From HODGKINE@prince.mm.wyeth.com Fri Sep 2 04:48:10 1994 Received: from mail1 for HODGKINE@prince.mm.wyeth.com by www.ccl.net (8.6.9/930601.1506) id EAA27451; Fri, 2 Sep 1994 04:28:08 -0400 Received: from mr.wyeth.com by mail1.wyeth.com (PMDF V4.2-14 #5660) id <01HGMGVE08O0000X1N@mail1.wyeth.com>; Fri, 2 Sep 1994 04:28:26 EST Received: with PMDF-MR; Fri, 2 Sep 1994 04:26:34 EST MR-Received: by mta PRIN1; Relayed; Fri, 02 Sep 1994 04:26:34 -0500 MR-Received: by mta MAIL1; Relayed; Fri, 02 Sep 1994 04:27:29 -0500 Disclose-recipients: prohibited Date: Fri, 02 Sep 1994 09:30:15 -0500 (EST) From: "Hodgkin, Ed" Subject: Van Der Waals Collapse To: "chemistry@ccl.net" Message-id: <01HGMGVEX70M000X1N@mr.wyeth.com> MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Content-transfer-encoding: 7BIT UA-content-id: Van Der Waals Collapse X400-MTS-identifier: [;43624020904991/204395@PRINCE] A1-type: MAIL Hop-count: 1 From: Hodgkin, Ed Date: Fri, Sep 2, 1994 9:30 AM Subject: Van Der Waals Collapse To: chemistry@ccl.net Dear All It is well known that molecular mechanics force fields favour 'folded' conformations which derive stability from large Van Der Waals terms. One could coin the phrase "Van Der Waals Collapse" to describe this effect. However I am not aware of any published work which addresses this issue. Are there any methods which compensate for the folding effect, thereby giving lower energies for extended conformations which are probably more relevant for molecules in solution or in binding sites. I'll summarize the replies, of course. Edward Hodgkin Wyeth Research (UK) E-mail: hodgkine@prince.mm.wyeth.com From states@ibc.wustl.edu Fri Sep 2 08:19:16 1994 Received: from wugate.wustl.edu for states@ibc.wustl.edu by www.ccl.net (8.6.9/930601.1506) id IAA28983; Fri, 2 Sep 1994 08:19:16 -0400 Received: by wugate.wustl.edu (5.67b/WUSTL-0.3) with SMTP id AA11290; Fri, 2 Sep 1994 07:19:12 -0500 Received: by ibc.WUStL.EDU (8.6.9/SMI-SVR4) id HAA11032; Fri, 2 Sep 1994 07:19:12 -0500 Date: Fri, 2 Sep 1994 07:19:12 -0500 From: states@ibc.wustl.edu (David J. States) Message-Id: <199409021219.HAA11032@ibc.WUStL.EDU> To: HODGKINE@prince.mm.wyeth.com, chemistry@ccl.net Subject: Re: CCL:Van Der Waals Collapse Content-Length: 928 |> From: Hodgkin, Ed |> |> It is well known that molecular mechanics force fields favour 'folded' |> conformations which derive stability from large Van Der Waals terms. |> One could coin the phrase "Van Der Waals Collapse" to describe this |> effect.... >From the earliest days of charmm development, this has been a concern. Globular proteins simulated in vacuo shrink when "true" atomic radii are used as the basis for nonbonded interaction parameters. Swaminathan spent alot of time working on a compensating force term, but I don't know what became of the work. The most direct way to control for the self-association of peptide chains is to do a simulation that includes solvation explicitly. Note that if you do this as a water droplet rather than a periodic box the internal pressure generated by surface tension is enormous so the system will still collapse some compared to physiologic conditions. David States From xiang@nemesis.rose.brandeis.edu Fri Sep 2 09:43:08 1994 Received: from nemesis.rose.brandeis.edu for xiang@nemesis.rose.brandeis.edu by www.ccl.net (8.6.9/930601.1506) id JAA29614; Fri, 2 Sep 1994 09:17:03 -0400 Received: by nemesis.rose.brandeis.edu (920330.SGI/920502.SGI) for CHEMISTRY@ccl.net id AA21948; Fri, 2 Sep 94 09:19:24 -0400 Date: Fri, 2 Sep 94 09:19:24 -0400 From: xiang@nemesis.rose.brandeis.edu (Phil Xiang) Message-Id: <9409021319.AA21948@nemesis.rose.brandeis.edu> To: CHEMISTRY@ccl.net Subject: CCL:user groups for MSI and TRIPOS Dear netters: Do discussion groups for MSI and TRIPOS users exist? Phil Xiang Brandeis University From lsaw00@risque.chem.rochester.edu Fri Sep 2 09:49:26 1994 Received: from risque.chem.rochester.edu for lsaw00@risque.chem.rochester.edu by www.ccl.net (8.6.9/930601.1506) id JAA29966; Fri, 2 Sep 1994 09:37:17 -0400 From: Received: by risque.chem.rochester.edu (AIX 3.1/UCB 5.61/4.03) id AA15678; Fri, 2 Sep 94 09:33:28 -0400 Date: Fri, 2 Sep 94 09:33:28 -0400 Message-Id: <9409021333.AA15678@risque.chem.rochester.edu> To: CHEMISTRY@ccl.net Subject: ignature The subroutine TRED2 in "Numerical Recipes" by Press et al.(p. 355) is used to reduce a hessian matrix to tridiagonal form prior to diagonalization. Has anyone had any experience using this routine(the so called Householder method)? It does not seem to generate the orthogonal Q matrix properly(the accumulated matrix that reduces the hessian to tridiagonal form). There appears to be a bug in the routine but I haven't been able to find it. Help from anyone who is familiar with this routine would be appreciated. From epw@ppco.com Fri Sep 2 09:50:33 1994 Received: from ppco.com for epw@ppco.com by www.ccl.net (8.6.9/930601.1506) id JAA29838; Fri, 2 Sep 1994 09:31:59 -0400 Received: from epwpc.ppco.com by ppco.com (/ ppco.1.0) id AA06975; Fri, 2 Sep 1994 08:31:25 -0500 Message-Id: <9409021331.AA06975@ppco.com> X-Sender: epw@charon.ppco.com Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Fri, 02 Sep 1994 08:35:19 +0100 To: del@ppco.com, gdp@ppco.com, pkd@ppco.com, epw@ppco.com, chemistry@ccl.net From: epw@ppco.com (Dr. Eric P. Wallis) Subject: Young Scientist Network address X-Mailer: Dear netters: I am looking for the address of the Young Scientist Bulletinboard (Network) and instructions on how to subscribe. Any help would be appreciated. Eric- *************************************************************** * Dr. Eric P. Wallis * * Computational Chemistry * * Phillips Petroleum Company Office (918)-661-7956 * * 331A PL PRC FAX: (918) 662-1097 * * Bartlesville, OK 74004 email: epw@ppco.com * *************************************************************** From LONCHARICH_RICHARD_J@Lilly.com Fri Sep 2 09:51:23 1994 Received: from Lilly.com for LONCHARICH_RICHARD_J@Lilly.com by www.ccl.net (8.6.9/930601.1506) id JAA29811; Fri, 2 Sep 1994 09:31:26 -0400 Received: from DECNET-MAIL (RX82788@MCVAX0) by INET.D48.LILLY.COM (PMDF V4.3-8 #6224) id <01HGMPALUZQO001P1E@INET.D48.LILLY.COM>; Fri, 2 Sep 1994 08:31:15 EST Date: Fri, 02 Sep 1994 08:31:15 -0500 (EST) From: Rick Loncharich Subject: CCL: VDW collapse To: chemistry@ccl.net Message-id: <01HGMPALXO76001P1E@INET.D48.LILLY.COM> X-VMS-To: MCDEV1::IN%"chemistry@ccl.net" MIME-version: 1.0 Content-transfer-encoding: 7BIT |> From: Hodgkin, Ed |> |> It is well known that molecular mechanics force fields favour 'folded' |> conformations which derive stability from large Van Der Waals terms. |> One could coin the phrase "Van Der Waals Collapse" to describe this |> effect.... |> From: David States |> . . . The most direct way to |> control for the self-association of peptide chains is to do a |> simulation that includes solvation explicitly. Note that if you do |> this as a water droplet rather than a periodic box the internal |> pressure generated by surface tension is enormous so the system will |> still collapse some compared to physiologic conditions. Furthermore, as one increases the amount of water in a water droplet simulation from 0 to 4000 water molecules the size of the protein (measured by rgyr) increases to the X-ray radius of gyration. See recent articles by B.R. Brooks et. al. Rick Loncharich Eli Lilly and Company From: LONCHARICH RICHARD J (MCVAX0::RX82788) To: FOREIGN TRANSPORT ADDRESSEE (MCDEV1::IN%"chemistry@ccl.net") From nauss@ucmod2.che.uc.EDU Fri Sep 2 09:52:30 1994 Received: from ROLL.SAN.UC.EDU for nauss@ucmod2.che.uc.EDU by www.ccl.net (8.6.9/930601.1506) id JAA29646; Fri, 2 Sep 1994 09:20:48 -0400 Received: from ucmod2.che.uc.edu by UCBEH.SAN.UC.EDU (PMDF V4.3-8 #4918) id <01HGMQO2AUCGHSIZ8X@UCBEH.SAN.UC.EDU>; Fri, 02 Sep 1994 09:08:50 -0500 (EST) Received: by ucmod2.che.uc.edu (920330.SGI/920502.SGI.AUTO) for @uc.edu:CHEMISTRY@ccl.net id AA28131; Fri, 2 Sep 94 09:11:17 -0400 Date: Fri, 02 Sep 1994 09:11:17 -0400 From: nauss@ucmod2.che.uc.EDU (Jeffrey L. Nauss) Subject: Re: CCL:Van Der Waals Collapse To: CHEMISTRY@ccl.net Message-id: <9409021311.AA28131@ucmod2.che.uc.edu> Content-transfer-encoding: 7BIT >From: states@ibc.wustl.edu (David J. States) >|> From: Hodgkin, Ed >|> >|> It is well known that molecular mechanics force fields favour 'folded' >|> conformations which derive stability from large Van Der Waals terms. >|> One could coin the phrase "Van Der Waals Collapse" to describe this >|> effect.... > >From the earliest days of charmm development, this has been a concern. >Globular proteins simulated in vacuo shrink when "true" atomic radii >are used as the basis for nonbonded interaction parameters... >The most direct way to >control for the self-association of peptide chains is to do a >simulation that includes solvation explicitly. I observed this phenomenon when I was running CHARMM a couple years ago. However, it does not appear to be a major problem with Biosym's Discover using the CVFF forcefield. I emphasis the word major as I do observe some collapse of proteins and peptides but never to the extent that CHARMM produced. Anyone have any comments on the difference between the two forcefields and this "Van Der Waals Collapse?" Is anything similar observed with AMBER or GROMOS? Jeff Nauss **************************************************************************** * UU UU Jeffrey L. Nauss, PhD * * UU UU Director, Molecular Modeling Services * * UU UU Department of Chemistry * * UU UU CCCCCCC University of Cincinnati * * UU UU CCCCCCCC Cincinnati, OH 45221-0172 * * UUUU CC * * CC Telephone: 513-556-0148 Fax: 513-556-9239 * * CC * * CCCCCCCC e-mail: nauss@ucmod2.che.uc.edu * * CCCCCCC * **************************************************************************** From A09039@VM.CC.METU.EDU.TR Fri Sep 2 10:43:10 1994 Received: from vm.cc.metu.edu.tr for A09039@VM.CC.METU.EDU.TR by www.ccl.net (8.6.9/930601.1506) id KAA01139; Fri, 2 Sep 1994 10:16:51 -0400 Message-Id: <199409021416.KAA01139@www.ccl.net> Received: from VM.CC.METU.EDU.TR by vm.cc.metu.edu.tr (IBM VM SMTP V2R2) with BSMTP id 0222; Fri, 02 Sep 94 17:14:53 TUR Received: from vm.cc.metu.edu.tr (NJE origin A09039@TRMETU) by VM.CC.METU.EDU.TR (LMail V1.2a/1.8a) with BSMTP id 8806; Fri, 2 Sep 1994 17:14:53 +0200 Date: Fri, 02 Sep 94 17:13:39 TUR From: hasan karaaslan Subject: XView installation on SGI To: chemistry@ccl.net Hello everybody, I have a problem with the installation of xview3 on SGI Indigo (IRIX 4.0.5) I have the following files from swedishchef.lerc.nasa.gov: [139.88.54.33] /libraries/xview3 files: xview3-sgi-patch.tar.Z libxview.a libolgx.a I need some help, to install the xview3 without any damage to my system... All helps appreciated... please send your comments to a09039@vm.cc.metu.edu.tr or hasan@indigo.chem.metu.edu.tr thanks From toni@athe.wustl.edu Fri Sep 2 10:59:47 1994 Received: from wugate.wustl.edu for toni@athe.wustl.edu by www.ccl.net (8.6.9/930601.1506) id KAA02152; Fri, 2 Sep 1994 10:59:47 -0400 Received: by wugate.wustl.edu (5.67b/WUSTL-0.3) with SMTP id AA16704; Fri, 2 Sep 1994 09:59:43 -0500 Received: by athe.WUStL.EDU (8.6.9/SMI-SVR4) id JAA04175; Fri, 2 Sep 1994 09:59:42 -0500 Date: Fri, 2 Sep 1994 09:59:42 -0500 From: toni@athe.wustl.edu (Toni Kazic) Message-Id: <199409021459.JAA04175@athe.WUStL.EDU> To: CHEMISTRY@ccl.net Subject: Dorothy Hodgkin died Cc: pm@mrc-lmb.cam.ac.uk Hello, I thought readers of this list would be interested to know that Dorothy Hodgkin, an eminent crystallographer and generally outstanding human being, died on approximately July 29th. Apart from the intrinsic merit and beauty of the structures she determined (mostly compounds of biochemical interest), her repeated findings of structures thought theoretically impossible helped significantly to push chemistry forward. Max Perutz' obituary of her for the Independent Newspaper (London), was posted to bionet.xtallography by Paul McLaughlin (article 947). He has graciously agreed to ask Max if it may be posted here, but in the meantime you might want to have a look at it there. Toni Kazic Institute for Biomedical Computing Washington University From heather@ramana.chem.yale.edu Fri Sep 2 11:44:23 1994 Received: from ramana.chem.yale.edu for heather@ramana.chem.yale.edu by www.ccl.net (8.6.9/930601.1506) id LAA02897; Fri, 2 Sep 1994 11:31:26 -0400 Received: by ramana.chem.yale.edu; Fri, 2 Sep 94 11:30:06 -0400 Date: Fri, 2 Sep 94 11:30:06 -0400 From: Heather Carlson Message-Id: <9409021530.AA21462@ramana.chem.yale.edu> To: chemistry@ccl.net Subject: collapsing water droplets Just another word on simulated water droplets (spherical caps)... During a simulation of a 12 A radius cap, we observed the compression previously mentioned on the net. In order to obtain the same O-O radial distribution function in a periodic cell, we have to set the NPT ensemble to 1500 atm. I realize this isn't addressing the vdw collapse, but since droplet compression was mentioned, I figured it would be of interest since adding an extra factor of compressiomn would be counter-productive. Heather Carlson heather@ramana.chem.yale.edu From SHAUN@jason.uthct.edu Fri Sep 2 11:58:29 1994 Received: from jason.uthct.edu for SHAUN@jason.uthct.edu by www.ccl.net (8.6.9/930601.1506) id LAA02500; Fri, 2 Sep 1994 11:11:47 -0400 Date: Fri, 2 Sep 1994 10:11:38 -0500 (CDT) From: "Shaun D. Black" To: chemistry@ccl.net Message-Id: <940902101138.8395@jason.uthct.edu> Subject: Re: CCL:Young Scientist Network address Dr. Eric Wallis writes: > Dear netters: > I am looking for the address of the Young Scientist Bulletinboard (Network) > and instructions on how to subscribe. Any help would be appreciated. > Eric- > (stuff deleted) The address for the Young Scientist Network (YSN) has changed recently and is, for subscriptions: ysnadm@crow-t-robot.stanford.edu Send the message: subscribe YSN (if you want to receive the full YSN digest each day) subscribe MYSN (if you want to receive the moderated YSN abou weekly) (you can subscribe to either or both if you like) The header of each digest contains all the e-mail addresses for posting, archives, advisors group, WWW server, Gopher, etc. Bye for now, and I hope this helps. Contact me if you have any problems with this. Best regards, Shaun (shaun@jason.uthct.edu) From yama@mol.biol.ethz.ch Fri Sep 2 12:17:02 1994 Received: from bernina.ethz.ch for yama@mol.biol.ethz.ch by www.ccl.net (8.6.9/930601.1506) id LAA02802; Fri, 2 Sep 1994 11:21:50 -0400 Received: from odin (actually odin.ethz.ch) by bernina.ethz.ch with SMTP inbound; Fri, 2 Sep 1994 17:21:24 +0200 From: Bernhard Anton Pabsch Received: from noldi by odin id AA15804; Fri, 2 Sep 94 17:21:23 +0200 Date: Fri, 2 Sep 94 17:21:41 +0200 Message-Id: <9409021521.AA07191@noldi> Received: by noldi id AA07191; Fri, 2 Sep 94 17:21:41 +0200 To: xiang@nemesis.rose.brandeis.edu, CHEMISTRY@ccl.net Subject: Re: CCL:user groups for MSI and TRIPOS Hi Phil, for MSI or to be more precise for CHARMM there is charmm-bbs-request@emperor.harvard.edu and for TRIPOS or SYBYL there is sybylreq@quant.chem.rpi.edu to join send them a subscribe mail. Information about modelin mail-exploders are listet in every Reviews in Computational Chemistry in the Appendix: Compendium of Software for Molecular Modeling. Una volta aperto, conservare in frigo! bap-man __________________________________________________________________________ Bernhard A. Pabsch yama@mol.biol.ethz.ch Laboratorium fuer organische Chemie MOM_10@CZHETH5A.bitnet ETH Hoenggerberg (HPM G32) Tel. ++41 1 633 34 89 CH-8093 Zuerich/Switzerland Fax ++41 1 372 00 53 __________________________________________________________________________ From sling@euclid.chem.washington.edu Fri Sep 2 12:43:09 1994 Received: from euclid.chem.washington.edu for sling@euclid.chem.washington.edu by www.ccl.net (8.6.9/930601.1506) id MAA03817; Fri, 2 Sep 1994 12:22:20 -0400 Received: by euclid.chem.washington.edu (AIX 3.2/UCB 5.64/4.03) id AA20824; Fri, 2 Sep 1994 09:21:04 -0700 Date: Fri, 2 Sep 1994 09:21:04 -0700 From: sling@euclid.chem.washington.edu (Song Ling) Message-Id: <9409021621.AA20824@euclid.chem.washington.edu> To: chemistry@ccl.net Subject: Young Scientists' Network ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ To send a message to entire distribution: ysn@crow-t-robot.stanford.edu Miscellaneous administration questions: ysnadm@crow-t-robot.stanford.edu for information: mail -s "help" ysn-request@crow-t-robot.stanford.edu ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ From IRIKURA@ENH.NIST.GOV Fri Sep 2 13:43:12 1994 Received: from ENH.NIST.GOV for IRIKURA@ENH.NIST.GOV by www.ccl.net (8.6.9/930601.1506) id MAA04382; Fri, 2 Sep 1994 12:59:40 -0400 From: Received: from ENH.NIST.GOV by ENH.NIST.GOV (PMDF V4.2-13 #4653) id <01HGMYK8V1TS006LAC@ENH.NIST.GOV>; Fri, 2 Sep 1994 12:58:09 EDT Date: Fri, 02 Sep 1994 12:58:08 -0400 (EDT) Subject: Ab initio spin-orbit codes? To: chemistry@ccl.net Message-id: <01HGMYK8WNPE006LAC@ENH.NIST.GOV> X-PS-Qualifiers: /LEFT_MARGIN=6/SIZE=11 X-VMS-To: IN%"chemistry@ccl.net" X-VMS-Cc: IRIKURA MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Content-transfer-encoding: 7BIT Is there a publicly-available (commercial or otherwise) ab initio program that can cope with spin-orbit coupling/splitting? For example, linear 2-Pi molecules. Thanks for any help--I'll post a summary of responses. Karl ---------------------------------------------- Dr. Karl Irikura Chemical Kinetics and Thermodynamics Division National Institute of Standards and Technology Gaithersburg, MD 20899 ---------------------------------------------- From zhu@Homer.PHYS.UH.EDU Fri Sep 2 14:43:13 1994 Received: from Homer.PHYS.UH.EDU for zhu@Homer.PHYS.UH.EDU by www.ccl.net (8.6.9/930601.1506) id OAA05135; Fri, 2 Sep 1994 14:02:38 -0400 Received: by Homer.PHYS.UH.EDU id AA07926 (5.65c+/IDA-1.4.4 for chemistry@ccl.net); Fri, 2 Sep 1994 13:02:28 -0500 From: Wie Zhu Message-Id: <199409021802.AA07926@Homer.PHYS.UH.EDU> Subject: 2D or 3D FFT code? To: chemistry@ccl.net Date: Fri, 2 Sep 94 13:02:27 CDT X-Mailer: ELM [version 2.3 PL11] Dear Netters, Could someone tell me where to get the 2D/3D-FFT (similar to CFFT2D on Cray) source code? Thanks for any information. zhu@homer.phys.uh.edu From mjf@iris120.biosym.com Fri Sep 2 14:55:40 1994 Received: from bioc1.biosym.com for mjf@iris120.biosym.com by www.ccl.net (8.6.9/930601.1506) id MAA04287; Fri, 2 Sep 1994 12:46:30 -0400 Received: from iris120.biosym.com by bioc1.biosym.com (5.64/0.0) id AA16625; Fri, 2 Sep 94 09:45:30 -0700 Received: by iris120.biosym.com (931110.SGI/930416.SGI) for @bioc1.biosym.com:chemistry@ccl.net id AA09777; Fri, 2 Sep 94 09:45:41 -0700 Date: Fri, 2 Sep 94 09:45:41 -0700 From: mjf@biosym.com (Mark J Forster ) Message-Id: <9409021645.AA09777@iris120.biosym.com> To: chemistry@ccl.net Subject: Routine TRED2 In response to > TRED2 in "Numerical Recipes"... > ...Has anyone had any experience using this routine Numerical recipes is available in C, FORTRAN, PASCAL even BASIC versions, which are you referring to ? Is only one version buggy or are they all ? I have previously used the C language TRED2/TQLI routines and performed a comparison with the Jacobi algorithm for diagonalizing a real symmetric matrix. I found the former to give the same results but to be 2-3 times quicker. Hope this helps. Best Wishes __________________________________________________________ Mark / ___ / / /| / Mark J Forster / / | / Biosym Technologies Inc, /__/__|/ \__O_/ 9685 Scranton Rd, /__/ | San Diego, CA 92121, USA. / | /| Tel: (619) 458 9990 / o |<-------- / | FAX: (619) 458 0136 /__ __| e-mail: mjf@biosym.com / Follower of Manchester United FC. / FA cup winners 1990, / European cup winners cup winners 1991, League cup winners 1992, / FA Premier League champions 1993, FA charity shield winners 1993/4. / FA Premier League champions AND FA cup winners 1994. / FA Charity shield winners 1994/5 /________________________________________________________________ ******************************************************************************* * DISCLAIMER: Unless indicated otherwise, everything in this note is * * personal opinion, not an official statement of Biosym Technologies, Inc. * ******************************************************************************* From ashy@rose.chem.wesleyan.edu Fri Sep 2 15:43:13 1994 Received: from rose.chem.wesleyan.edu for ashy@rose.chem.wesleyan.edu by www.ccl.net (8.6.9/930601.1506) id NAA05034; Fri, 2 Sep 1994 13:52:57 -0400 Received: by rose.chem.wesleyan.edu (AIX 3.2/UCB 5.64/4.03) id AA20763; Fri, 2 Sep 1994 13:49:23 -0400 Date: Fri, 2 Sep 1994 13:49:23 -0400 Message-Id: <9409021749.AA20763@rose.chem.wesleyan.edu> From: Ashwin Dinakar To: xiang@nemesis.rose.brandeis.edu Cc: CHEMISTRY@ccl.net In-Reply-To: <9409021319.AA21948@nemesis.rose.brandeis.edu> (xiang@nemesis.rose.brandeis.edu) Subject: Re: CCL:user groups for MSI and TRIPOS Hi ! Iam interested in discussing about CHARMm and QUANTA and some of the problems I have encountered using the above programs. I was wondering whether anyone else would be interested. Ashwin Dinakar, Wesleyan University. From psubram@texaco.com Fri Sep 2 15:50:44 1994 Received: from texaco.com for psubram@texaco.com by www.ccl.net (8.6.9/930601.1506) id OAA05838; Fri, 2 Sep 1994 14:34:18 -0400 Received: by texaco.com (4.1/SMI-4.1) id AA16704; Fri, 2 Sep 94 13:34:04 CDT Date: Fri, 2 Sep 94 13:34:04 CDT From: psubram@texaco.com (Palavo Subramanian) Message-Id: <9409021834.AA16704@texaco.com> To: chemistry@ccl.net Subject: Monolayer modeling I am looking for information on modeling monolayer formation. I am mainly intersted in the monolayer formed from a polymer(s) in solvent(s). Any suggestions, references will be greatly appreciated. I will summarize the results. Thanks , P.S.Subramanian psubram@texaco.com From bear@ellington.pharm.arizona.edu Fri Sep 2 16:43:13 1994 Received: from ellington.pharm.arizona.edu for bear@ellington.pharm.arizona.edu by www.ccl.net (8.6.9/930601.1506) id PAA06967; Fri, 2 Sep 1994 15:30:04 -0400 Received: by ellington.pharm.arizona.edu (931110.SGI/920502.SGI) for chemistry@ccl.net id AA27292; Fri, 2 Sep 94 12:29:26 -0700 Date: Fri, 2 Sep 94 12:29:26 -0700 From: bear@ellington.pharm.arizona.edu (Soaring Bear) Message-Id: <9409021929.AA27292@ellington.pharm.arizona.edu> To: chemistry@ccl.net Subject: CCL:Van Der Waals Collapse |> From: Hodgkin, Ed |> force fields favour 'folded' conformations |> From: David States |> most direct way to control for the self-association |> of peptide chains is to do a simulation that includes |> solvation explicitly... |> From: Jeff Nauss |>Is anything similar observed with AMBER... In my work with solvated DNA under AMBER dynamics with periodic boundary, water does NOT stop collapse. bear * UU UU SOARING BEAR * * UU UU Computer Aided Drug Design * * UU UU A University of Arizona, New Pharmacy 404 * * UUUU AAA Tucson, AZ 85721 602-626-6133 * * AA AA where the sun shines * * AAAAAAA * * AA AA e-mail:bear@ellington.pharm.arizona.edu * From jesus@canarylab.chem.nyu.edu Fri Sep 2 16:49:38 1994 Received: from acf6.acf.nyu.edu for jesus@canarylab.chem.nyu.edu by www.ccl.net (8.6.9/930601.1506) id PAA07038; Fri, 2 Sep 1994 15:38:51 -0400 Received: from canarylab.chem.nyu.edu by ACFcluster.NYU.EDU (PMDF V4.3-8 #5342) id <01HGN4AJOLAOQUFV5D@ACFcluster.NYU.EDU>; Fri, 2 Sep 1994 15:38:51 EDT Received: by canarylab.chem.nyu.edu (940406.SGI/931108.SGI.AUTO.ANONFTP) for @acfcluster.nyu.edu:CHEMISTRY@ccl.net id AA29869; Fri, 2 Sep 94 15:45:57 -0400 Date: Fri, 02 Sep 1994 15:45:57 -0400 From: jesus@canarylab.chem.nyu.edu (Jesus M. Castagnetto Mizuaray) Subject: Summary: PD EHT packages To: CHEMISTRY@ccl.net Message-id: <9409021945.AA29869@canarylab.chem.nyu.edu> Content-transfer-encoding: 7BIT This is the summary of repsonses to my query on PD EHT software. I couldn't send it before because I am writing my Thesis Research Proposal. I'll respond to all who answered. For what it seems we are going to stick with CACAO at least for now, because we are in process of upgrading our systems and connections. But we seriously will consider using the QCMP #116 QCPE package, as soon as things get settle down (hardware-wise) around here. Thanks for the help/tips to compile/use forticon in a SGI machine, and thosw who gave more info about CACAO, and thanks to Leif Laaksonen for his offer of a modified version of FORTICON8. Hope this helps somebody else. Greetings P.S. The answers have been stripped of non-esential to save bandwith. My apologies to all who were confused my signature. In my country of origin (Peru) we use the father's and mother's last name ;-) *** Initial query > Mon Aug 29 05:52:31 1994 > Hello all. Does anybody know about any PD EHT program (or programs) > for Unix. I got CACAO from the CCL server, but would prefer to have > something running in our Indigo, because transfering data to a PC > is not an easy task, because of the way the machines are connected > Also found in the CCL archives: forticon8.f, but no documentation > except the one in the program, but for what I can see it was written > with a VAX in mind. > Thanks in advance for any lead/hint/idea. I prefer to receive info > to my mailbox (below), I'll summarize to the list as soon as I got > some answers. > Greetings. *** From braendle@solar.iac.unibe.ch (Martin Braendle) > Date: Mon, 29 Aug 1994 11:54:44 +0200 (DFT) > Subject: Re: CCL:PD EHT software? > > Dear Dr. Mizuaray > > An extended-Hueckel package called ICONC&INPUTC, which should be easily portable > to UNIX, is available at QCPE (QCMP #116), including sources and manual. It in- > volves FMO, a modified distance-dependent Wolfsberg-Helmholz approximation, and > an electrostatic core-core repulsion term. We are running it under IBM RS/6000 > AIX 3.2.3, VMS and MS/DOS. For operating-system-specific implementation que- > stions you may contact me. > > With kind regards > > Martin Braendle > > -------------------------------------------------------------------------------- > Martin Braendle, PhD, Institute for Inorganic and Physical Chemistry, > University of Berne, Freiestr. 3, CH-3012 Berne, Switzerland, > Tel. ~41 31 631 42 25, Fax ~41 31 631 39 94, Email braendle@solar.iac.unibe.ch > -------------------------------------------------------------------------------- *** From: Leif Laaksonen > Date: Mon, 29 Aug 1994 12:57:36 +0300 (EET DST) > Subject: ICON8 > > Hi, > > I have a modified version of FORTICON8 which I have enhanced: > (1) Dynamic memory allocation through a small c-program > (2) Number of atoms up to 5000 (eats horrible much of memory) > (3) Understands the atom names used in protein modelling > (4) Changed a bit of the output to satisfy my needs > (5) Produces the input to an molecular electrostatic potential > program VSS. > (6) ICON8 runs on all Unix boxes. > > If you want the code I can mail the stuff to you. > Regards, > > -leif laaksonen > ------------------------------------------------------------------- > Leif Laaksonen | > Center for Scientific Computing | Phone: 358 0 4572378 > P.O. Box 405 | Telefax: 358 0 4572302 > FIN-02101 Espoo | Voice Mail: 358 486257407 > FINLAND | Mail: Leif.Laaksonen@csc.fi > --------URL: http://www.csc.fi/lul/leif/leif.laaksonen.html-------- > Who has seen the wind? > Neither you nor I: > But when the trees bow down their heads > The wind is passing by. > > Christina Rossetti > ------------------------------------------------------------------- *** From: ascanio@salve3.salve.edu > Date: Mon, 29 Aug 1994 09:27:40 EDT > Subject: "The Last Word....." > Jesus: > 1. Who publishes "The Last Word-The Ultimate Scientific > Dictionary" > 2. You can print CACAO*.HGL and MOAN1.HGL using a PC Graphics > Star NX10 and IBM 6-color Pen Plotter. You don't need the > Laser printers. > 3. Can't help you on your request for other EHT program. > > Ciao > Pacem in Calcio > /////////// > |/////| > | 3 | > Ascanio Giuseppe DiPippo, C.H.S.,C.A.O.S. ////// / liter \ > Salve Regina University ___ |//| / \ > Newport, Roe Dylin 02840 ___| |__ / \ | et cum | > ascanio@salve3.salve.edu |___ ___| | H2O | | spiriti | > 401-847-6650 | | | | | vini | > 41 30'N 71 20'W |__| -------- -------------- > **************************************************************** > * " Neva trusst n nee won whoo kan ownly spel a wird won whey" * > ******************** Mock Twane ******************************** *** From: SATYAM@vms.cis.pitt.edu > Date: Mon, 29 Aug 1994 11:15:00 -0500 (EST) > Subject: Re: CCL:PD EHT software? > > Dear Mizuaray, > The forticon8 will work on INDIGO.. > IMPORTANT... while compiling remember to give flag -static i.e. > f77 -static forticon8.f -o executable.file > > Have fun. > Satyam *** From: bowlus@palres.dnet.sandoz.com (Steve Bowlus) > Date: Mon, 29 Aug 94 10:18:13 -0400 > Subject: EHT > > I've used forticon on my ESV/4D35/Indigo2 without incident. The conversion > from the VAX code is straightforward -- if I remember correctly, a few > things get changed to keep the compiler from complaining, but there was > nothing even a non-programmer (like myself) couldn't fix. > > sb > > =========================================================================== > Stephen B. Bowlus, Ph.D. Computer-Aided Molecular Design > Research Division > e-mail: bowlus@sandoz.com Sandoz Agro, Inc. > Phone: + 1 415 354 3904 975 California Ave. > Fax: + 1 415 857 1125 Palo Alto, CA 94304 > =========================================================================== *** From: slee@theochem.uwaterloo.ca (Tom Slee) > Date: Mon, 29 Aug 94 21:57:15 -0400 > Subject: Re: CCL:PD EHT software? > > I don't have any specific address for you, although most > Extended Huckel programs I've seen around have their origins > in Roald Hoffmann's laboratory. Really, I'm writing to point > out that in order to get the most from Extended Huckel as a > method you need not only an EHT program (such as forticon), > which produces the MO's etc., but also a program such as FMO > (developed in Hoffmann's lab I believe), which allows you to > construct the fragment interaction diagrams which make the > method so useful. Cacao is particularly attractive because > it contains both programs. > > Yours > > Tom Slee ----- Jesus M. Castagnetto Mizuaray | "Organic Chemistry: The practice Dep.of Chemistry - New York University | of transmuting vile substances 4 Washington Pl, Room 514. NY 10003 | into publications" (The Last Word- jesus@canarylab.chem.nyu.edu | The Ultimate Scientific Dictionary) From bobf@msi.com Fri Sep 2 17:43:14 1994 Received: from msi.com for bobf@msi.com by www.ccl.net (8.6.9/930601.1506) id RAA08470; Fri, 2 Sep 1994 17:00:38 -0400 Received: from wednesday (wednesday.msi.com) by msi.com (4.1/SMI-4.1) id AA12769; Fri, 2 Sep 94 17:00:55 EDT Received: by wednesday (931110.SGI/911001.SGI) for CHEMISTRY@ccl.net id AA07863; Fri, 2 Sep 94 17:03:35 -0400 Message-Id: <9409022103.AA07863@wednesday> From: Bob Funchess Date: Fri, 2 Sep 1994 17:03:34 -0400 Organization: Molecular Simulations Inc. Phone: (617) 229-9800 ext. 202 To: CHEMISTRY@ccl.net Subject: RE: CCL:user groups for MSI and TRIPOS > Do discussion groups for MSI and TRIPOS users exist? Molecular Simulations does maintain several mailing lists for its users. I'll append a copy of the announcement document below describing how to subscribe and some information about these lists. Regards, Bob Funchess PS Some fonts do not sufficiently distinguish between the number "1" and the lowercase letter L. All the lists below end with -L, not with -1. Commands sent to listproc are not case sensitive. ------------------------------------------------------------------------- The MSI Scientific Support Bulletin Board mailing lists are intended to provide an informal forum for users of MSI products to discuss various aspects of the programs. The lists are NOT designed to be an official channel for product support; all requests for technical product support should continue to go through the Scientific Support hotline or via e-mail to the phone, fax, and e-mail addresses provided on this page. There are currently three mailing lists generally available on the MSI Scientific Support Bulletin Board which uses the ListProcessor 6.0(c) software. The lists are: QUANTA-L (address: quanta-l@msi.com) This list is for users of QUANTA and related programs (e.g. ChemNote). 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In order to subscribe to any of the lists, a user should send e-mail to the server (for MSI, this address is: listproc@msi.com) with a request of the format: subscribe where should let people know who the subscriber is. For example, if Bob Funchess wanted to subscribe to the QUANTA-L mailing list, he would send an e-mail message to listproc@msi.com consisting of the line: subscribe quanta-l Bob Funchess A subscriber may send messages to the list. This is a regular e-mail message addressed to the list address itself (not the server address!). Any messages sent to the list address will be automatically distributed to all subscribers. A subscriber who wishes to be taken off the distribution list should send this message to the server listproc@msi.com; for example: unsubscribe quanta-l For information on other commands, the server accepts help requests of the form: help [topic] If no topic is specified, the general help file will be sent. Each mailing list has its messages automatically archived on a monthly basis. In addition, some of the archives contain other useful files that can be sent via e-mail upon request. To access the archives, an 'index' request is sent to listproc@msi.com to find out what archives are available and what files may be obtained from these archives. A user then may request one or more files via a 'get' request. For example: get xplor xplor.bat will send the file xplor.bat from that archive. In the case of binary files, what the user receives is a uuencoded file, possibly split into several parts depending on its size. Archives may be searched with the 'search' command. We hope you find this new service to be of use to you. Please send any comments or suggestions to the MSI Scientific Support group or to the bulletin board itself! -- Dr. Robert B. Funchess Molecular Simulations Inc. Senior Support Scientist 16 New England Executive Park bobf@msi.com Burlington, MA 01803-5297 (617) 229-9800 x202 FAX (617) 229-9899 From jgonda@kosice.upjs.sk Fri Sep 2 18:43:13 1994 Received: from kosice.upjs.sk for jgonda@kosice.upjs.sk by www.ccl.net (8.6.9/930601.1506) id RAA09224; Fri, 2 Sep 1994 17:53:26 -0400 Received: by kosice.upjs.sk id AA25916 (5.65c/IDA-1.4.4 for CHEMISTRY@ccl.net); Fri, 2 Sep 1994 23:53:53 +0100 Date: Fri, 2 Sep 1994 23:53:53 +0100 (WET DST) From: "RNDr. Jozef Gonda" Subject: user groups for Gaussian 92 and GAMESS To: CHEMISTRY@ccl.net Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear netters, do discussion groups for Gaussian 92 and GAMESS user exists? Jozef Gonda Safarik University