From vkitzing@silia.mpimf-heidelberg.mpg.de Tue Sep 30 08:27:37 1997 Received: from otto.mpimf-heidelberg.mpg.de for vkitzing@silia.mpimf-heidelberg.mpg.de by www.ccl.net (8.8.3/950822.1) id HAA08830; Tue, 30 Sep 1997 07:34:42 -0400 (EDT) Received: from [149.217.50.47] (mac20.mpimf-heidelberg.mpg.de) by otto.mpimf-heidelberg.mpg.de (4.1/SMI-4.1) id AA18308; Tue, 30 Sep 97 12:34:31 +0100 Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Tue, 30 Sep 1997 13:29:39 +0200 To: berriz@chasma.harvard.edu (Gabriel Berriz), chemistry@www.ccl.net From: vkitzing@silia.mpimf-heidelberg.mpg.de (Eberhard von Kitzing) Subject: CCL:Dihedral angle restoring force Dear CCLlers, At 13:29 Uhr 29.09.1997, Gabriel Berriz wrote: >I'm looking for computationally efficient code (or algorithm) to >compute the restoring forces (magnitudes and directions) corresponding >to a potential dependent on the dihedral angle formed by three >consecutive bonds along a chain. The desired forces act on the four >atoms forming the three bonds. Any pointers would be much >appreciated. Thank you. In the quote give below numerically stable derivatives for the complete range of angles of the dihedral potential are give (except for an obvious typo in Eq 2): Eberhard von Kitzing (1992). Modeling DNA Structures. Progress in Nucleic Acids Research and Molecular Biology. San Diego, Academic Press. 89-110. ====================================================================== Eberhard von Kitzing Max-Planck-Institut fuer Medizinische Forschung Jahnstr. 29 D 69115 Heidelberg Germanny email: vkitzing@silia.mpimf-heidelberg.mpg.de WWW: http://sunny.mpimf-heidelberg.mpg.de/people/vkitzing/ From campagne@incm.u-nancy.fr Tue Sep 30 10:27:49 1997 Received: from brown.incm.u-nancy.fr for campagne@incm.u-nancy.fr by www.ccl.net (8.8.3/950822.1) id KAA09478; Tue, 30 Sep 1997 10:15:04 -0400 (EDT) Received: from yellow.incm.u-nancy.fr by brown.incm.u-nancy.fr via ESMTP (940816.SGI.8.6.9/940406.SGI.AUTO) for <@brown.incm.u-nancy.fr:chemistry@www.ccl.net> id QAA08178; Tue, 30 Sep 1997 16:16:27 +0100 Received: from incm.u-nancy.fr (localhost [127.0.0.1]) by yellow.incm.u-nancy.fr (950413.SGI.8.6.12/950213.SGI.AUTOCF) via ESMTP id QAA28819 for ; Tue, 30 Sep 1997 16:16:25 +0100 Sender: campagne@incm.u-nancy.fr Message-ID: <343117C6.629625CD@incm.u-nancy.fr> Date: Tue, 30 Sep 1997 16:16:23 +0100 From: Fabien Campagne Organization: Lab. Chimie theorique Nancy X-Mailer: Mozilla 4.03 [en] (X11; I; IRIX64 6.2 IP28) MIME-Version: 1.0 Newsgroups: bionet.molbio.proteins.7tms_r To: chemistry@www.ccl.net Subject: CCL: protein sequence alignment HTML representations Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear all, The following service is available for converting MSF Multiple Sequence Alignment (MSA) to HTML. Three methods are proposed that render MSA as colored, possibly hyperlinked (last two) HTML pages: text-based HTML. grahical HTML (for netscape3-, xmosaic, InternetExplorer2-) style-sheet HTML (for netscape4+, InternetExplorer3+) Illustrations are available from the service root page: http://www.lctn.u-nancy.fr/viseur/services.html The WWW conversion service uses the Viseur program (http://www.lctn.u-nancy.fr/viseur/viseur.html ) to create the representations. People interested in creating a lot of these representations are encouraged to register the program for local use. PS: This service was proposed a few month ago to bionet.molbio.proteins.7tms_r users, for beta test. I'd like to thanks people who reported previous unexpected behaviours for their collaboration. These methods will be presented and discussed at MGM EC-2, ftp://www.ccl.net/pub/chemistry/info/conferencelist/mess0139.html, next month. Fabien Campagne -- campagne@incm.u-nancy.fr | Lab. de Chimie Theorique phone: +33 (0)3 83 91 20 00 extension 3236 | Nancy, France. http://www.lctn.u-nancy.fr/viseur/FC.html From usenet@ciril.fr Tue Sep 30 10:37:42 1997 Received: from ciril.fr for usenet@ciril.fr by www.ccl.net (8.8.3/950822.1) id KAA09480; Tue, 30 Sep 1997 10:15:05 -0400 (EDT) Received: (from usenet@localhost) by ciril.fr (8.8.7/8.8.7) id QAA11141; Tue, 30 Sep 1997 16:14:49 +0200 (METDST) To: bionet-molbio-proteins-7tms_r@net.bio.net Path: not-for-mail From: Fabien Campagne Newsgroups: bionet.molbio.proteins.7tms_r Subject: CCL: protein sequence alignment HTML representations Date: Tue, 30 Sep 1997 16:16:23 +0100 Organization: Lab. Chimie theorique Nancy Lines: 37 Message-ID: <343117C6.629625CD@incm.u-nancy.fr> NNTP-Posting-Host: yellow.incm.u-nancy.fr Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.03 [en] (X11; I; IRIX64 6.2 IP28) To: chemistry@www.ccl.net Dear all, The following service is available for converting MSF Multiple Sequence Alignment (MSA) to HTML. Three methods are proposed that render MSA as colored, possibly hyperlinked (last two) HTML pages: text-based HTML. grahical HTML (for netscape3-, xmosaic, InternetExplorer2-) style-sheet HTML (for netscape4+, InternetExplorer3+) Illustrations are available from the service root page: http://www.lctn.u-nancy.fr/viseur/services.html The WWW conversion service uses the Viseur program (http://www.lctn.u-nancy.fr/viseur/viseur.html ) to create the representations. People interested in creating a lot of these representations are encouraged to register the program for local use. PS: This service was proposed a few month ago to bionet.molbio.proteins.7tms_r users, for beta test. I'd like to thanks people who reported previous unexpected behaviours for their collaboration. These methods will be presented and discussed at MGM EC-2, ftp://www.ccl.net/pub/chemistry/info/conferencelist/mess0139.html, next month. Fabien Campagne -- campagne@incm.u-nancy.fr | Lab. de Chimie Theorique phone: +33 (0)3 83 91 20 00 extension 3236 | Nancy, France. http://www.lctn.u-nancy.fr/viseur/FC.html From MMENDEZ@DELTA.IS.TCU.EDU Tue Sep 30 15:27:39 1997 Received: from DELTA.IS.TCU.EDU for MMENDEZ@DELTA.IS.TCU.EDU by www.ccl.net (8.8.3/950822.1) id OAA10553; Tue, 30 Sep 1997 14:50:34 -0400 (EDT) Received: from DELTA.IS.TCU.EDU by DELTA.IS.TCU.EDU (PMDF V5.1-7 #20456) id <01IO97P3NSJM007NST@DELTA.IS.TCU.EDU> for CHEMISTRY@www.ccl.net; Tue, 30 Sep 1997 13:40:30 CDT Date: Tue, 30 Sep 1997 13:40:30 -0500 (CDT) From: "Miguel A. Mendez Rojas" Subject: unsuscribe... In-reply-to: To: Pablo Vitoria Garcia Cc: ccl Message-id: MIME-version: 1.0 Content-type: TEXT/PLAIN; charset=US-ASCII /////////////////////////////////////////////////////////////////////////// Miguel Angel Mendez Rojas, Editor & Director of the Chemistry Ph.D. Journal ALEPHZERO, of Sciences Texas Christian University Divulgation. Fort Worth, TX 76120 http://rico.pue.udlap.mx/~aleph http://delta.is.tcu.edu/~mmendez/ aleph@udlapvms.pue.udlap.mx e-mail: mmendez@delta.is.tcu.edu \\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\ From MMENDEZ@DELTA.IS.TCU.EDU Tue Sep 30 15:36:55 1997 Received: from DELTA.IS.TCU.EDU for MMENDEZ@DELTA.IS.TCU.EDU by www.ccl.net (8.8.3/950822.1) id PAA10645; Tue, 30 Sep 1997 15:19:03 -0400 (EDT) Received: from DELTA.IS.TCU.EDU by DELTA.IS.TCU.EDU (PMDF V5.1-7 #20456) id <01IO972MGV7S007NST@DELTA.IS.TCU.EDU> for chemistry@www.ccl.net; Tue, 30 Sep 1997 13:22:23 CDT Date: Tue, 30 Sep 1997 13:22:23 -0500 (CDT) From: "Miguel A. Mendez Rojas" Subject: Re: CCL:New Issue of NetSci In-reply-to: To: Network Science Cc: chemistry@www.ccl.net Message-id: MIME-version: 1.0 Content-type: TEXT/PLAIN; charset=US-ASCII The current issue of ALEPHZERO, Journal of Science Divulgation and Education is available in: http://rico.pue.udlap.mx/~aleph/index.html /////////////////////////////////////////////////////////////////////////// Miguel Angel Mendez Rojas, Editor & Director of the Chemistry Ph.D. Journal ALEPHZERO, of Sciences Texas Christian University Divulgation. Fort Worth, TX 76120 http://rico.pue.udlap.mx/~aleph http://delta.is.tcu.edu/~mmendez/ aleph@udlapvms.pue.udlap.mx e-mail: mmendez@delta.is.tcu.edu \\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\ From cklein@uic.edu Tue Sep 30 15:42:51 1997 Received: from tigger.cc.uic.edu for cklein@uic.edu by www.ccl.net (8.8.3/950822.1) id OAA10503; Tue, 30 Sep 1997 14:39:04 -0400 (EDT) Received: from draco (MMAD1.PMMP.UIC.EDU [128.248.78.171]) by tigger.cc.uic.edu (8.8.5/8.8.5) with SMTP id LAA239888 for ; Tue, 30 Sep 1997 11:52:09 -0500 Sender: klein@tigger.cc.uic.edu Message-ID: <34312EA1.794B@uic.edu> Date: Tue, 30 Sep 1997 11:53:53 -0500 From: Christian Klein Organization: Lab. Molecular Modeling & Design, UIC X-Mailer: Mozilla 3.0 (X11; I; IRIX 5.3 IP22) MIME-Version: 1.0 To: CCL Subject: FORTRAN compiler for Irix 6.x ? [2] Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCLers, please forgive me for some wrong statements in my request for FOTRTAN compilers. SGI does provide FORTRAN as part of the MIPSproTMCompilers package. Anyway, if some freeware is available, I would like to know about it. Thanks, Chris ================================================================== Christian Klein | email: cklein@uic.edu Laboratory of Molecular Modeling & Design | voice: (312) 996-6004 Dept. of Medicinal Chemistry M/C 781 | fax: (312) 996-7107 College of Pharmacy, UIC | 833 South Wood Street | Chicago, IL 60612 | U.S.A. | ================================================================== A neutron goes into a bar and asks the bartender, "How much for a beer?" The bartender replies, "For you, no charge." From cklein@uic.edu Tue Sep 30 15:47:26 1997 Received: from tigger.cc.uic.edu for cklein@uic.edu by www.ccl.net (8.8.3/950822.1) id OAA10514; Tue, 30 Sep 1997 14:43:03 -0400 (EDT) Received: from draco (MMAD1.PMMP.UIC.EDU [128.248.78.171]) by tigger.cc.uic.edu (8.8.5/8.8.5) with SMTP id LAA130252 for ; Tue, 30 Sep 1997 11:08:56 -0500 Sender: klein@tigger.cc.uic.edu Message-ID: <3431247F.446B@uic.edu> Date: Tue, 30 Sep 1997 11:10:39 -0500 From: Christian Klein Organization: Lab. Molecular Modeling & Design, UIC X-Mailer: Mozilla 3.0 (X11; I; IRIX 5.3 IP22) MIME-Version: 1.0 To: CCL Subject: FORTRAN compiler for Irix 6.x ? Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCLers, does anybody have experience with commercial or public domain FORTRAN compilers for the more recent Irix Versions? To my knowledge, SGI does not provide Fortran compilers (any more), so where do I get one? F2C does not work satisfactorily. We considered re-building g77 from the public domain source, but this seems to be a rather difficult task. I will summarize any helpful answers. Greetings, Chris -- ================================================================== Christian Klein | email: cklein@uic.edu Laboratory of Molecular Modeling & Design | voice: (312) 996-6004 Dept. of Medicinal Chemistry M/C 781 | fax: (312) 996-7107 College of Pharmacy, UIC | 833 South Wood Street | Chicago, IL 60612 | U.S.A. | ================================================================== A neutron goes into a bar and asks the bartender, "How much for a beer?" The bartender replies, "For you, no charge." From schrecke@t12.lanl.gov Tue Sep 30 15:51:48 1997 Received: from mailhost.lanl.gov for schrecke@t12.lanl.gov by www.ccl.net (8.8.3/950822.1) id PAA10630; Tue, 30 Sep 1997 15:16:12 -0400 (EDT) Received: from [128.165.22.209] (machgs.lanl.gov [128.165.22.209]) by mailhost.lanl.gov (8.8.7/8.8.7) with SMTP id NAA21615 for ; Tue, 30 Sep 1997 13:16:11 -0600 (MDT) Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable Date: Tue, 30 Sep 1997 13:19:06 -0700 To: CHEMISTRY@www.ccl.net (CCL) From: schrecke@t12.lanl.gov (Georg Schreckenbach) Subject: summary: solid state/band structures Dear CCL readers, some two weeks ago, I posted a query about solid state methods. Here now is the promised summary. Thanx to those who replied. I didn't get too many answers although they were certainly useful. I would like to also mention again the older summary on the same subject, CCL archives, Feb. 20, 96. In a sense, it complements this new posting. If anybody wants to comment further, please do so! Best regards, Georg Here is the original question: I am interested in solid state (band structure) programs for a research proposal that I am just starting to think about. A CCL archive search shows that this question pops up regularly in one form or another. The last time was just a few days ago! However, the same archive search revealed that there are, unfortunately, mostly questions, and not many answers: The only related summary that I could find is dated 20 Feb. 1996. Some of the relevant programs mentioned briefly in this summary are: - ADF-BAND (http://www.scm.com/) - WIEN97 (http://www.tuwien.ac.at/theochem/wien97/) - and then there are the Car-Parinello type codes, including "PAW" of P. Blochl et al. So far for the background, and here are my questions in more detail. Since this is a very early state of a possible future project, I am trying to gain a broad overview. Basically what I want to learn is the state of the art in the field of doing solid state calculations from a chemical point of view. My questions are, e.g.: - What kinds of programs are out there? (relevant literature?) - What methods do they use (e.g., plane waves or other basis sets; DFT or ab initio -- I am not interested in semiempirical approaches in the moment). Which method might be superior over another? - What functionality is available (ECPs or other ways to include relativistic effects, geometry optimizations, properties ...)? - General experience of users of, e.g., the mentioned programs (source code available?, numerical stability, user friendliness, number of bugs that one runs into, cost ...) - Any other info that you would deem useful. 1) Reply by Keith Refson Georg Schreckenbach writes: > A CCL archive search shows that this question pops up regularly in > one form or another. The last time was just a few days ago! However, the > same archive search revealed that there are, unfortunately, mostly > questions, and not many answers: The only related summary that I > could find is dated 20 Feb. 1996. > Some of the relevant programs mentioned briefly in this summary are: > - ADF-BAND (http://www.scm.com/) > - WIEN97 (http://www.tuwien.ac.at/theochem/wien97/) > - and then there are the Car-Parinello type codes, including "PAW" of P. = Bl=3D > =3DF6chl > et al. A few other programs to add to your list: CRYSTAL (http://www.dl.ac.uk/TCSC/Software/CRYSTAL/). This does periodic Hartree-Fock calculations on solids using standard Gaussian basis sets. No forces or geometry optimization. CASTEP (http://www.msi.com/info/products/modules/CASTEP.html, http://www.tcm.phy.cam.ac.uk/castep/) - Unfortunately now available only to but from MSI, this is Mike Payne's plane-wave pseudopotential code. Also from MSI, the Cornell PWPP code: PLANE_WAVE (http://www.msi.com/info/products/modules/I2_QP.html) CETEP: The parallel version of CASTEP used by the UK Car-Parrinello consortium. Collaboration may be possible. (http://www.dl.ac.uk/TCSC/projects/UKCP/ukcp.html) VASP ( http://tph.tuwien.ac.at/~vasp/) The Vienna ab-initio simulation package. One of the best and most highly developed plane-wave pseudopotential codes. Not free but the price is modest. There's Ali Alavi's FEMD The most widely avaliable LAPW code is WIEN97 which you already have. The other thing to mention is Methfessel's FP-LMTO program. I don't have a WWW address, but I may be able to dig out a literature reference. There are also other 3 or 4 other plane-wave pseudopotential codes which aren't generally avaliable - Parrinello's group amongst others. > > Basically what I want to learn > is the state of the art in the field of doing solid state > calculations from a chemical point of view. You could do a lot worse than look at the UKCP publications list and work in progress, see the URL above. > - What kinds of programs are out there? (relevant literature?) You should find this from the URLs listed. > - What methods do they use (e.g., plane waves or other basis sets; Most of the ones I listed are plane-wave + pseudopotential codes and use DFT. The exception you listed was WIEN97 which uses the LAPW basis set. I believe there is a version which uses pseudopotentials but it's primarily an all-electron method. The exception in my list is CRYSTAL which is a Hartree-Fock program using the usual Gaussian basis sets. > DFT or ab initio Be aware that physicists don't share the chemists' view of using ab-initio to refer only to Harfree Fock and methods based on it. DFT is definitely ab-initio in the physics lexicon. > Which method might be superior over another? DFT is always superior [ :) ]. This is more seriously true in the solid state world (a) because no periodic program implements any higher-level of Hartree-Forck - not even MP2. The best that can be done is the non-self-consistent density-functional correlation correction in CRYSTAL. (b) Hartree-Fock gets the metallic state so badly wrong that there's no point in even trying, so it has a bad name in the physics world. > - What functionality is available (ECPs or other ways to include > relativistic effects, CRYSTAL has ECPs. All plane-wave codes use pseudopotentials, which in the fashionable form are ab-initio, (sometimes) norm-conserving and nodeless. I can't remember whether WIEN97 handles relativistic effects or not but there is an experimental version which uses pseudopotentials. > geometry optimizations, All but CRYSTAL have forces and do geometry optimizations + molecular dynamics. VASP has a pretty extensive list of properties, but you'll have to check on the web sites for the rest. > - General experience of users of, e.g., the mentioned programs > (source code available?, numerical stability, user friendliness, number o= f > bugs that one runs into, cost ...) If you make up a table I can add comments on those I know about. FYI the UKCP is currently running a comparitive evaluation of FEMD, CASTEP/CETEP and VASP. I don't know whether the results are being made public but I will try to determine that in our meeting on Monday and let you know if it's allowed. There's certainly a comprehensive "features" list for them. At the moment most of the excitement is still with the plane-wave pseudopotential methods because of the O(N**2) scaling with system size. O(N) methods are under development (including the UCKP code) but I don't know of any which are in a useable state for general research as yet. There are also many post-LDA developments foing on such as SIC, LDA+U, exact exchange and others which I can't recall at the moment which all promise a much better approximation to "true dft" and hopefully to reality. I'm sure we will find out which of them deliver in the next few years. Hope this info is helpful. sincerely Keith Refson -- ----------------------------------------------------------------------------= -- Email: Keith.Refson@ | Tel: +44 1865 272026 | Dr Keith Refson, = | earth.ox.ac.uk | Fax: +44 1865 272072 | Dept of Earth Sciences = | | Parks Road, Oxford OX1 3PR, U= K| ----------------------------------------------------------------------------= -- 2) Another reply by Keith Refson: Ome more program I nearly for got - "fhi93cp" which is Matthias Scheffler's plane-wave pseudopotential code. It's available from the Computer Physics Communications program library: - see http://www.cpc.cs.qub.ac.uk/cpc/ Keith Refson 3) Yet another reply by Keith Refson, answering a specific question of mine: I have talked to David Sherman of Bristol Uni who has tried out ADF-BAND and who spoke highly of its useability. However as far as I know it can not calculate forces and therefore can't do geometry optimizations which rather rules it out for most things I'd want it for. 4) From: d3g359@fido.pnl.gov (John Nicholas) (I asked him about the results of a similar posting earlier on the CCL) Georg, I'm not sure how easy it would be to get all the replies together, but I can pretty much tell you what's available: Crystal (RHF and DFT), DSolid, CASTEP, Bloch-Demon, VASP, QUEST, DECAPO are all availble in various forms. I think the plane wave methods have such an advatage (speed) over the other basis-sets that they are far preferred. Also amsterdam-DFT. Regards, John -------------------------------------------------------------------- John Nicholas Office: (509) 375-6559 Senior Research Scientist FAX: (509) 375-6631 Environmental Molecular Sciences Laboratory Pacific Northwest National Laboratory Mailstop K1-96 Richland, WA 99352 -------------------------------------------------------------------- (End of summary) -- =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D Dr. Georg Schreckenbach Tel: (USA)-505-667 7605 Theoretical Chemistry T-12 FAX: (USA)-505-665 3909 M.S. B268, Los Alamos National E-mail: schrecke@t12.lanl.gov Laboratory, Los Alamos, New Mexico, 87545, USA Internet: http://www.t12.lanl.gov/~schrecke/ =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D From shenkin@still3.chem.columbia.edu Tue Sep 30 16:27:42 1997 Received: from mailrelay1.cc.columbia.edu for shenkin@still3.chem.columbia.edu by www.ccl.net (8.8.3/950822.1) id QAA10991; Tue, 30 Sep 1997 16:24:36 -0400 (EDT) Received: from still3.chem.columbia.edu (still3.chem.columbia.edu [128.59.112.36]) by mailrelay1.cc.columbia.edu (8.8.5/8.8.5) with SMTP id QAA01443; Tue, 30 Sep 1997 16:24:32 -0400 (EDT) Received: by still3.chem.columbia.edu (950413.SGI.8.6.12/930416.SGI.AUTO) id QAA09968; Tue, 30 Sep 1997 16:24:31 -0400 From: "Peter Shenkin" Message-Id: <9709301624.ZM9966@still3.chem.columbia.edu> Date: Tue, 30 Sep 1997 16:24:31 -0400 In-Reply-To: Christian Klein "CCL:FORTRAN compiler for Irix 6.x ?" (Sep 30, 11:10am) References: <3431247F.446B@uic.edu> X-Mailer: Z-Mail (3.2.3 08feb96 MediaMail) To: Christian Klein , CCL Subject: Re: CCL:FORTRAN compiler for Irix 6.x ? Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii On Sep 30, 11:10am, Christian Klein wrote: > Subject: CCL:FORTRAN compiler for Irix 6.x ? > ... To my knowledge, SGI does > not provide Fortran compilers (any more), so where do I get one? F2C > does not work satisfactorily. ... Your knowledge is mistaken in this case. :-) SGI supplies f77 and f90, and in fact has just released a new set of compilers (Version 7.2) that includes these as well as C and C++. -P. -- ******************* Jimmy Witherspoon, 1923 - 1997, RIP ******************* * Peter S. Shenkin; Chemistry, Columbia U.; 3000 Broadway, Mail Code 3153 * ** NY, NY 10027; shenkin@columbia.edu; (212)854-5143; FAX: 678-9039 *** *MacroModel WWW page: http://www.columbia.edu/cu/chemistry/mmod/mmod.html * From Bernard.B.Pirard@GBJHA.zeneca.com Tue Sep 30 17:28:30 1997 Received: from bath.mail.pipex.net for Bernard.B.Pirard@GBJHA.zeneca.com by www.ccl.net (8.8.3/950822.1) id QAA11074; Tue, 30 Sep 1997 16:42:30 -0400 (EDT) X400-Received: by mta bath.mail.pipex.net in /PRMD=pipex/ADMD=pipex/C=gb/; Relayed; Tue, 30 Sep 1997 21:40:59 +0100 X400-Received: by /PRMD=ZENECA/ADMD=PIPEX/C=GB/; Relayed; Tue, 30 Sep 1997 21:16:57 +0100 Date: Tue, 30 Sep 1997 21:16:57 +0100 X400-Originator: Bernard.B.Pirard@GBJHA.zeneca.com X400-Recipients: chemistry@www.ccl.net X400-MTS-Identifier: [/PRMD=ZENECA/ADMD=TMAILUK/C=GB/;970930201657] X400-Content-Type: P2-1984 (2) Content-Identifier: CSI NC V3.0 From: Pirard Bernard B Message-ID: <001AFEED.MAI*/I=B/G=Bernard/S=Pirard/OU=GBJHA/PRMD=ZENECA/ADMD=PIPEX/C=GB/@MHS> To: cclq Subject: Electrostatic potential derived charges MIME-version: 1.0 Content-type: multipart/mixed; boundary="AZfvOmbr2HjGr3QzUSb4Z5VNfBGmxU15" --AZfvOmbr2HjGr3QzUSb4Z5VNfBGmxU15 Content-type: text/plain; charset="us-ascii" [[ CCL1.TXT : 4186 in CCL1.TXT ]] --AZfvOmbr2HjGr3QzUSb4Z5VNfBGmxU15 Content-type: text/plain; charset="us-ascii" Dear colleagues, I am currently looking for references dealing with STO-3G electrostatic potential derived (EPD) charges computed for drug-like molecules or for fragments found in drug-like molecules. The rationale for STO-3G EPD charges is as follows : they are to be used in AMBER 4.0.1 computations, as available through TRIPOS Force Field Engine. I will post a summary of the replies. Thanks in advance, Bernard Pirard, PhD Computational Chemistry Group ZENECA AGROCHEMICALS Jealott's Hill Research Station Bracknell Berks RG42 6EY UK --AZfvOmbr2HjGr3QzUSb4Z5VNfBGmxU15-- From gryko@jsucc.jsu.edu Tue Sep 30 18:27:41 1997 Received: from jsucc.jsu.edu for gryko@jsucc.jsu.edu by www.ccl.net (8.8.3/950822.1) id RAA11694; Tue, 30 Sep 1997 17:47:11 -0400 (EDT) Received: from localhost (gryko@localhost) by jsucc.jsu.edu (8.8.7/8.8.5) with SMTP id VAA18410 for ; Tue, 30 Sep 1997 21:45:45 GMT Date: Tue, 30 Sep 1997 16:45:45 -0500 (CDT) From: Jan Gryko cc: CCL Subject: MD (or DFT) under Linux/Alpha In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Does anyone have experience runing typical MD or DFT code under Linux on Alpha system? Is it true that Alpha system with IDE hard drive is unstable under Linux? (There are such rumors...) I will summarize answers to the list. Thanks, Jan Gryko Jacksonville State Univ. From d3e102@emsl.pnl.gov Tue Sep 30 20:27:44 1997 Received: from pnl.gov for d3e102@emsl.pnl.gov by www.ccl.net (8.8.3/950822.1) id TAA12140; Tue, 30 Sep 1997 19:53:27 -0400 (EDT) From: Received: from odyssey.emsl.pnl.gov by pnl.gov (PMDF V5.1-10 #21283) with ESMTP id <01IO9EG4RF00AW84FA@pnl.gov> for chemistry@www.ccl.net; Tue, 30 Sep 1997 16:53:19 PDT Received: from ames.emsl.pnl.gov (ames.emsl.pnl.gov [130.20.182.110]) by odyssey.emsl.pnl.gov (8.8.5/8.8.5) with ESMTP id QAA16093 for ; Tue, 30 Sep 1997 16:53:17 -0700 (PDT) Received: (from d3e102@localhost) by ames.emsl.pnl.gov (8.8.5/8.8.5) id QAA17772 for chemistry@www.ccl.net; Tue, 30 Sep 1997 16:53:18 -0700 (PDT) Date: Tue, 30 Sep 1997 16:53:17 -0700 Subject: AM1/PM3 parameters for K,Rb,Cs To: chemistry@www.ccl.net Message-id: <9709301653.ZM17770@ames.emsl.pnl.gov> MIME-version: 1.0 X-Mailer: Z-Mail (3.2.0 06sep94) Content-type: text/plain; charset=us-ascii Could someone provide me with a reference to AM1 or PM3 parameters for K, Rb and Cs? Thank you. Dave -- David Feller | Mail Stop K1-96 Environmental Molecular Sciences Laboratory | 906 Battelle Blvd Battelle Pacific Northwest National Lab | Richland, WA 99352 | e-mail:d3e102@emsl.pnl.gov | Fax: (509)-375-6631 From brunob@helix.nih.gov Tue Sep 30 20:44:33 1997 Received: from mgcct6.nci.nih.gov for brunob@helix.nih.gov by www.ccl.net (8.8.3/950822.1) id TAA12159; Tue, 30 Sep 1997 19:59:01 -0400 (EDT) Received: from mgcct6 (localhost [127.0.0.1]) by mgcct6.nci.nih.gov (950413.SGI.8.6.12/950213.SGI.AUTOCF) via SMTP id WAA08303 for ; Tue, 30 Sep 1997 22:09:12 -0400 Sender: brunob@helix.nih.gov Message-ID: <3431B0C8.31DF@helix.nih.gov> Date: Tue, 30 Sep 1997 22:09:12 -0400 From: Bruno Bienfait Organization: National Cancer Institute X-Mailer: Mozilla 3.01SGoldC-SGI (X11; I; IRIX 6.3 IP32) MIME-Version: 1.0 To: Computer Chemistry List Subject: Definition of molecular flexibility Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit I am looking for a definition of molecular flexibility. Does anyone know a paper or a book which defines this concept ? Furthermore, are molecular flexibility and conformational flexibility the same concept ? Thanks, Bruno Bienfait -- [ 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://schiele.organik.uni-erlangen.de/Bruno_Bienfait ]