From Jeffrey.Gosper@brunel.ac.uk Mon Nov 7 06:24:32 1994 Received: from monge.brunel.ac.uk for Jeffrey.Gosper@brunel.ac.uk by www.ccl.net (8.6.9/930601.1506) id GAA20212; Mon, 7 Nov 1994 06:00:17 -0500 Received: from chem-pc-13.brunel.ac.uk by monge.brunel.ac.uk with SMTP (PP) id <16063-0@monge.brunel.ac.uk>; Mon, 7 Nov 1994 11:00:01 +0000 Date: Mon, 7 Nov 1994 10:58:08 GMT From: Jeffrey J Gosper Reply-To: Jeffrey.Gosper@brunel.ac.uk Subject: Animation of chemical information To: chemistry@ccl.net Message-ID: Priority: Normal MIME-Version: 1.0 Content-Type: TEXT/PLAIN; CHARSET=US-ASCII I have recently developed a program (originally called mop2xyz now entitled RE_VIEW) which is capable of animating chemical reactions/phenomena given the coordinates on steps along the process. My program is capable of producing excellent quality images (ray-traced) and I am using these images to prepare animation sequences (.flc files) that run under windows using the freely available AAplay. I am now looking for interesting files to animate (what I need are concatinated multi-structure xyz formated files, although other coordinate files could be used). Such files could be a chemical reaction, dynamics run, docking experiment, etc as long as the coordinates of the steps are known. I will happily distribute any animation sequences I develop to the net. Yours sincerely Dr Jeff Gosper - Brunel From krasimir@qtp.ufl.edu Mon Nov 7 09:24:30 1994 Received: from crunch for krasimir@qtp.ufl.edu by www.ccl.net (8.6.9/930601.1506) id JAA21858; Mon, 7 Nov 1994 09:15:42 -0500 Received: by crunch (5.x/4.11) id AA21456; Mon, 7 Nov 1994 09:15:41 -0500 Date: Mon, 7 Nov 1994 09:15:41 -0500 From: "Stavrev Krassimir" Message-Id: <9411071415.AA21456@crunch> To: chemistry@ccl.net Subject: Mac software inquiry Dear Netters, I need to download big binary files from Macintosh hard drive to diskettes. Does anybody know about a software that can transfer such files (several Mb each) onto 2 or more diskettes ? Thank you. Krassimir Stavrev krasimir@qtp.ufl.edu From gotwals@mcnc.org Mon Nov 7 09:30:48 1994 Received: from robin.mcnc.org.mcnc.org for gotwals@mcnc.org by www.ccl.net (8.6.9/930601.1506) id JAA21734; Mon, 7 Nov 1994 09:09:32 -0500 Received: from [128.109.178.39] by robin.mcnc.org.mcnc.org (8.6.9/MCNC/8-10-92) id JAA06680; Mon, 7 Nov 1994 09:09:06 -0500 for Message-Id: <199411071409.JAA06680@robin.mcnc.org.mcnc.org> Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Mon, 7 Nov 1994 09:12:38 +0500 To: chemistry@ccl.net From: gotwals@mcnc.org (Bob Gotwals) Subject: ANNOUNCEMENT: Molecular Modeling Workshop Introduction to Molecular Modeling and Drug Design January 24-26,1995 North Carolina Supercomputing Center Research Triangle Park, North Carolina The North Carolina Supercomputing Center (NCSC) is pleased to offer "Introduction to Molecular Modeling and Drug Design." World-renowned experts from pharmaceutical companies and academia will lecture on the state-of-the-art techniques in molecular modeling and drug design such as molecular dynamics, ligand based drug design, receptor based drug design, protein structure prediction, molecular databases, application of quantum mechanical methods to molecular modeling, and information retrieval from World Wide Web using Mosaic. In the hands-on sessions, workshop participants will learn how to apply the techniques using the state-of-the-art modeling programs from three leading software companies (Biosym Technologies, Inc., Molecular Simulations Inc. and Tripos Associates, Inc.). After completion of the workshop, participants will be able to enhance their research and shorten their drug design cycle considerably by applying the techniques learned in the workshop. Attendance will be limited to fifteen to allow adequate training to all attendees. For more information please contact Dr. Hong Ma via e-mail to hongma@ncsc.org or by calling 919-248-1176. Registration fees are $120.00 for North Carolina academic institutions, $180.00 for out-of-state academic institutions. Industrial fees are $750.00. Agenda January 24, 1995 - Tuesday ----------------- 8:30 - 8:45 AM Remarks and Course Overview 8:45 - 10:00 AM Molecular Modeling in Drug Design 10:00 - 10:15 AM Break 10:15 - 12:00 AM Lab I: Graphic Interface 12:00 - 1:00 PM Lunch 1:00 - 2:30 PM Ligand Based Drug Design 2:30 - 5:00 PM Lab II: Pharmacophore Model Generation 5:00 - 7:00 PM Dinner 7:00 - 8:00 PM Molecular Databases 8:00 - 10:00 PM Lab III: Molecular Database January 25, 1995 - Wednesday ----------------- 8:30 - 10:00 AM Molecular Mechanics and Dynamics 10:00 - 10:15 AM Break 10:15 - 12:00 AM Lab IV: Minimization and Dynamics 12:00 - 1:00 PM Lunch 1:00 - 2:00 PM Ab Initio and Semi-empirical Methods 2:00 - 2:05 PM Break 2:05 - 3:05 PM Density Functional Method 3:05 - 5:00 PM Lab V: Application of Quantum Mechanics Methods 5:00 - 7:00 PM Dinner 7:00 - 10:00 PM Optional Lab Time January 26, 1995 - Thursday ----------------- 8:30 - 10:00 AM Protein Structure Prediction 10:00 - 12:00 AM Lab VI: Protein Structure Prediction 12:00 - 1:00 PM Lunch 1:00 - 2:00 PM Receptor Based Drug Design 2:00 - 4:00 PM Lab VII: Receptor Based Drug Design 4:00 - 5:15 PM Drug Design -- A Practical Example LECTURERS: Mike Agostino Glaxo Inc. (RTP, NC) Webb Andrews Burroughs Wellcome (RTP, NC) Frank Brown Glaxo Inc. (RTP, NC) Lee Bartolotti North Carolina Supercomputing Center (RTP, NC) Alexander Tropsha School of Pharmacy, University of North Carolina (Chapel Hill, NC) Mike Mitchell Becton Dickinson Research Center (RTP, NC) Mark Murcko Vertex (Cambridge, MA) Lee Pedersen Department of Chemistry, University of North Carolina (Chapel Hill, NC) INSTRUCTORS: Lee Bartolotti North Carolina Supercomputing Center (RTP, NC) Hong Ma North Carolina Supercomputing Center (RTP, NC) Scott Kahn Biosym Technologies, Inc. K. Raghavan Molecular Simulations Inc. Chris Van Dyke Tripos Associates, Inc. From cletner@remcure.bmb.wright.edu Mon Nov 7 09:32:40 1994 Received: from remcure.bmb.wright.edu for cletner@remcure.bmb.wright.edu by www.ccl.net (8.6.9/930601.1506) id JAA21963; Mon, 7 Nov 1994 09:20:21 -0500 Received: by remcure.bmb.wright.edu (931110.SGI/921111.SGI.AUTO) for CHEMISTRY@ccl.net id AA08075; Mon, 7 Nov 94 09:11:05 -0800 Date: Mon, 7 Nov 1994 09:06:10 -0800 (PST) From: Charles Letner Subject: SUmmary: more AMBER types To: Computational Chemistry List Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello, Last week I asked about the validity of using standard atom type for non-protein molecules. As promised here is the summary of responses. Thanks to all who responded, Chuck Charles Letner Wright State University Department of Biochemistry Dayton, OH 45435 e-mail: cletner@remcure.bmb.wright.edu -------------------------- From: Irene Newhouse The question is, do you believe in mystical properties for amino acids, or are they just chemicals? If you believe they're just chemicals, then you can use the atom types anywhere. You MAY, in certain cases, have a chemical in which the particular bond/angle/torsion you're interested in has properties that differ significantly from the norm, in which case you need to derive your own parameters. Otherwise, a cetain sting of 3 atoms is that string is that string.... (I wouldn't use the tetrahedral C parameters from AMBER for a cyclopropyl group, for example. On the other hand, I've been doing some work with carvone, a cyclohexenone, & find no reason not to use standard parameters for it. You may find, as I did, that not all your bend parameters have been defined in AMBER, & have to the H & P method to get THOSE.) Irene Newhouse --------------------------- From: Ajay Hi Charles, Re: your question about using AMBER atom types for MD on substrates. i/we have successfully done this on two projects: a) Free energy perturbation calculations involving distamycin & DNA b) Molecular docking of protein ligand complexes. Both have worked out successfully. In general, of course, this is a difficult question to answer. Also, i have no idea how new parameters work in conjuction with AMBER. It would be interesting to see other's experiences. ------------------------------------------ From: George Seibel > I just finished reading the summary of kd7@tower.york.ac.uk about >atom types in AMBER. It seems that this approach of taking a atom type >from the AMBER force field and using this as an atom type in a non-protein >molecule is OK. However, I'm wondering how general this is. I'm planning >on including substrates in some of my upcoming MDs. As these only contain >C, H, N, and O, I can probably find similar atoms among the standard atoms >of AMBER. So, is this reasonable or should I still think about creating >new parameters (ala tha Hopfinger & Pearlstein, 1984 article)? I'd be >very interested in opinions as well as aspects that should be considered >when making this decision. It's fine for a first approximation. You should do a few minimizations of your small molecule and compare the results to experimental structures. The Cambridge Crystallographic Database is very useful in this regard. You would also like to get conformational energy differences right, at least within reason... These days, you can often obtain the needed energies from QM calcs with a healthy basis set. ------------------------------------------ From: Brad Isbister Charles Letner writes about the selection of atom types in AMBER. The selection of atom types should always use a data set which resembles the compounds to be investigated. The original AMBER parameters which were derived for proteins and nucleic acids are pretty good for the functional groups found in such systems (peptide backbone, AA sidechains, C, T, G, A, etc). If your system includes other functional groups, a literature search for AMBER parameters which better reflect the 'real' system is a good idea. These new atom types can be included in an frcmod file for addition to the standard parameter set. Several papers have been written on 'non-standard' functional groups. In my work, I use the parameters for carbohydrates from S.W Homans, Biochemistry, 1990, 29, 9110-9118. If you want to know just what compounds were used to derive the standard AMBER parameter set, get the original AMBER papers: Kollman, Case, et al, JACS, 1984, 106, 765-784 and Kollman, Case, et al, J. Comp. Chem., 1986, 7, 230-252. You should also look in the AMBER manual p23-24 for more info on the parameter databases. I've seen rumblings of "Does anyone(else) want to set up a database of published AMBER parameters (or references to such)?" But I don't think anyone has taken the plunge and volunteered. There is always the possibility that your compound is very different from anything you can find. In that case, refer to some papers on deriving atom, bond, angle, and torsion parameters from spectroscopic data and/or Quantum Mechanical simulation. I haven't had to go that route yet. Perhaps some others on the CCL can help out with the references? In the end, Molecular Mechanics is a game of assumptions. Too many guesses and your results are worthless or misleading; too few and you'll be running very long and inefficient simulations. You'll have to determine how similar the database compounds are to the compound of interest. Good Luck! -Brad From janrad@tiger.chem.uw.edu.pl Mon Nov 7 16:24:35 1994 Received: from tiger.chem.uw.edu.pl for janrad@tiger.chem.uw.edu.pl by www.ccl.net (8.6.9/930601.1506) id PAA28458; Mon, 7 Nov 1994 15:32:19 -0500 Received: by tiger.chem.uw.edu.pl (AIX 3.2/UCB 5.64/4.03) id AA12702; Mon, 7 Nov 1994 20:25:43 +0100 Date: Mon, 7 Nov 1994 20:25:43 +0100 From: janrad@tiger.chem.uw.edu.pl (Jan Radomski) Message-Id: <9411071925.AA12702@tiger.chem.uw.edu.pl> To: chemistry@ccl.net Subject: SUMMARY: problems running MOPAC from Sybyl ver. 6.1 Cc: janrad@tiger.chem.uw.edu.pl ------ Dear All, many thanks to all of you who replied to my plea for urgent help with the problems running MOPAC from Sybyl ver. 6.1. As it turns out the reason is more complex than simple file permission settings. Read mesage from Wayne Steinmetz below. Have a good day, Regards, Jan P. Radomski ---------------------------- > Date: Sun, 6 Nov 1994 07:33:08 +0100 > From: janrad (Jan Radomski) > Subject: problem running MOPAC from SYBYL 6.1 > ---- > Dear Netters, > I have problem running MOPAC from SYBYL ver. 6.1, > any attempt ends with some mysterious crashes. > Any pointers would be greatly appreciated asap, > I must prepere class for students and there is no > support during weekends. > Regards, > Jan Radomski =============================================================== Date: Sun, 6 Nov 1994 10:27:16 -0600 From: Mr. Berkley Shands ------ See if your working directory is NFS mounted. You might have the classic "SYSVR4" security problem as follows... server foo: exports disk /a. client machine xxx: mounts foo:/a on /b (not an identical names path). You can use the /b device, but if you cd /b; pwd; system V reams you with can't determine current directory. Sometimes (on suns) you could fake the system out by aliasing "pwd" as "echo $cwd". Hope this helps... berkley Shands ================================================================ Date: Sun, 06 Nov 1994 11:30:51 -0700 (PDT) From: Wayne Steinmetz Subject: MOPAC with Sybyl ------ I just installed the R4000 version of Sybyl Version 6.1 and MOPAC on an Indy. Sybyl worked but MOPAC crashed. The problem was solved with one call to Tripos. Here is what worked here. 1) You need swap space. Tripos recommends 150 MB. I reserved 200 MB. The following UNIX commands were used. mkdir -p /var/swap /usr/sbin/mkfile 200m /var/swap/swap1 /sbin/swap -a /var/swap/swap1 To make the change permanent, add the following line to your /etc/fstab file. /var/swap/swap1 swap swap pri=3 You can get a report on your current swap capacity by entering /etc/swap -l 2) The V6.1 code for a R4000 processor has a bug! You'll have to settle for the R3000 code. To install the code which works, insert your CD-ROM in the drive and enter the following: cd /$TA_ROOT tar -xvf /CDROM/sybexe.tar bin/mopac 3) Make sure that NetBatch works and has been installed correctly. I hope this works for your. With best wishes, Wayne Steinmetz ======================================================================== From: BAELL@mel.dah.csiro.au (Jonathan Baell) Date: Mon, 07 Nov 94 13:23 ----- I have had a similar problem before. It happened after I had run sybyl inadvertantly as root. I subsequently tried to run some files in batch as a general user and wasn't allowed to because I didn't own the files....i.e. check the ownership of the user (I'm sure you have and you wouldn't think it a problem if rwx is OK, but it sounds like you want any help possible). +----------------------------------------------------------------------+ Dr Jonathan Baell Senior Research Scientist CSIRO, Division of Animal Health Private Bag 1, Parkville, Victoria 3052, Australia Internet email: baell@mel.dah.csiro.au Tel: +61 3 342-9782 Fax: +61 3 347-4042 +______________________________________________________________________+ Date: Sun, 06 Nov 1994 09:57:43 EST From: breneman@XRAY.CHEM.RPI.EDU ----- Jan, Check the underlying directory permissions of disk mount points. We had a similar problem when a mounted filesystem had good permissions but the underlying mount point directory was only allowed restricted access. To test this, simply dismount the filesystem and ls -l the directory containing the mount point directory. I hope this helps. Curt Breneman RPI Chemistry =========================================================================== from: Jussi Eloranta Subject: Re: CCL:problem running MOPAC from SYBYL 6.1 Date: Mon, 7 Nov 1994 09:11:15 +0200 (EET) ------ Have you checked the permissions on sybyl directories? (mopac interface works on our system). Esp. check $TA_ROOT/bin, $TA_ROOT/bin/mopac* and $TA_ROOT/batch/cmd or simply just do as root: chmod -R go+rx $TA_ROOT Regards, jussi ========================================================================== From: Bob Funchess Date: Mon, 7 Nov 1994 09:45:10 -0500 Organization: Molecular Simulations Inc. Phone: (617) 229-9800 ext. 202 ------ Dear Jan, We've had this problem reported from time to time. It usually seems to involve a directory somewhere in the path which doesn't have read permissions (that is, while your current directory is 755, the parent directory, or its parent, etc. might not be readable by you). This sometimes happens through some weird interactions with NFS, especially the automounter. Regards, Bob Funchess -- Dr. Robert B. Funchess bobf@msi.com Senior Support Scientist Tel (617) 229-9800 x202 Molecular Simulations Inc. FAX (617) 229-9899 16 New England Executive Park http://www.msi.com/~bobf/bobf.html Burlington, MA 01803-5297 From sgustaf@rhea.cray.com Mon Nov 7 17:24:36 1994 Received: from timbuk.cray.com for sgustaf@rhea.cray.com by www.ccl.net (8.6.9/930601.1506) id QAA29272; Mon, 7 Nov 1994 16:28:27 -0500 Received: from giraf.cray.com (giraf.cray.com [128.162.171.5]) by timbuk.cray.com (8.6.9/8.6.9M) with SMTP id PAA03987 for ; Mon, 7 Nov 1994 15:28:26 -0600 Received: by giraf.cray.com (931110.SGI/CRI-5.14) id AA03760; Mon, 7 Nov 94 15:28:26 -0600 From: sgustaf@rhea.cray.com (Susan M. Gustafson) Message-Id: <9411072128.AA03760@giraf.cray.com> Subject: UniChem Mosaic Page To: CHEMISTRY@ccl.net Date: Mon, 7 Nov 1994 15:28:26 -0600 (CST) Cc: raeuchle@rhea.cray.com (Thomas Raeuchle), george@rhea.cray.com, kryan@rhea.cray.com X-Mailer: ELM [version 2.4 PL23] Content-Type: text Content-Length: 918 Greetings all, Cray Research, Inc. announces the UniChem Mosaic Home Page. You will find the page at "http://www.cray.com/apps/UNICHEM/Mainpage.html". This page gives you access to a wealth of information, including: - The UniChem package and latest release information - Recent results in high performance computational chemistry - News about DGauss analytical vibrational frequencies - DGauss basis sets at no cost The UniChem is the Cray Research molecular simulation package. It consists of a graphical interface and a set of quantum chemistry codes integrated into a seamless environment. The UniChem page can also be accessed via the Cray Research Home Page (http://www.cray.com). For more information about UniChem, contact the Cray Research Applications Dept. at 1-800-289-CRAY or send e-mail to unichem@cray.com. Susan M. Gustafson UniChem Support Cray Research, Inc. e-mail: sgustaf@cray.com From FOX@cmchem.chem.cmu.edu Mon Nov 7 18:24:36 1994 Received: from cmchem.chem.cmu.edu for FOX@cmchem.chem.cmu.edu by www.ccl.net (8.6.9/930601.1506) id RAA00666; Mon, 7 Nov 1994 17:43:14 -0500 From: Date: Mon, 7 Nov 1994 17:43:40 -0500 (EST) To: chemistry@ccl.net CC: FOX@cmchem.chem.cmu.edu Message-Id: <941107174340.25402a04@cmchem.chem.cmu.edu> Subject: G92: What are "concise" subgroups? John Sichel asks, >Can someone tell me the meaning of the word "concise" in symmetry group theory.>This term occurs in the output of the Gaussian programs, as in the following >examples: I am not sure this concept is exploited in standard group theory but it referes to the subgroup formed by those two-fold operations which interchange equivalent atoms. This subgroup contians the operations useful in the evaluation of integrals and integral derivatives. More information on the use of symmetry by the Gaussian 92 system of programs can be found in the Gaussian 92 Programmer's Reference Manual, Section 11.7. Douglas J. Fox Director of Technical Support help@gaussian.com