From chemistry-request@server.ccl.net Wed Jul 14 01:37:10 1999 Received: from enterprise.fuse.net (mail.fuse.net [206.230.21.15]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id BAA09921 for ; Wed, 14 Jul 1999 01:37:09 -0400 Received: from as1-695.fuse.net (as1-695.fuse.net [216.68.39.187]) by enterprise.fuse.net (8.8.5/8.8.5) with SMTP id BAA20314 for ; Wed, 14 Jul 1999 01:30:27 -0400 (EDT) Received: by as1-695.fuse.net with Microsoft Mail id <01BECD98.8D843F10@as1-695.fuse.net>; Wed, 14 Jul 1999 01:31:10 -0500 Message-ID: <01BECD98.8D843F10@as1-695.fuse.net> From: "Jason L. Douglas" To: "'chemistry@ccl.net'" Subject: OpenGL library for Scientific Research; Genetic Algorithms; Gaussian Curve Regression in Force Fields Date: Wed, 14 Jul 1999 01:30:22 -0500 MIME-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id BAA09923 I have just posted two new products free to anyone who wishes to download and use them; both compiled binaries and source is included. The first is an MS-DOS program which finds protein tertiary conformations using a very extensive genetic algorithm, with many features such as quantitative inheritance and implementation of Fischer's theorem (which balances exploration versus exploitation). The force field used is a new method, using the classical Coulumb expression of nuclear energy coupled with an electronic energy term calculated using Gaussian curves regressed to quantum mechanics calculations on dielectronic species. The term also attempts to take into account electron-electron repulsion and shielding effects. In tests, it seems to have done a well job predicting hydrogen-bonding distances as well as London dispersion forces, though the total energy curve is not quite shaped right at very far distances (this can be dealt with in several ways). A paper in PDF format is also available, to help you understand the theory and methodology behind these methods. The program is available both as a compiled DOS executable, and also contains complete C source code. The second product is an OpenGL library for scientific researchers to implement in their programs. This can save a great amount of time in reducing your graphics code to a minimum, off-loading everything to this library. The full code is included so you can modify it as you wish. It is tailored for Windows 95/98/NT platforms, but can be easily modified to work on other operating systems (XWindows, Mac OS, OS/2, etc.) that support OpenGL. It does, of course, support hardware acceleration, which can help give more processor time to CPU-intensive calculations while still providing real-time graphics. The code is in C++, and is thus only of use to C++ programmers. An example, both in source code and compiled, is also provided to demonstrate the capabilities of this library. The library can also be interfaced with PC-GAMESS (or other versions of GAMESS) to render Connolly surfaces, geodesic surfaces, electron density contours, electrostatic potential contours, and full electron density plots, all with complete control over alpha-blending! You can also display your molecular models in vector, tube, ball-and-stick, and CPK models, and control wire-frame rendering or semi-transparency values, add dynamic lighting, and varying levels of rendering quality. Support for protein models will hopefully be added soon. All of these are available through my website at: http://home.fuse.net/douglas/index.htm NOTE: All downloads must come through this website for informational tracking purposes. You can contact me at: Jason Douglas douglas@fuse.net From chemistry-request@server.ccl.net Wed Jul 14 01:36:11 1999 Received: from enterprise.fuse.net (oldradius2.fuse.net [206.230.21.72]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id BAA09913 for ; Wed, 14 Jul 1999 01:36:11 -0400 Received: from as1-695.fuse.net (as1-695.fuse.net [216.68.39.187]) by enterprise.fuse.net (8.8.5/8.8.5) with SMTP id BAA19753 for ; Wed, 14 Jul 1999 01:29:28 -0400 (EDT) Received: by as1-695.fuse.net with Microsoft Mail id <01BECD98.6A03CE70@as1-695.fuse.net>; Wed, 14 Jul 1999 01:30:11 -0500 Message-ID: <01BECD98.6A03CE70@as1-695.fuse.net> From: "Jason L. Douglas" To: "'chemistry@ccl.net'" Subject: OpenGL library for Scientific Research; Genetic Algorithms; Gaussian Curve Regression in Force Fields Date: Wed, 14 Jul 1999 01:30:03 -0500 MIME-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id BAA09914 I have just posted two new products free to anyone who wishes to download and use them; both compiled binaries and source is included. The first is an MS-DOS program which finds protein tertiary conformations using a very extensive genetic algorithm, with many features such as quantitative inheritance and implementation of Fischer's theorem (which balances exploration versus exploitation). The force field used is a new method, using the classical Coulumb expression of nuclear energy coupled with an electronic energy term calculated using Gaussian curves regressed to quantum mechanics calculations on dielectronic species. The term also attempts to take into account electron-electron repulsion and shielding effects. In tests, it seems to have done a well job predicting hydrogen-bonding distances as well as London dispersion forces, though the total energy curve is not quite shaped right at very far distances (this can be dealt with in several ways). A paper in PDF format is also available, to help you understand the theory and methodology behind these methods. The program is available both as a compiled DOS executable, and also contains complete C source code. The second product is an OpenGL library for scientific researchers to implement in their programs. This can save a great amount of time in reducing your graphics code to a minimum, off-loading everything to this library. The full code is included so you can modify it as you wish. It is tailored for Windows 95/98/NT platforms, but can be easily modified to work on other operating systems (XWindows, Mac OS, OS/2, etc.) that support OpenGL. It does, of course, support hardware acceleration, which can help give more processor time to CPU-intensive calculations while still providing real-time graphics. The code is in C++, and is thus only of use to C++ programmers. An example, both in source code and compiled, is also provided to demonstrate the capabilities of this library. The library can also be interfaced with PC-GAMESS (or other versions of GAMESS) to render Connolly surfaces, geodesic surfaces, electron density contours, electrostatic potential contours, and full electron density plots, all with complete control over alpha-blending! You can also display your molecular models in vector, tube, ball-and-stick, and CPK models, and control wire-frame rendering or semi-transparency values, add dynamic lighting, and varying levels of rendering quality. Support for protein models will hopefully be added soon. All of these are available through my website at: http://home.fuse.net/douglas/index.htm NOTE: All downloads must come through this website for informational tracking purposes. You can contact me at: Jason Douglas douglas@fuse.net From chemistry-request@server.ccl.net Mon Jul 12 07:50:28 1999 Received: from aquarius.ime.eb.br (aquarius.ime.eb.br [200.20.120.34]) by server.ccl.net (8.8.7/8.8.7) with SMTP id HAA16844 for ; Mon, 12 Jul 1999 07:50:21 -0400 Received: from by aquarius.ime.eb.br (4.1/SMI-4.1) id AC00454; Mon, 12 Jul 99 08:44:51 EST Received: from EPQ/SpoolDir by epq.ime.eb.br (Mercury 1.44); 12 Jul 99 08:43:44 -0200 Received: from SpoolDir by EPQ (Mercury 1.44); 10 Jul 99 13:32:06 -0200 Received: from sdio (200.20.123.210) by epq.ime.eb.br (Mercury 1.44); 10 Jul 99 13:32:01 -0200 Message-Id: <003701becaf1$bba90d20$d27b14c8@ime.eb.br> From: "Teodorico Ramalho" To: Subject: Force Field to metals. Date: Sat, 10 Jul 1999 13:31:59 -0300 Mime-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0034_01BECAD8.9632A240" X-Priority: 3 X-Msmail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.00.2314.1300 X-Mimeole: Produced By Microsoft MimeOLE V5.00.2314.1300 This is a multi-part message in MIME format. ------=_NextPart_000_0034_01BECAD8.9632A240 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable HI all, I'm a little confused. I would like calculte propriets to = co-ordinated complexes, by example with zinc. Are there field force by = this element ? Another idea I want to try is changing level of theory to = higher but Irealy appreciate any comments and advices. And some could = give some references about =20 =20 Many thanks Teodorico C. Ramalho Departamento de Qu=EDmica IME =20 ------=_NextPart_000_0034_01BECAD8.9632A240 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
HI all,

    I'm a little=20 confused. I would like calculte propriets to co-ordinated = complexes,=20 by example with zinc.  Are there field force by this element=20 ? Another idea I want to try is changing level of theory to higher = but=20 Irealy appreciate any comments and advices. And some could give some = references=20 about 
 
Many thanks
 
Teodorico C. Ramalho
Departamento de Qu=EDmica
IME

 
------=_NextPart_000_0034_01BECAD8.9632A240-- From chemistry-request@server.ccl.net Mon Jul 12 16:23:00 1999 Received: from unet.univie.ac.at (unet.univie.ac.at [131.130.230.7]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id QAA22498 for ; Mon, 12 Jul 1999 16:23:00 -0400 Received: from brain (uvo-84.univie.ac.at [131.130.230.84]) by unet.univie.ac.at (8.8.8/8.8.7) with ESMTP id WAA129370 for ; Mon, 12 Jul 1999 22:16:32 +0200 Received: from 192.168.0.1 by brain ([192.168.0.1] running VPOP3) with SMTP for ; Mon, 12 Jul 1999 22:12:46 +0200 Message-ID: <000501becca2$e8159790$0100a8c0@brain> Reply-To: "Alexander Klinsky" From: "Alexander Klinsky" To: Subject: SQ Program questions Date: Mon, 12 Jul 1999 22:12:46 +0200 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 8bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.00.2014.211 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2014.211 X-Server: VPOP3 V1.3.1 - Registered to: Lukundoo [HPA] Dear Colleaques ! I have two questions: First: Does someone know about the SQ (molecular alignment) algorithm by Miller, Sheridan and Kearsley published in the May issue of J. Med. Chem. of 1999 ? In particular i would like to know if this algorthm is available as a program and where/or how to obtain it. Second: Is there a program freely available to calculate atomic lipophilicity constants based on fragment lipophilicity contributions ? Kind regards, Alexander Klinsky Institute of Theoretical Chemistry Department of Applied Theoretical Biochemistry University of Vienna Währinger Strasse 17, A-1090 Wien Österreich From chemistry-request@server.ccl.net Mon Jul 12 23:12:38 1999 Received: from web103.yahoomail.com (web103.yahoomail.com [205.180.60.68]) by server.ccl.net (8.8.7/8.8.7) with SMTP id XAA27757 for ; Mon, 12 Jul 1999 23:12:37 -0400 Message-ID: <19990713030616.20126.rocketmail@web103.yahoomail.com> Received: from [208.165.103.2] by web103.yahoomail.com; Mon, 12 Jul 1999 20:06:16 PDT Date: Mon, 12 Jul 1999 20:06:16 -0700 (PDT) From: Gustavo Mercier Reply-To: gamercier@yahoo.com Subject: Amber 5.0 Makefile PGC compiler? To: chemistry@ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Hi! Before I rediscover the wheel... Amber 5.0 has a makefile under Linux using f2c. I have the Portland Group fortran and c/c++ compilers for my linux box, and would like to use them instead of f2c. Is anyone willing to share a makefile using these compiler or any other words of wisdom regarding porting Amber 5.0 to a Linux box? Thanks! Gus Mercier, Jr. === -- ("`-/")_.-'"``-._ Gustavo A. Mercier,Jr.,MD,PhD (. . `) -._ )-;-,_() Hillcrest Medical Center (v_,)' _ )`-.\ ``- Dept. of Radiology _;- _,-_/ / ((,' Tulsa X-Ray Laboratory ((,.-' ((,/ 5840 South Memorial Suite 301 gamercier@yahoo.com Tulsa, OK 74145-9082 voice: 918-664-9892/fax: 918-664-6120 _________________________________________________________ Do You Yahoo!? Get your free @yahoo.com address at http://mail.yahoo.com From chemistry-request@server.ccl.net Tue Jul 13 11:14:10 1999 Received: from gatekeeper.itqb.unl.pt (qmailr@gatekeeper.itqb.unl.pt [193.136.177.1]) by server.ccl.net (8.8.7/8.8.7) with SMTP id LAA01987 for ; Tue, 13 Jul 1999 11:14:08 -0400 Received: (qmail 14475 invoked from network); 13 Jul 1999 15:07:29 -0000 Received: from brutus.itqb.unl.pt (193.136.176.2) by gatekeeper.itqb.unl.pt with SMTP; 13 Jul 1999 15:07:29 -0000 Received: from model.itqb.unl.pt by brutus.itqb.unl.pt (5.65v4.0/1.1.8.2/30Apr98-1221PM) id AA10308; Tue, 13 Jul 1999 16:07:29 +0100 Message-Id: <3.0.6.32.19990713160616.0086e910@brutus.itqb.unl.pt> X-Sender: claudio@brutus.itqb.unl.pt X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.6 (32) Date: Tue, 13 Jul 1999 16:06:16 +0100 To: CHEMISTRY@ccl.net From: =?iso-8859-1?Q?Cl=E1udio?= Soares Subject: Solvation energies of iodide organic compounds Cc: claudio@itqb.unl.pt, nunoe@itqb.unl.pt Mime-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id LAA01988 Dear CClers We need solvation parameters for iodine to apply in molecular docking methods (G=alpha*SAS like methods). So far we did not find any parameter for iodine in the literature. Is anyone aware of these parameters for iodine somewhere? Alternatively, we can try to derive these parameters for iodine ourselves, but for that we need solvation energies (in water) of organic molecules containing iodine and that hasn't been easy either. Regards, Cláudio Soares -------------------------------------------------------------------- Cláudio Soares | Instituto de Tecnologia | Química e Biológica |Phone:(351-1)4469610/4469100 6º Piso, Av. da Republica | Fax :(351-1)4411277 Apartado 127 |email:claudio@itqb.unl.pt 2781-901 OEIRAS Portugal |http://www.itqb.unl.pt/~claudio From chemistry-request@server.ccl.net Tue Jul 13 14:58:40 1999 Received: from mgcct6.nci.nih.gov (mgcct6.nci.nih.gov [137.187.211.216]) by server.ccl.net (8.8.7/8.8.7) with SMTP id OAA04593 for ; Tue, 13 Jul 1999 14:58:40 -0400 Received: from helix.nih.gov (localhost [127.0.0.1]) by mgcct6.nci.nih.gov (950413.SGI.8.6.12/950213.SGI.AUTOCF) via ESMTP id QAA03037 for ; Tue, 13 Jul 1999 16:19:45 -0400 Sender: brunob@helix.nih.gov Message-ID: <378B9F60.F4FA5CB5@helix.nih.gov> Date: Tue, 13 Jul 1999 16:19:44 -0400 From: Bruno Bienfait Organization: National Cancer Institute X-Mailer: Mozilla 4.6 [en] (X11; I; IRIX 6.3 IP32) X-Accept-Language: en MIME-Version: 1.0 To: Computer Chemistry List Subject: Re: CCL:autodock 3.0 References: <378B6873.872EB196@carrier2.pharmacy.ohio-state.edu> <378B784A.C0CB3D0B@scripps.edu> Content-Type: multipart/alternative; boundary="------------7421FB11F1624F98BFAF4634" --------------7421FB11F1624F98BFAF4634 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit With Insight 97, load the receptor first and import the docked ligand in pdb-format using the "reference name" option which must points to the atoms of the receptor. With Quanta 97, there is no special trick, just import the two files. The freely available Gopenmol can import both structure and trajectory files from Autodock. Hopes this can help, Bruno Maneesh Yadav wrote: > When some modellers load up multiple molecules, they sometimes apply wierd > transforms so you can't see the true docked complex (insightII). Use a modeller > like SPOCK and load up the macromolecule and ligand and it gives you no problems. > > Freek Helsper wrote: > > > I'm trying to run Autodock to find a putative binding site in a model > > I've just finished. > > When I analyze the docking logfile (dlg-file), I only get the > > coordinates of the docked ligand in pdb-format. How can I view the > > complex of the ligand with the macromolecule (I don't have AVS, so > > that's not an option). There's nothing about this in the Autodock > > manual. > > Has anyone an idea how to solve this problem? > > > > Freek Helsper > > > > -- > > ##################################################################### > > Freek Helsper Tel:+1 614 292 9646 > > College of Pharmacy Fax:+1 614 292 9977 > > The Ohio-State University > > Parks Hall, room 357 > > 500 W 12th Ave > > Columbus, OH 43210 > > > > http://carrier2.pharmacy.ohio-state.edu/~helsper/Public/homepage.html > > ##################################################################### > > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net -- [ Bruno Bienfait, Ph. D. Laboratory of Medicinal Chemistry ] [ National Cancer Institute ] [ Email : brunob@helix.nih.gov National Institutes of Health ] [ Phone : (301) 402-3111 Building 37, Room 5B20 ] [ Fax : (301) 496-5839 Bethesda Maryland 20892 , USA ] [ WWW : http://www.brunob.org ] --------------7421FB11F1624F98BFAF4634 Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit With Insight 97, load the receptor  first and import the  docked ligand in pdb-format  using the "reference name" option which must points to the atoms of  the receptor.

With Quanta 97, there is no special trick, just import the two files.

The freely available Gopenmol can import both structure and trajectory files  from Autodock.

Hopes this can help,

Bruno
 

Maneesh Yadav wrote:

When some modellers load up multiple molecules, they sometimes apply wierd
transforms so you can't see the true docked complex (insightII).  Use a modeller
like SPOCK and load up the macromolecule and ligand and it gives you no problems.

Freek Helsper wrote:

> I'm trying to run Autodock to find a putative binding site in a model
> I've just finished.
> When I analyze the docking logfile (dlg-file), I only get the
> coordinates of the docked ligand in pdb-format. How can I view the
> complex of the ligand with the macromolecule (I don't have AVS, so
> that's not an option). There's nothing about this in the Autodock
> manual.
> Has anyone an idea how to solve this problem?
>
> Freek Helsper
>
> --
> #####################################################################
> Freek Helsper                   Tel:+1 614 292 9646
> College of Pharmacy             Fax:+1 614 292 9977
> The Ohio-State University
> Parks Hall, room 357
> 500 W 12th Ave
> Columbus, OH 43210
>
> http://carrier2.pharmacy.ohio-state.edu/~helsper/Public/homepage.html
> #####################################################################
>

-= This is automatically added to each message by mailing script =-
CHEMISTRY@ccl.net -- To Everybody    |   CHEMISTRY-REQUEST@ccl.net -- To Admins
MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH
CHEMISTRY-SEARCH@ccl.net -- archive search    |    Gopher: gopher.ccl.net 70
Ftp: ftp.ccl.net  |  WWW: http://www.ccl.net/chemistry/   | Jan: jkl@ccl.net

-- 
[ Bruno Bienfait, Ph. D.            Laboratory of Medicinal Chemistry ]
[                                   National Cancer Institute         ]
[ Email : brunob@helix.nih.gov      National Institutes of Health     ]
[ Phone : (301) 402-3111            Building 37, Room 5B20            ]
[ Fax   : (301) 496-5839            Bethesda Maryland 20892 , USA     ]
[ WWW   : http://www.brunob.org                                       ]
  --------------7421FB11F1624F98BFAF4634-- From chemistry-request@server.ccl.net Wed Jul 14 05:43:23 1999 Received: from inch.uia.ac.be (inch.uia.ac.be [143.169.4.1]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id FAA12890 for ; Wed, 14 Jul 1999 05:43:22 -0400 Received: from uia.ac.be by inch.uia.ac.be; (8.8.8/1.1.8.2/22Feb95-0943AM) id LAA08495; Wed, 14 Jul 1999 11:36:36 +0200 (MET DST) Sender: roussea@uia.ua.ac.be Message-ID: <378C56C3.34C3CDAB@uia.ac.be> Date: Wed, 14 Jul 1999 11:22:11 +0200 From: Bart Rousseau Organization: University of Antwerp (UIA) X-Mailer: Mozilla 4.06 [en] (X11; I; OSF1 V4.0 alpha) MIME-Version: 1.0 To: CCL Subject: SUMMARY: atoms in a specific state Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi all, I was looking for a program that allows calculations on atoms in a specific state (eg the spectroscopic ground state). I found two programs for doing atomic calculations - atomscf - atomci I have a copy of the former, and have contacted the authors of the latter in order to obtain a copy. The atomscf program performs ROHF calculations using coupling coefficients. More information on atomic SCF calculations can be found in (references provided by B. Fink): G.L. Malli, J.P. Olive, J. Chem. Phys, 43 (1965) 861. G.L. Malli, J.P. Olive, Technical Report, LMSS (Laboratory of Molecular Structure and Spectroscopy), p. 257-294, 1962-63, University of Chicago. Other responses to my question: - J. Kerkines: perform MCSCF calculation using MOLPRO - P. Bultinck and M. Thomas: explained how to use the CUBE keyword in G94 - S. Fau: use the scf(wfnsymm) keyword in G94 to constrain the symmetry of the wavefunction similar to the well known constraint on nuclear symmetry use of the density=current and iop(6/8=3) keywords to print the density matrix - M. Reinhold: suggested to use ADF1999? (http://www.scm.com/SCM/Doc/ADFUG/) Thanks to Patrick Bultinck, University of Ghent, Ghent, Belgium. Stefan Fau, Univeristy of Marburg, Marburg, Germany. Bill Fink, University of California, Davis, USA. John Kerkines, Athens, Greece. Meike Reinhold, University of York, York, UK. Masahiro Sekiya, Hokkaido University, Japan. Mehnert Thomas, Munich, Germany. Thanks again, Bart -- Bart Rousseau, Ph.D. student University of Antwerp - Dep. of Chemistry Structural Chemistry - Quantum Chemistry http://sch-www.uia.ac.be/struct/quantum/ From chemistry-request@server.ccl.net Wed Jul 14 07:48:44 1999 Received: from ct2.mpibpc.gwdg.de (ct2.mpibpc.gwdg.de [134.76.213.214]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id HAA14621 for ; Wed, 14 Jul 1999 07:48:41 -0400 Received: (from gkaeb@localhost) by ct2.mpibpc.gwdg.de (AIX4.2/UCB 8.7/8.7) id NAA18136; Wed, 14 Jul 1999 13:40:59 +0200 (MESZ) Date: Wed, 14 Jul 1999 13:40:59 +0200 (MESZ) From: Guenter Kaeb Message-Id: <199907141140.NAA18136@ct2.mpibpc.gwdg.de> To: chemistry@server.ccl.net Subject: MD program ROAR 1.0 Cc: gkaeb@gwdg.de Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-MD5: uoSlLHTzehg8/HYKdWoTgw== Dear CCLers, I have recently come across a research article (JPC B 103 (1999) 5396.) by Ailan Cheng and Kenneth M Merz, Jr., dealing with the implementation of a time-reversible symplectic molecular dynamics integrator (of rRESPA type) in biomolecular dynamics simulations using the program ROAR 1.0. Does anybody have information on this MD package, whether it is available freely to people working in the field of MD, and can somebody tell me an appropriate web page for getting in contact to the authors and receiving more information? P.S.: The authors are affiliated at Pennsylvania State, but I was not able to find their web location. Thanks in advance, and I will summarize all responses. Sincerely, Guenter Kaeb ============================================================================== = = = Dr. Guenter Kaeb = = Max-Planck-Institute of Biophysical Chemistry = = (Department 010: Spectroscopy and photochemical kinetics) = = Am Fassberg 11 = = D-37077 Goettingen = = = = Tel.: +49-551/201-1344 = = Fax: +49-551/201-1006 = = = = e-mail: gkaeb@gwdg.de = = = ============================================================================== From chemistry-request@server.ccl.net Wed Jul 14 10:22:15 1999 Received: from alpha.luc.ac.be (alpha.luc.ac.be [193.190.2.30]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id KAA16315 for ; Wed, 14 Jul 1999 10:22:14 -0400 Received: from sbg-ts (sbg-ts.luc.ac.be [193.190.1.15]) by alpha.luc.ac.be (8.9.3/8.9.3) with SMTP id QAA09943 for ; Wed, 14 Jul 1999 16:17:43 +0200 (MET DST) Date: Wed, 14 Jul 1999 16:17:43 +0200 (MET DST) Message-Id: <199907141417.QAA09943@alpha.luc.ac.be> X-Sender: skwasnie@mail.luc.ac.be X-Mailer: Windows Eudora Pro Version 2.1.2 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: chemistry@ccl.net From: sergiusz kwasniewski Subject: TD-HF Hi all, Just a short question: Is it true that TD-HF (Time-Dependent HF) is the same as RPA (Random Phase Approximation) ? Because I find it a bit confusing in the literature ... Thanks in advance S. Kwasniewski _________________________________________________ Sergiusz Kwasniewski LUC SBG/TS Universitaire Campus Gebouw D 3590 Diepenbeek BELGIUM tel(direct): 011/268315 fax : 011/268301 email : sergiusz.kwasniewski@luc.ac.be _________________________________________________ From chemistry-request@server.ccl.net Wed Jul 14 14:51:56 1999 Received: from dali.chem.uab.edu (dali.chem.uab.edu [138.26.72.17]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id OAA19298 for ; Wed, 14 Jul 1999 14:51:56 -0400 Received: from dali (localhost [127.0.0.1]) by dali.chem.uab.edu (AIX4.2/UCB 8.7/8.7) with SMTP id NAA29990; Wed, 14 Jul 1999 13:45:08 -0500 (CDT) Sender: prasad@dali.chem.uab.edu Message-ID: <378CDAB4.69D8@dali.chem.uab.edu> Date: Wed, 14 Jul 1999 13:45:08 -0500 From: "Dr. Bharatam V. Prasad" X-Mailer: Mozilla 3.0Gold (X11; I; AIX 2) MIME-Version: 1.0 To: Computational Chemistry List Subject: Chemistry Educational software Content-Type: text/plain; charset=us-ascii; name="chemsoft" Content-Transfer-Encoding: 7bit Content-Disposition: inline; filename="chemsoft" Chemistry Educational Packages Dear CCLers, This is a request from an upcoming Chemistry School which does not have funds for the purchase of chemisty Educational software. If any of the members of the CCL can spare the Educational software packages (at least the old versions) for an upcoming chemistry school please send them to the address given below. Software related to to any branch of chemistry is welcome. If any of the members can freely give the old versions of their theoretical chemistry packages (quantum mechanics, statistical mechanics, molecular mechanics, molecular modeling, biological activity type, polymer chemistry, neural networks, molecular building, molecular graphics, drug design etc.) it will clearly help. The platforms available are the IBM compatible PC pentium. Silicon Graphics O2. Executable versions and / or the source codes will be useful. My current address is Prasad V. Bharatam Department of Chemistry University of Alabama at Birmingham Birmingham, AL 35294-1240 Phone : 205-934-2481 I shall carry the material to Department of Chemistry Guru Nanak Dev University Amritsar - 143 005 India Thanking you, Prasad From chemistry-request@server.ccl.net Wed Jul 14 16:25:08 1999 Received: from macgw.chem.iupui.edu (macgw.chem.iupui.edu [134.68.137.71]) by server.ccl.net (8.8.7/8.8.7) with SMTP id QAA20665 for ; Wed, 14 Jul 1999 16:25:08 -0400 Message-ID: Date: 14 Jul 1999 15:22:12 -0500 From: "Boyd" Subject: re: free books To: "Amber list" , "Cache list" , "CHMINF-L" , "MacroModel list" , "MEDI ACS Listserv" , "OSC CCL" , "PDB list" , "QSAR and Modelling Society" X-Mailer: Mail*Link SMTP for Quarterdeck Mail; Version 4.1.0 Hello, I would like to thank everyone who responded to the survey on the "Reviews in Computational Chemistry" books (http://chem.iupui.edu/rcc/rcc.html). We appreciate the many compliments about the chapters we have published. We also appreciate the many helpful suggestions. The 2 respondents randomly selected to receive a free volume of Reviews in Computational Chemistry are: 1. Dr. Jose Ignacio Garcia-Laureiro, Zaragoza, Spain 2. Dr. David E. Clark, Dagenham, England Thanks again, Don Donald B. Boyd, Ph.D. Editor, Reviews in Computational Chemistry Editor, Journal of Molecular Graphics and Modelling (publication of the ACS COMP division) Department of Chemistry Indiana University-Purdue University at Indianapolis 402 North Blackford Street Indianapolis, Indiana 46202-3274, U.S.A. Telephone 317-274-6891, FAX 317-274-4701 E-mail boyd@chem.iupui.edu ____________________________________________________________ >Hello, > >The 13th volume of Reviews in Computational Chemistry (RCC) >was published last month. Vol. 14 is in press. As editors, Ken >Lipkowitz and I have been glad to provide a steady stream of >introductory tutorials and advanced reviews on many facets of >computational chemistry, molecular modeling, molecular design, >and so on. > >To better serve our readers, we ask your help in completing the >following survey. Your answers can be as short as you like. As a >expression of our thanks for your help with this survey, we will >select at random 2 respondents and give each a FREE volume of >RCC. > >1. Of the 86 chapters that have been published in RCC: > > A. Which have been most useful in your teaching? > > B. Which have been most useful in your research? > > C. Which have you enjoyed the most for your personal >use? > >2. You wish there were chapters on the following subjects: > >3. A way RCC could better meet your needs is to: > >._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._ >Thanks very much for your help with this survey. > >Donald B. Boyd, Ph.D. >Editor, Reviews in Computational Chemistry From chemistry-request@server.ccl.net Wed Jul 14 16:43:57 1999 Received: from tbone.agouron.com (tbone.agouron.com [198.182.177.3]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id QAA20878 for ; Wed, 14 Jul 1999 16:43:57 -0400 Received: (from gproxy@localhost) by tbone.agouron.com (8.9.3/8.9.3) id NAA16063; Wed, 14 Jul 1999 13:37:04 -0700 (PDT) Received: from dns3-wla.agouron.com(192.135.144.6), claiming to be "dns3.agouron.com" via SMTP by gauntlet.agouron.com, id smtpdAAAa003pS; Wed Jul 14 13:36:55 1999 Received: from agouron.com (Russell-Anna.dhcp.agouron.com [10.0.29.72]) by dns3.agouron.com (8.9.3/8.9.1) with ESMTP id NAA87285; Wed, 14 Jul 1999 13:36:31 -0700 (PDT) (envelope-from anna.russell@agouron.com) Message-ID: <378CF466.F620BC4B@agouron.com> Date: Wed, 14 Jul 1999 13:35:23 -0700 From: Anna Russell Organization: Agouron Pharamceuticals X-Mailer: Mozilla 4.05 (Macintosh; U; PPC) MIME-Version: 1.0 To: "Dr. Bharatam V. Prasad" CC: Computational Chemistry List Subject: Re: CCL:Chemistry Educational software References: <378CDAB4.69D8@dali.chem.uab.edu> Content-Type: text/plain; charset=us-ascii; x-mac-type="54455854"; x-mac-creator="4D4F5353" Content-Transfer-Encoding: 7bit Try to call Science Media in San Diego :619-6259261 Anna Dr. Bharatam V. Prasad wrote: > Chemistry Educational Packages > > Dear CCLers, > > This is a request from an upcoming Chemistry School > which does not have funds for the purchase of chemisty > Educational software. > > > If any of the members of the CCL can spare the Educational > software packages (at least the old versions) > for an upcoming chemistry school please send them to the > address given below. Software related to to any > branch of chemistry is welcome. > > If any of the members can freely give the old versions of > their theoretical chemistry packages (quantum mechanics, > statistical mechanics, molecular mechanics, molecular modeling, > biological activity type, polymer chemistry, neural networks, > molecular building, molecular graphics, drug design etc.) > it will clearly help. > > The platforms available are the IBM compatible PC pentium. > Silicon Graphics O2. > > Executable versions and / or the source codes will be useful. > > My current address is > > Prasad V. Bharatam > Department of Chemistry > University of Alabama at Birmingham > Birmingham, AL 35294-1240 > Phone : 205-934-2481 > > I shall carry the material to Department of Chemistry > Guru Nanak Dev University > Amritsar - 143 005 > India > > Thanking you, > > > Prasad > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net