From mrigank@imtech.ernet.in Tue Mar 21 14:49:31 1995 Received: from sangam.ncst.ernet.in for mrigank@imtech.ernet.in by www.ccl.net (8.6.10/930601.1506) id OAA16676; Tue, 21 Mar 1995 14:49:27 -0500 Received: (from uucp@localhost) by sangam.ncst.ernet.in (8.6.8.1/8.6.6) with UUCP id BAA01738 for chemistry@ccl.net; Wed, 22 Mar 1995 01:19:16 +0530 Received: from imtech.UUCP by doe.ernet.in (4.1/SMI-4.1-MHS-7.0) id AA13078; Tue, 21 Mar 95 23:30:50+050 Message-Id: <9503211830.AA13078@doe.ernet.in> Received: by imtech.ernet.in (DECUS UUCP w/Smail); Tue, 21 Mar 95 09:23:48 +0530 Date: Tue, 21 Mar 95 09:23:48 +0530 From: Mrigank To: chemistry@ccl.net Subject: RE: CCL:H-bond analysis of MD X-Vms-Mail-To: UUCP%"bishop@london.ks.uiuc.edu" ==>dear netters, ==> ==>I am looking for a program which takes an x-plor format ==> ==>molecular dynamics trajectory file (a DCD file), determines ==>the hydrogen bonds and formats the output in a suitable fashion ==>for reporting. ==>(This information can be extracted from x-plor but it's no simple matter ==>to accumulate the data in a reportable format, as far as I know) ==> ==>The system we wish to analyze contains DNA and excess water and we would like ==>to analyze only the h-bonding of the water to the DNA, and not DNA-DNA h-bonds ==>or water-water hbonds. ==> ==>Any suggestions would be very much appreciated. In my previous organization, I have written a package in Fortran 77 called DNAlys which include this, it was mainly to read AMBER/GROMOS files but X-Plor can be introduced without difficulty. Only due ti some mishap I lost the tape, you can contact DR. V. Kothekar at koth@medinst.ernet.in or vkoth@aiims.ernet.in and seek the program if desired, she might be having a copy. Mrigank ---- /Mrigank \/ Phone +91 172 690557 \ \Institute of Microbial Technology /\ Email: mrigank@imtech.ernet.in / /Sector 39A, \/ FAX: +91 172 690585 \ \Chandigarh 160 014 India. /\ / \//\//\//\//\//\//\//\//\//\//\//\//\//\//\//\//\//\//\//\//\//\//\//\//\// -- When I feed the poor, they call me saint. When I ask why the poors do not have food, they call me communist - Archbishop Camaran From busse@chemie.fu-berlin.de Wed Mar 22 10:14:37 1995 Received: from spider.chemie.fu-berlin.de for busse@chemie.fu-berlin.de by www.ccl.net (8.6.10/930601.1506) id JAA00631; Wed, 22 Mar 1995 09:30:25 -0500 Received: by spider.chemie.fu-berlin.de (1.37.109.10G/16.2) id AA107942576; Wed, 22 Mar 1995 15:29:36 +0100 Date: Wed, 22 Mar 1995 15:29:36 +0100 (MEZ) From: Holger Busse To: CHEMISTRY@ccl.net Subject: OFFER: (Theoret. Chem. Berlin, GER) 3 doctoral positions Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Subject: B: (Theoret. Chem. Berlin, GER) 3 doctoral positions Newsgroups: bln.jobs Summary: Keywords: Opportunities for 3 doctoral positions (BAT IIa/2) are available in the Instiut fuer Physikalische und Theoretische Chemie der Freien Universitaet Berlin starting with 1st April 1995 or later. *** Interests quantum dynamics of elementary reactions *** Experience required M.Sc. in Theoretical Chemistry or Theoretical Physics Programming (Fortran77/90) *** Contact Freie Universitaet Berlin Prof. Dr. J. Manz Takustrasse 3 D-14195 Berlin phone: xx49 30 838 3338 FAX: xx49 30 838 4792 mail: manz@eagle.chemie.fu-berlin.de -- Holger Busse =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- | | Holger Busse | | busse@chemie.fu-berlin.de | FU Berlin - Theoretical Chemistry | | Tel. ++49/30/838 5383 (2351) | Takustrasse 3 | | FAX. ++49/30/838 4792 | D-14195 Berlin | =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- From WALKERD@sask.usask.ca Wed Mar 22 12:14:32 1995 Received: from skycat.usask.ca for WALKERD@sask.usask.ca by www.ccl.net (8.6.10/930601.1506) id LAA03367; Wed, 22 Mar 1995 11:53:20 -0500 From: Received: from SKYCAT.USask.CA by SKYCAT.USask.CA (PMDF V4.3-11 #5952) id <01HOFMUTSGV48WXD2W@SKYCAT.USask.CA>; Wed, 22 Mar 1995 10:52:52 -0600 (CST) Date: Wed, 22 Mar 1995 10:52:51 -0600 (CST) Subject: Molecular Modeling Packages for ALPHA systems To: chemistry@ccl.net Message-id: <01HOFMUU7QMQ8WXD2W@SKYCAT.USask.CA> X-Envelope-to: chemistry@ccl.net X-VMS-To: IN%"chemistry@ccl.net" MIME-version: 1.0 Content-transfer-encoding: 7BIT Hello, We have a dec alpha LX workstation. For molecular modeling we used to use the package BIOGRAF on an older Kubota TITAN. We are looking for a package similar to that for our alpha. The package must be able to draw molecules on screen as well as read from a variety of formats such as PDB. It should contain Molecular Mechanics engines suitable for both smaller molecules and especially for proteins and polypeptides. I would like to here from others using such a package on smaller workstations such as ours. all information appreciated Duane Walker Mathematical Chemistry Research Unit University of Saskatchewan Saskatoon, Saskatchewan, Canada walkerd@usask.sask.ca From markm@portal.vpharm.com Wed Mar 22 14:14:41 1995 Received: from portal.vpharm.com for markm@portal.vpharm.com by www.ccl.net (8.6.10/930601.1506) id NAA05541; Wed, 22 Mar 1995 13:45:41 -0500 Received: by portal.vpharm.com (AIX 3.2/UCB 5.64/4.03) id AA15621; Wed, 22 Mar 1995 13:38:26 -0500 From: markm@portal.vpharm.com (Mark Murcko) Message-Id: <9503221838.AA15621@portal.vpharm.com> Subject: protein - protein interactions To: chemistry@ccl.net Date: Wed, 22 Mar 1995 13:38:25 -0500 (EST) X-Mailer: ELM [version 2.4 PL21] Content-Type: text Content-Length: 344 I am looking for software that takes two proteins and attempts to "dock" them together. I know that this has been an area of interest to many code developers. I would be interested in recent references to this field, but even more exciting would be an actual program that I could play with on a few test cases. Thanks for any help. / Mark From kaupp@vsibm1.mpi-stuttgart.mpg.de Wed Mar 22 14:17:26 1995 Received: from vsibm1.mpi-stuttgart.mpg.de for kaupp@vsibm1.mpi-stuttgart.mpg.de by www.ccl.net (8.6.10/930601.1506) id NAA04948; Wed, 22 Mar 1995 13:19:15 -0500 Received: by vsibm1.mpi-stuttgart.mpg.de (AIX 3.2/UCB 5.64/4.03) id AA37755; Wed, 22 Mar 1995 19:11:23 +0100 From: kaupp@vsibm1.mpi-stuttgart.mpg.de (Martin Kaupp) Message-Id: <9503221811.AA37755@vsibm1.mpi-stuttgart.mpg.de> Subject: Partridge basis sets To: CHEMISTRY@ccl.net (Comp. Chem. List OSC) Date: Wed, 22 Mar 1995 19:11:23 +0100 (MEZ) Cc: kaupp@vsibm1.mpi-stuttgart.mpg.de (Martin Kaupp), uachmalk@savba.sk (Vladimir Malkin), malkina@fns.uniba.sk (Malkina Olga) Content-Type: text Content-Length: 1686 Dear netters, We are looking for an online source for the near-HF-limit Gaussian basis sets of Partridge for 4th-5th period elements. These have been tested in: J. Chem. Phys. 1989, 90, 1043 (2nd and 4th period) Theor. Chim. Acta. 1992, 82, 207 (5th period), but printed NASA or QCPE sources were indicated for the parameter sets. We found files with 3rd-period bases (J. Chem. Phys. 1987, 87, 6643), but in an inconvenient format, therefore a better source for these would be nice as well. Any hint on where to find these parameter sets on the net or on how to best contact Harry Partridge by e-mail would be greatly appreciated. Please e-mail to me directly. In case of useful replies I will summarize for the list. Regards, Martin Kaupp ------------------------------------------------------------------ | Dr. Martin Kaupp | | | | Max-Planck-Institut fuer Festkoerperforschung, | | Heisenbergstrasse 1, D-70569 Stuttgart, Germany, | | Tel.: country-code+711/689-1532 | | Fax.: country-code+711/689-1562 | | email: kaupp@vsibm1.mpi-stuttgart.mpg.de | | | | and Institut fuer Theoretische Chemie, Universitaet Stuttgart, | | Pfaffenwaldring 55, D-70569 Stuttgart, Germany | | Tel.: country-code+711/685-4399 | | Fax.: country-code+711/685-4442 | ------------------------------------------------------------------ From garciae@ucsub.colorado.edu Wed Mar 22 15:14:35 1995 Received: from ucsub.colorado.edu for garciae@ucsub.colorado.edu by www.ccl.net (8.6.10/930601.1506) id PAA07161; Wed, 22 Mar 1995 15:04:08 -0500 Received: (from garciae@localhost) by ucsub.colorado.edu (8.6.11/8.6.9/CNS-3.5) id NAA06322; Wed, 22 Mar 1995 13:04:04 -0700 Date: Wed, 22 Mar 1995 13:04:04 -0700 (MST) From: Garcia Edgardo To: chemistry@ccl.net Subject: CCL: BSSE & semiempirical energies Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi netters, o Is there any BSSE with semiempirical methods like AM1 ? o Also, how reliable are the intermolecular interactios energies obtained with semiempirical methods ? Are they consistent and show correct general trends ? Thanks in advance for any comments or references. Edgardo Garcia Univ. of Colorado BOULDER CO USA From st-amant@theory.chem.uottawa.ca Wed Mar 22 15:20:16 1995 Received: from theory.chem.uottawa.ca for st-amant@theory.chem.uottawa.ca by www.ccl.net (8.6.10/930601.1506) id PAA07083; Wed, 22 Mar 1995 15:00:58 -0500 Received: by theory.chem.uottawa.ca (AIX 3.2/UCB 5.64/4.03) id AA18733; Wed, 22 Mar 1995 14:57:13 -0500 Date: Wed, 22 Mar 1995 14:57:13 -0500 From: st-amant@theory.chem.uottawa.ca (Alain St-Amant) Message-Id: <9503221957.AA18733@theory.chem.uottawa.ca> To: chemistry@ccl.net, praa2@cluster1.urz.uni-halle.de Subject: Re: CCL:new version of DeFT available praa2@cluster1.urz.uni-halle.de writes: > Dear colleagues, > > Since several days I'm using DeFT-code from Alain St-Amant, provided by a > colleague of mine, for some test calculations. > Unfortunately my colleague do not know exactly , if this is the latest > available release. He told me that his version is from Febr./March of the > last year. > > So there is my question. Is this version the actual release or if not > where I can get a newer version. > > I have tried to contact Dr. St Amant directly, but since several weeks I > do not get any response. It seems that he is very busy. Hi, I'd first like to apologize for taking so long to respond to so many. Things have really gotten a bit out of hand. The answer to your question is that there is no substantially new version of the DeFT program. I am hoping to have some worthwhile new stuff by the end of this summer to warrant the release of a new version. This would primarily be related to the introduction of model core potentials. However, to simplify distribution of the code, I have decided to place the source code in the OSC archives. The instructions for downloading the code are appended. Please remember that even though it is given out free of charge, the code is still copyrighted. Just to very briefly remind you, DeFT is a linear combination of gaussian type orbitals density functional program very similar to deMon or DGauss. It only has analytic first derivatives, so geometry optimizations are efficient, but vibrational analyses can become quite time consuming as this must be done by finite differentiation of the analytic first derivatives. Gradient-corrected functionals are included. I have only included basis sets up to fluorine since these are the only ones officially published. Basis sets for heavier elements are freely available from Cray Research's WWW site (we greatly appreciate their doing so). Documentation on the methodology and the program is included. I hope the code can be of some use to some of you, and if you have any questions after downloading the code, feel free to e-mail me and I'll try to get back to you as soon as my busy schedule permits :-) Alain p.s. thanks to Jan for doing the necessary work in setting up everything in the archives for me and providing the following instructions: --------------------- instructions on retrieving --------- There are 2 files: 813702 Mar 21 17:27 DeFT.tar.Z 1334 Mar 21 17:24 README They can be retrieved using: Anonymous ftp (use binary mode!): www.ccl.net in directory: /pub/chemistry/software/SOURCES/FORTRAN/DeFT WWW: gopher://www.ccl.net:73/11/software/SOURCES/FORTRAN/DeFT Gopher: gopher www.ccl.net 73 software -> SOURCES -> FORTRAN -> DeFT E-mail: send a message: select chemistry cd software/SOURCES/FORTRAN/DeFT limit 1.5MB size 60kB get README get DeFT.tar.Z quit to MAILSERV@ccl.net and you will get about several uuencoded chunks which you need to combine with an editor in the proper order (cutting the headers) and then run uudecode program. To unpack the compressed tar archive use the command (under UNIX): zcat DeFT.tar.Z | tar xvof - From thep@risc1.lrm.fi.cnr.it Wed Mar 22 16:07:35 1995 Received: from risc1.lrm.fi.cnr.it for thep@risc1.lrm.fi.cnr.it by www.ccl.net (8.6.10/930601.1506) id PAA08196; Wed, 22 Mar 1995 15:45:44 -0500 Received: by risc1.lrm.fi.cnr.it (AIX 3.2/UCB 5.64/4.03) id AA23948; Wed, 22 Mar 1995 21:36:00 +0100 From: thep@risc1.lrm.fi.cnr.it (Pornthep Sompornpisut) Message-Id: <9503222036.AA23948@risc1.lrm.fi.cnr.it> Subject: chirality problem after MD To: chemistry@ccl.net Date: Wed, 22 Mar 1995 21:35:59 +0100 (NFT) X-Mailer: ELM [version 2.4 PL23] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Length: 416 Dear Amber-users Does anyone have or used to have a chirality problem of ALPHA-C in the first residue of the proteins after refining by the restraint energy minimized or restraint molecular dynamics (I am using the program AMBER v4.0)? My problem is that the first N-terminal residue of the calculated structure is D-aminoacid, even the residue started from L- . Any opinions are welcome. Thank you Pornthep From dimitris@3dp.com Wed Mar 22 16:22:38 1995 Received: from boris.3dp.com for dimitris@3dp.com by www.ccl.net (8.6.10/930601.1506) id QAA08972; Wed, 22 Mar 1995 16:11:57 -0500 Received: from europa.3dp.com by boris.3dp.com via SMTP (931110.SGI/930416.SGI) for chemistry@ccl.net id AA08560; Wed, 22 Mar 95 16:14:43 -0500 Received: by europa.3dp.com (931110.SGI) id AA11654; Wed, 22 Mar 95 16:14:02 -0500 From: "Dimitris Agrafiotis" Message-Id: <9503221614.ZM11652@europa.3dp.com> Date: Wed, 22 Mar 1995 16:14:01 -0500 X-Mailer: Z-Mail (3.1.0 22feb94 MediaMail) To: chemistry@ccl.net Subject: [Q] Programs for peptide sequence design Content-Type: text/plain; charset=us-ascii Mime-Version: 1.0 Are there any programs that given a 3D structure of a peptide (or peptides) bound to a receptor, will suggest other peptide sequences of equal length that are expected to bind to that receptor with equal or higher affinity? Thanks. -- Dimitris K. Agrafiotis, PhD | e-mail: dimitris@3dp.com 3-Dimensional Pharmaceuticals, Inc. | tel: (610) 458-6045 665 Stockton Drive, Suite 104 | fax: (610) 458-8249 Exton, PA 19341 From raman@bioc01.uthscsa.edu Wed Mar 22 16:37:33 1995 Received: from thorin.uthscsa.edu for raman@bioc01.uthscsa.edu by www.ccl.net (8.6.10/930601.1506) id QAA09576; Wed, 22 Mar 1995 16:36:50 -0500 Received: from bioc01.uthscsa.edu by thorin.uthscsa.edu with SMTP; Wed, 22 Mar 1995 15:39:29 -0600 (CST) Received: by bioc01.uthscsa.edu (4.1/SMI-4.1) id AA11386; Wed, 22 Mar 95 15:36:48 CST From: raman@bioc01.uthscsa.edu (C.S.RAMAN) Message-Id: <9503222136.AA11386@bioc01.uthscsa.edu> Subject: Re: CCL:protein - protein interactions To: markm@portal.vpharm.com (Mark Murcko) Date: Wed, 22 Mar 1995 15:36:47 -0600 (CST) Cc: chemistry@ccl.net In-Reply-To: <9503221838.AA15621@portal.vpharm.com> from "Mark Murcko" at Mar 22, 95 01:38:25 pm X-Mailer: ELM [version 2.4 PL3] Content-Type: text Content-Length: 2028 Mark: > > I am looking for software that takes two proteins and attempts to > "dock" them together. I know that this has been an area of interest > to many code developers. I would be interested in recent references > to this field, but even more exciting would be an actual program You need the program DOCK from Tack Kuntz at UCSF. He can be reached at: kuntz@cgl.ucsf.edu Mike Connolly was working on an upgrade of the program and I am not sure if it has been released to the public yet. It is free for academia. Cheers -raman _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ _/ _/ _/ C.S.RAMAN _/ _/ Department of Biochemistry _/ _/ University of Texas Health Science Center _/ _/ 7703 Floyd Curl Drive _/ _/ San Antonio, TX 78284-7760 _/ _/ USA _/ _/ _/ _/ Tel: (210) 567-6623 _/ _/ Fax: (210) 567-6595 _/ _/ E-mail: raman@bioc01.uthscsa.edu _/ _/ _/ _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ _/ _/ _/ How can it be that mathematics, a product of human thought _/ _/ independent of experience, is so admirably adapted to the _/ _/ objects of reality? "-Albert Einstein" _/ _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ From hcj@mazda.wavefun.com Wed Mar 22 17:22:32 1995 Received: from volvo.wavefun.com for hcj@mazda.wavefun.com by www.ccl.net (8.6.10/930601.1506) id RAA10306; Wed, 22 Mar 1995 17:18:17 -0500 Received: from mazda.wavefun.com by volvo.wavefun.com via SMTP (931110.SGI/930416.SGI) for chemistry@ccl.net id AA16921; Wed, 22 Mar 95 14:18:32 -0800 Received: by mazda.wavefun.com (931110.SGI/930416.SGI) for @volvo.wavefun.com:chemistry@ccl.net id AA24701; Wed, 22 Mar 95 14:18:25 -0800 Date: Wed, 22 Mar 95 14:18:25 -0800 From: hcj@mazda.wavefun.com (Harry C. Johnson) Message-Id: <9503222218.AA24701@mazda.wavefun.com> To: chemistry@ccl.net Subject: Spartan WWW Page Reply-To: hcj@wavefun.com Dear net surfers, For those who are interested, the computational chemistry package, Spartan, now has a web page, http://wavefun.com. It is fairly technical since I am not a marketing person, but should be informative. Please feel free to browse and/or put a link in your own page(s). Any comments and criticisms are welcome as this is my first attempt at such things. Thanks! -Harry +-----------------------+--------------------------------------------+ |Harry C. Johnson | /--- ----\ /---/ ---\ ----- /---/ /| / | |Computational Chemist | \ / / / / / / / / / / | / | |Wavefunction Inc. | \ /---/ /---/ /---/ / /---/ / | / | |E-mail: hcj@wavefun.com|---/ / / / / \ / / / / |/ | +-----------------------+--------------------------------------------+ From que@still3.chem.columbia.edu Wed Mar 22 18:52:33 1995 Received: from mailhub.cc.columbia.edu for que@still3.chem.columbia.edu by www.ccl.net (8.6.10/930601.1506) id SAA11151; Wed, 22 Mar 1995 18:51:03 -0500 Received: from still3.chem.columbia.edu by mailhub.cc.columbia.edu with SMTP id AA15356 (5.65c+CU/IDA-1.4.4/HLK for <@mailhub.cc.columbia.edu:chemistry@ccl.net>); Wed, 22 Mar 1995 18:50:54 -0500 Received: by still3.chem.columbia.edu (931110.SGI/930416.SGI.AUTO) for @mailhub.cc.columbia.edu:MMODINFO@UOFT02.UTOLEDO.EDU id AA24137; Wed, 22 Mar 95 18:50:52 -0500 Date: Wed, 22 Mar 95 18:50:52 -0500 From: que@still3.chem.columbia.edu (Quentin McDonald) Message-Id: <9503222350.AA24137@still3.chem.columbia.edu> To: chemistry@ccl.net, MMODINFO@UOFT02.UTOLEDO.EDU, que@still3.chem.columbia.edu Subject: Seeking papers describing MacroModel applications Dear All, We are seeking to expand our MacroModel WWW page: http://www.cc.columbia.edu/~chempub/mmod/mmod.html to include a collection of references to modeling studies which used MacroModel. At present we have a number of references to papers from within the Still group but we would like to expand this to include the work of other MacroModel users. If you are the author (or know of) a paper which uses the MacroModel package please mail the reference (including paper title please) to: mmod@still3.chem.columbia.edu We will welcome any papers reporting results obtained with MacroModel - it does not have to be a "success story" or an exclusively computational study. By building a collection of such papers we hope to provide a resource which will be available for MacroModel users to consult, get ideas from and see how others have applied this software. Thanks, Quentin =============================================================================== Quentin McDonald (que@still3.chem.columbia.edu) Dept. of Chemistry, Columbia University, New York, NY. =============================================================================== From pak@cgl.ucsf.EDU Wed Mar 22 20:37:34 1995 Received: from socrates.ucsf.EDU for pak@cgl.ucsf.EDU by www.ccl.net (8.6.10/930601.1506) id UAA12593; Wed, 22 Mar 1995 20:35:05 -0500 From: Received: (from pak@localhost) by socrates.ucsf.EDU (8.6.11/GSC4.24) id RAA21290 for chemistry@ccl.net; Wed, 22 Mar 1995 17:35:04 -0800 Date: Wed, 22 Mar 1995 17:35:04 -0800 Message-Id: <199503230135.RAA21290@socrates.ucsf.EDU> To: chemistry@ccl.net Subject: amber4.1 It gives us great pleasure to announce the release of AMBER 4.1. This code is a joint effort of the Kollman group at UCSF, the Case group at The Scripps Research Institute, David Pearlman of Vertex Pharmaceuticals and David Ferguson of the University of Minnesota. We are very excited about the fact that this version of AMBER will be jointly supported by the company Oxford Molecular (OM) as well as by the various authors. Oxford Molecular will offer commercial-level support and update services and the option of bundling AMBER with their other complementary software. We expect that this partnership will combine the best of univer- sity science with the benefits of commercial ease of use. We are very pleased with this arrangement because: (1) commercial and noncommercial users can receive standalone AMBER exactly as before or get it from OM (the price for standalone remains unchanged from 4.0); (2) source code will be distributed from both places, as has always been the case; (3) Oxford Molecular can also include the programs compiled and ready to run; and (4) OM will help us develop the graphical interface program LEAP to their "Gold Pro- duct" level. Contact information for OM is given below. AMBER 4.1 has a number of exciting new features: (1) The free energy module, GIBBS, has the capability of calcu- lating free energy derivatives, free energy components by residue and free energies involving non-additive force fields. It also supports free energy perturbation, thermo- dynamic integration and slow growth within both dual and single topologies. PMF and constraint contributions are now fully implemented within thermodynamic integration. Optional dual cutoff and alternate cutoff for the perturbed group have been implemented. (2) TIP3P water systems in both GIBBS and the molecular dynam- ics / NMR fitting program SANDER have been speeded up by the incorporation of Shuichi Miyamoto's analytical shake for three-point water, and the water-water non-bonded code has been made more efficient. This speedup can be as large as 30%. Both programs have been parallelized under a gen- eralized MPI (Message Passing Interface) for MIMD architectures with the contributions of Jim Vincent and Ken Merz of Penn State, and also for shared memory parallel machines with the help of Silicon Graphics Incorporated. (3) A fast, "particle mesh" implementation of the Ewald sum method for simulating an infinite lattice has been contri- buted by Tom Darden of the National Institute of Environ- mental and Health Science and installed in SANDER by Tom Cheatham (UCSF) and Darden. (4) SPASMS, an MD and perturbation program originally developed by David Spellmeyer of UCSF (now at Chiron), Bill Swope (IBM) and Erik Evensen (now at Harvard), is being further developed mainly by David Ferguson of the University of Minnesota. It incorporates a number of new approaches not available in SANDER and GIBBS. (5) INTERFACE, a program written by David Pearlman, which allows an efficient way to set up multiple and complex runs involving the computationally intensive parts of AMBER 4.1, is being distributed with the rest of the code. It is a general program that allows front ends to be generated for other programs as well. (6) LEAP, the graphical user interface written by Christian Schafmeister (UCSF), has been significantly improved by Bill Ross and Vladimir Romanovski, and is included in AMBER 4.1. It has had a long, ongoing debugging process but we feel it is now sufficiently robust for general use. (7) The new additive force field, developed mainly by Wendy Cornell and Piotr Cieplak (manuscript in press in JACS), will be available with the code. The /dat directory will also support the force fields of Weiner et al. (1984-United atom; 1986-All atom) and OPLS/AMBER by William Jorgensen and co-workers. We hope to make other force fields avail- able as well (e.g. the Merz group and Rob Woods of the University of Georgia have carbohydrate ones). The Cornell et al. force field will be publically available through anonymous ftp, but AMBER 4.1 users will have it in advance. (8) The code to calculate RESP charges (Bayly et al. JPC, 1993 and Cornell et al., JACS, 1993) will be distributed with AMBER 4.1 (9) A number of new features related to structural refinement using NMR data have been added to the SANDER and NMODE modules, including order parameter analysis, spectral simu- lation, quasiharmonic refinement and improved simulated annealing facilities. If you are interested in obtaining a copy of AMBER 4.1, please contact Willa Crowell of UCSF (willa@cgl.ucsf.edu) or Oxford Molecular at one of the following sites: USA: California: toll free 1-800-876-9994 phone (415) 962 7300 fax (415) 962 7302 email support@presto.ig.com Oregon: toll free 1-800-544-6634 phone (503) 526 5000 fax (503) 526 5099 email support@cache.com UK: phone +44 1865 784600 fax +44 1865 784601 email support@oxmol.co.uk France: phone +33 1 69 33 35 90 fax +33 1 69 30 41 email support@madison.polytechnique.fr Germany: phone +49 9131 8796 0 fax +49 9131 8796 11 email onciul@oml.ccc.uni-erlangen.de Thank you for your interest and continued support. Sincerely yours, Peter Kollman Bill Ross Jim Caldwell Tom Cheatham David Pearlman David Ferguson David Case From cmartin@rainbow.uchicago.edu Wed Mar 22 20:52:34 1995 Received: from midway.uchicago.edu for cmartin@rainbow.uchicago.edu by www.ccl.net (8.6.10/930601.1506) id UAA12731; Wed, 22 Mar 1995 20:49:05 -0500 Received: from rainbow.uchicago.edu (rainbow.uchicago.edu [128.135.136.33]) by midway.uchicago.edu (8.6.10/8.6.4) with SMTP id TAA09765 for <@midway.uchicago.edu:chemistry@ccl.net>; Wed, 22 Mar 1995 19:49:05 -0600 Received: by rainbow.uchicago.edu (931110.SGI/930416.SGI) for @midway.uchicago.edu:chemistry@ccl.net id AA10613; Wed, 22 Mar 95 19:48:43 -0600 From: cmartin@rainbow.uchicago.edu (Charles Martin) Message-Id: <9503230148.AA10613@rainbow.uchicago.edu> Subject: COLUMBUS query To: chemistry@ccl.net Date: Wed, 22 Mar 1995 19:48:42 -0600 (CST) X-Mailer: ELM [version 2.4 PL24] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Length: 437 Netters, I am currently using the COLUMBUS package for some aspects of my research. I would like to know who else in cyberspace uses this package. I would, in particular, like to know what kinds of programs are available that interface with COLUMBUS and with the SIFS library routines. I will post a summary if so desired. with best regards Charles Martin Theoretical Biophysics University of Illinois at Urbana-Champaign