anything in it. . Finally, I'd like to invite you to comment on possible roles of "Prestige, power and money" in science and philosophy, as I commented in the PhilChem List just a few weeks ago in response to an internet post from Yuehui Zhou. Frankly, Yuehui's post reminded me whether your FOCH journal like some other scientific journals is influenced in some degree by "Prestige, power and money" and contains some biased political tricks. What are your measures or philosophy to make sure that you are free from these bad influences. I think it benefits your FOCH journal to clarify this issue. . Thanks. Good luck to your philosophy and your FOCH journal/your books. . Best regards, . Sengen __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com From owner-chemistry@ccl.net Wed Sep 6 21:01:00 2006 From: "Daria Khvostichenko dkhvosti++uiuc.edu" To: CCL Subject: CCL:G: vibrational analysis for transition states in G03 Message-Id: <-32498-060906205747-32720-ITwqf9hzcZYTHBxE0HWfAA]-[server.ccl.net> X-Original-From: "Daria Khvostichenko" Date: Wed, 6 Sep 2006 20:57:46 -0400 Sent to CCL by: "Daria Khvostichenko" [dkhvosti ~~ uiuc.edu] Dear CCL subscribers, Does anybody know how vibrational analysis for transition states is done in G03? Is the mode with imaginary frequency excluded from calculations of ZPE and thermal correction to energy? Thank you! Daria