From chemistry-request@www.ccl.net Mon Feb 22 05:43:31 1999 Received: from ipruniv.cce.unipr.it (alpha1.cce.unipr.it [160.78.48.100]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id FAA06847 Mon, 22 Feb 1999 05:43:26 -0500 (EST) From: A.Romani@leonardo.biomed.unipr.it Received: from leonardo.biomed.unipr.it (leonardo.biomed.unipr.it [160.78.84.228]) by ipruniv.cce.unipr.it (8.9.0/8.8.7) with SMTP id LAA06436 for ; Mon, 22 Feb 1999 11:43:23 +0100 (MET) Received: from localhost by leonardo.biomed.unipr.it (5.65v3.2/1.1.10.5/10Feb99-0618PM) id AA20738; Mon, 22 Feb 1999 11:43:40 +0100 Message-Id: <9902221043.AA20738@leonardo.biomed.unipr.it> To: chemistry@www.ccl.net Subject: Molecular Modeling Date: Mon, 22 Feb 99 11:43:40 +0100 X-Mts: smtp -------- Dear netters, my name is Antonello Romani and I am a medicine graduated. During last two years my field of interest was focused on structure-based ligand design, with particularly interest in tyrosine protein kinases inhibitors. At present, I'm interested in the design and development of an inhibitor of the tyrosine kinase associated to Epidermal Growth Factor Receptor (EGFR). As far as I know, experimental atomic coordinates for the EGFR are not available in the Protein Data Bank . Therefore, I have built a model for the tyrosine kinase domain using two different approach like standard similarity search and a new approach called "inverse fording approach"(THREADING). This model was built using the methods of "spatial restrain" implemented in Modeller program. The structure refinement and other calculations were carried out "in vacuum" with the AMBER 5.0 software package with dielectric constant that changes with distance, in order to obtain a rough implicit simulation of aqueous solvent around protein. Some programs used were: ProsaII and 1D-3D profile to verify structure consistency while Errat,Verify_3D,Procheck and What_Check to test steric parameter. I have not found in my University a research group interested and qualified to compare my results and to verify the methods used. Since I'm not fully acquainted with this field,I apply to your kind attention to obtain, if possible, suggestion and criticism about my work.I am available, if you agree, to send detailed informations and to meet soon you. Thanking in advance, Yours Faithfully, Antonello Romani ___________________________________________ Antonello Romani Istituto di Patologia Generale Plesso Biotecnologico Integrato Facolta' di Medicina e Chirurgia Universita' degli Studi di Parma via Volturno 39 43100 Parma Tel : +39 0521 903 764 Fax : +39 0521 903 742 E-Mail : A.Romani@leonardo.biomed.unipr.it ___________________________________________ From chemistry-request@www.ccl.net Mon Feb 22 08:33:33 1999 Received: from send203.yahoomail.com (send203.mail.yahoo.com [128.11.68.127]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id IAA07542 Mon, 22 Feb 1999 08:33:33 -0500 (EST) Message-ID: <19990222133513.23701.rocketmail@send203.yahoomail.com> Received: from [129.43.6.38] by send203.mail.yahoo.com; Mon, 22 Feb 1999 05:35:13 PST Date: Mon, 22 Feb 1999 05:35:13 -0800 (PST) From: Aaron Hu Subject: C Program To: chemistry@www.ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Hi, Could someone tell me how to call a FORTRAN subroutine in a C program on SGI workstation or PC ? Thanks Aaron _________________________________________________________ DO YOU YAHOO!? Get your free @yahoo.com address at http://mail.yahoo.com From chemistry-request@www.ccl.net Mon Feb 22 08:54:47 1999 Received: from fsmail.pace.edu (fsmail.pace.edu [205.232.111.6]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id IAA07670 Mon, 22 Feb 1999 08:54:47 -0500 (EST) Received: from fsmail.pace.edu [205.232.102.18] by fsmail.pace.edu with ESMTP (SMTPD32-4.07) id A26E46020052; Mon, 22 Feb 1999 08:58:06 EDT Message-ID: <36D1641E.B4B6B8CC@fsmail.pace.edu> Date: Mon, 22 Feb 1999 09:05:18 -0500 From: "Francis T. Marchese" Reply-To: marchesf@pace.edu Organization: Pace University X-Mailer: Mozilla 4.08 [en] (Win95; I) MIME-Version: 1.0 To: CHEMISTRY@www.ccl.net, Brian Williams Subject: 2 Photon spectra of organic molecules Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi Brian, The application of theory to 2 photon absorption by organic molecules is nearly 30 years old. See the work by Marchese and Jaffe for application of CNDO/S to singlet and doublet states and other references therein: Singlet - f.t. marchese, c.j.seliskar, and h.h.jaffe, j. chem. phys., 72(7), 4194 (1980) Doublet - f.t. marchese, c.j.seliskar, and h.h.jaffe, j. chem. phys., 72(7), 4207 (1980) also see work by Hohlneicher and Dick, j. chem. phys. 70, 5427 (1979). Regards, Dr. Francis T. Marchese Professor Dept. of Computer Science Pace University New York, NY 10038 fmarchese@fsmail.pace.edu From chemistry-request@www.ccl.net Mon Feb 22 10:06:50 1999 Received: from mail.wesleyan.edu (mail.wesleyan.edu [129.133.1.51]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id KAA08447 Mon, 22 Feb 1999 10:06:49 -0500 (EST) Received: from sunfish (sunfish.chem.wesleyan.edu [129.133.20.34]) by mail.wesleyan.edu (8.9.1/8.9.1) with SMTP id KAA06510 for ; Mon, 22 Feb 1999 10:06:50 -0500 (EST) Message-Id: <3.0.5.32.19990222100759.01279ec0@wesleyan.edu> X-Sender: yliu@wesleyan.edu X-Mailer: QUALCOMM Windows Eudora Pro Version 3.0.5 (32) Date: Mon, 22 Feb 1999 10:07:59 -0500 To: chemistry@www.ccl.net From: Yongxing Liu Subject: Re: CCL:C Program In-Reply-To: <19990222133513.23701.rocketmail@send203.yahoomail.com> Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" On a PC, It depends on which OS you are using, WIN32, Linux or DOS? On a SGI workstation, You compile c code and fortran code separatly, and then link them together. Notice that, in c code, the name of a Fortran function should be followed by an underscore. When you pass parameters, C always pass by value(copy) and Fortran 77 always call by reference (address). The column and row order of multidimensional arrays is also inversed when passing between languages. At 05:35 AM 2/22/99 -0800, you wrote: >MIME-Version: 1.0 >Content-Type: text/plain; charset=us-ascii > >Hi, > >Could someone tell me how to call a FORTRAN subroutine in a C program >on SGI workstation or PC ? > >Thanks > >Aaron > > > > >_________________________________________________________ >DO YOU YAHOO!? >Get your free @yahoo.com address at http://mail.yahoo.com > > >-------This is added Automatically by the Software-------- >-- Original Sender Envelope Address: chemistry-request@www.ccl.net >-- Original Sender From: Address: aaronguyue@yahoo.com >CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator >MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73 >Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search > Web: http://www.ccl.net/chemistry.html > > > -------------------------------------------------------------------- Yongxing Liu |Tel : (860)-685-2777 Department of Chemistry|Fax : (860)-685-2211 Wesleyan University |EMAIL: yliu@wesleyan.edu Middletown CT 06459 |URL : http://ludwig.chem.wesleyan.edu/yliu --------------------------------------------------------------------- From chemistry-request@www.ccl.net Mon Feb 22 10:36:48 1999 Received: from syr.edu (syr.edu [128.230.1.49]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id KAA08727 Mon, 22 Feb 1999 10:36:47 -0500 (EST) Received: from [128.230.187.108] (jello.cat.syr.edu [128.230.187.108]) by syr.edu (8.8.8/8.8.8) with ESMTP id KAA05785; Mon, 22 Feb 1999 10:31:30 -0500 (EST) Mime-Version: 1.0 Content-Type: multipart/alternative; boundary="============_-1292424324==_ma============" X-Sender: desingh@mailbox.syr.edu Message-Id: In-Reply-To: <199902191614.LAA05183@mail.bucknell.edu> Date: Mon, 22 Feb 1999 10:42:45 -0500 To: Brian Williams From: Deepak Singh Subject: Re: CCL:Two-photon spectroscopy Cc: CHEMISTRY@www.ccl.net --============_-1292424324==_ma============ Content-Type: text/plain; charset="us-ascii" You could refer to papers by Robert Birge on the theory of two-photon spectroscopy. I added on one by Dick as well. What you want is a program that can handle CISD i.e. singles and doubles. Birge, R., & Pierce, B. (1986) International Journal of Quantum Chemistry 29, 639- 656. Birge, R. R. (1983) in Ultrasensitive laser spectroscopy (Kliger, D. S., Ed.) pp 109-174, Academic Press, Inc., New York. Birge, R. R. (1984) in Spectroscopy of biological molecules (Sandorfy, C., & Theophanides, T., Eds.) pp 457-471, D. Reidel, Boston. Birge, R. R., & Pierce, B. M. (1979) J. Chem Phys. 70, 165-178. Dick, B., & Hohlneicher, G. (1982) J. Chem. Phys. 76, 5755-5760. Regards Deepak. ********************************************************************** Deepak Singh Email: desingh@syr.edu Graduate Fellow URL: http://web.syr.edu/~desingh Department of Chemistry and Biochemistry, Tel: (315) 443 1739 -- work Syracuse University (315) 472 9659 -- home 1-014 Scitech Syracuse NY 13244 Fax: (315) 443 4070 "Violence is the last resort of the incompetent". -- Salvor Hardin ********************************************************************** --============_-1292424324==_ma============ Content-Type: text/html; charset="us-ascii" Re: CCL:Two-photon spectroscopy
You could refer to papers by Robert Birge on the theory of two-photon spectroscopy.   I added on one by Dick as well.  What you want is a program that can handle CISD i.e. singles and doubles.




Birge, R., & Pierce, B. (1986) International Journal of Quantum Chemistry 29, 639- 656.
Birge, R. R. (1983) in Ultrasensitive laser spectroscopy (Kliger, D. S., Ed.) pp 109-174, Academic Press, Inc., New York.
Birge, R. R. (1984) in Spectroscopy of biological molecules (Sandorfy, C., & Theophanides, T., Eds.) pp 457-471, D. Reidel, Boston.
Birge, R. R., & Pierce, B. M. (1979) J. Chem Phys. 70, 165-178.
Dick, B., & Hohlneicher, G. (1982) J. Chem. Phys. 76, 5755-5760.


Regards

Deepak.
**********************************************************************
Deepak Singh                              Email: desingh@syr.edu
Graduate Fellow                           URL: http://web.syr.edu/~desingh
Department of Chemistry and Biochemistry,       Tel: (315) 443 1739 -- work
Syracuse University                         (315) 472 9659 -- home
1-014 Scitech Syracuse NY 13244            Fax: (315) 443 4070
                    
"Violence is the last resort of the incompetent". -- Salvor Hardin
**********************************************************************
--============_-1292424324==_ma============-- From chemistry-request@www.ccl.net Mon Feb 22 10:39:00 1999 Received: from hartree.chem.kuleuven.ac.be (hartree.quantchem.kuleuven.ac.be [134.58.49.1]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id KAA08765 Mon, 22 Feb 1999 10:38:57 -0500 (EST) Received: from localhost (alexei@localhost) by hartree.chem.kuleuven.ac.be (8.9.0/8.9.0) with ESMTP id QAA39782; Mon, 22 Feb 1999 16:34:08 +0100 Date: Mon, 22 Feb 1999 16:34:08 +0100 (NFT) From: Alexei Arbouznikov To: aplincou@host11.lctn.u-nancy.fr cc: chemistry@www.ccl.net Subject: Re: CCL:reviews on MCSCF methods In-Reply-To: <199902211103.MAA18772@host11.lctn.u-nancy.fr> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Phil, I can recommend you at least two reviews, I would say, from the hands of their developpers: B. O. Roos, K. Andersson, M. P. Flscher, P.-. Malmqvist, L.Serrando-Andres, "Multiconfigurational perturbation theory: applications in electronic spectroscopy", in: Advances in Chemical Physics, Vol. XCIII, (Ed. by I.Prigogine and S.A.Rice), Wiley, New York, 1996, p. 219. B. O. Roos, "The complete active space SCF method ...", in: Ab Initio Methods in Quantum Chemistry, (Ed. by K. P. Lawley), Wiley, New York, 1987, p.399. Good luck! Alexei ------------------------------------------------------------------------- Dr. Alexei ARBOUZNIKOV Katholieke Universiteit Leuven Departement Scheikunde Afdeling Quantumchemie Celestijnenlaan 200F B-3001 Heverlee BELGIUM Tel. (32) 16.32.74.76 Fax. (32) 16.32.79.92 E-mail: alexei@hartree.quantchem.kuleuven.ac.be On Sun, 21 Feb 1999 aplincou@host11.lctn.u-nancy.fr wrote: > Dear all, > > Does anyone know reviews on MCSCF methods (CASSCF, CASPT2, MRDCI...) ? > I thank you in advance. > I will summarize. > > Phil > > ------------------------------------------------------------------------ > APLINCOURT Philippe > Laboratoire de Chimie Theorique ___ > UMR 7565 S2RMC __n/ \__ > Faculte des Sciences \___ * ) > Domaine Scientifique Victor Grignard B.P. 239 / / > 54506 VANDOEUVRE-LES-NANCY Cedex / _ | > Tel : 03 83 91 20 00 Poste 35 52 \___/ \_\ > Fax : 03 83 91 25 30 > E-mail : Philippe.Aplincourt@lctn.u-nancy.fr > ------------------------------------------------------------------------ > > > > > > -------This is added Automatically by the Software-------- > -- Original Sender Envelope Address: chemistry-request@www.ccl.net > -- Original Sender From: Address: aplincou@host11.lctn.u-nancy.fr > CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator > MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73 > Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search > Web: http://www.ccl.net/chemistry.html > > From chemistry-request@www.ccl.net Mon Feb 22 11:03:57 1999 Received: from mercury.ih.org (mercury.ih.org [206.9.152.243]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id LAA09610 Mon, 22 Feb 1999 11:03:56 -0500 (EST) Received: from [206.9.152.161] (206.9.152.161) by mercury.ih.org with ESMTP (Eudora Internet Mail Server 2.2); Mon, 22 Feb 1999 10:03:38 -0600 X-Sender: mpugmire@mercury.ih.org Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Mon, 22 Feb 1999 10:07:34 -0500 To: chemistry@www.ccl.net From: Matt Pugmire Subject: Protein-protein docking software I am currenlty looking for protein-protein docking software. Are there any methods available that give reasonable results? I have found a few packages, but am interested to know what people in this field are presently using. I would appreciate any information. ****************************** Matt Pugmire, Ph. D. Hughes Institute 2665 Long Lake Road, Suite 330 Roseville, MN 55113 Tel: 651-697-9228 ext. 626 Fax: 651-697-0645 email: mpugmire@ih.org ****************************** From chemistry-request@www.ccl.net Mon Feb 22 11:26:43 1999 Received: from ifisicam.unam.mx (ce.fis.unam.mx [132.248.33.1]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id LAA11516 Mon, 22 Feb 1999 11:26:27 -0500 (EST) Message-Id: <199902221626.LAA11516@www.ccl.net> Received: by ce.ifisicam.unam.mx (1.38.193.4/16.2) id AA26382; Mon, 22 Feb 1999 09:53:02 -0600 From: Ramon Garduno Subject: Seeking NAOMI software..... To: CHEMISTRY@www.ccl.net (CCL POST MSG) Date: Mon, 22 Feb 99 9:53:02 CST Mailer: Elm [revision: 70.85] Dear CCLers: A couple of weeks ago I posted the following message. It seems that it did not go through since I have not even seen my own message funneled to my address. So, I am going to tamper with your patience one more and hopefully someone can give a pointer. I have used most of the Web search engines to get in touch with Prof. Simon M. Brocklehurst, author of NAOMI, without success. My query is in order to obtain the most recent version (2.4c) of this software but apparently he has moved from smb@bioch.ox.ac.uk to how knows where. Does any of you have information leading to the appropiate email or URL address, either for Prof. Brocklehurst or NAOMI?. Much obliged, Ramon Garduno -- "...De los 260 musculos que tiene el cuerpo humano, el mas dificil de mantener en forma es el corazon...." ___________________________________________________________________________ Dr. Ramon Garduno-Juarez Research Professor in Biophysics CENTRO DE CIENCIAS FISICAS | EMAIL: ramon@ce.ifisicam.unam.mx UNIVERSIDAD NAL. AUTONOMA DE MEXICO | Apdo. Postal 48-3 | VOICE: +52(5)6227749 ; +52(73)291749 62251 Cuernavaca, Morelos | +52(73)111611 & +52(73)175388 MEXICO | FAX: +52(5)6227775 & +52(73)291775 | +52(73)173077 ___________________________________EOF ____________________________________ From chemistry-request@www.ccl.net Mon Feb 22 14:06:43 1999 Received: from nmr-v.ioc.ac.ru (root@nmr-v.ioc.ac.ru [193.233.3.213]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id OAA10764 Mon, 22 Feb 1999 14:06:36 -0500 (EST) Received: from cacr.ioc.ac.ru (val@localhost [127.0.0.1]) by nmr-v.ioc.ac.ru (8.8.7/8.8.7) with ESMTP id UAA03035 for ; Mon, 22 Feb 1999 20:01:08 +0300 Sender: val@nmr-v.ioc.ac.ru Message-ID: <36D18D53.6569889A@cacr.ioc.ac.ru> Date: Mon, 22 Feb 1999 20:01:07 +0300 From: val Reply-To: val@cacr.ioc.ac.ru Organization: IOC X-Mailer: Mozilla 4.5 [en] (X11; I; Linux 2.0.30 i686) X-Accept-Language: en MIME-Version: 1.0 To: CCL_post Subject: TS imaginary freq. value Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCL'ers, I have got a Transition State (TS) structure with unusually low imaginary frequency value, about 17 CM**-1. However, the gradient convergence criterion is satisfied, Hessian is correct (only one imaginary freq.), visualization of the normal mode gives right picture and Intrinsic Reaction Coordinate optimization connects the TS to reactants and products. Is this enough to proof that the saddle point is true TS of the reaction of interest? Does it make any sense to take into account the value of the imaginary frequency? In what range should it be for the most common cases? Any references on TS imaginary frequency value interpretation are really welcome. Thanks in advance, I will summarize as usual. sincerely yours, Valentin. ==================================================================== , , , , Valentin P. Ananikov |\\\\ ////| /////| NMR Group | \\\|/// | ///// | ND Zelinsky Institute of Organic Chemistry | |~~~| | |~~~| | Leninsky Prospect 47 | |===| | |===| | Moscow 117913 | | | | | | | Russia | | A | | | Z | | \ | | / | | / e-mail: val@cacr.ioc.ac.ru \|===|/ |===|/ http://nmr.ioc.ac.ru/Staff/AnanikovVP/ '---' '---' Fax +7 (095)1355328 Phone +7 (095)9383536 ==================================================================== From chemistry-request@www.ccl.net Mon Feb 22 23:37:28 1999 Received: from mail02.rapidsite.net (mail02.rapidsite.net [207.158.192.68]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id XAA07765 Mon, 22 Feb 1999 23:37:28 -0500 (EST) Received: from www.mdpi.org (207.158.232.88) by mail02.rapidsite.net (RS ver 1.0.2) with SMTP id 11921 for ; Mon, 22 Feb 1999 23:30:52 -0500 (EST) Message-ID: <36D22F49.2D6E5267@mdpi.org> Date: Tue, 23 Feb 1999 05:32:09 +0100 From: "Dr. Shu-Kun Lin" Reply-To: lin@mdpi.org Organization: MDPI (http://www.mdpi.org) X-Mailer: Mozilla 4.5 [en] (Win98; I) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@www.ccl.net Subject: ENTROPY (http://mdpi.org/entropy/) calling for papers Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Loop-Detect: 1 I kindly invite you to contribute any related papers for consideration and publication in ENTROPY, an International and Interdisciplinary Journal of Entropy and Information Studies (ISSN 1099-4300) at the http://www.mdpi.org/entropy/ website. The first issue will be published in March, 1999. It has a very strong scientific editorial board. Sincerely, Shu-Kun Lin, The Editor -- Dr. Shu-Kun Lin MDPI, Saengergasse 25, CH-4054 Basel, Switzerland Tel. +41 79 322 3379, Fax +41 61 302 8918 E-mail: lin@mdpi.org URL: http://mdpi.org/lin/