From chemistry-request@server.ccl.net Thu Sep 23 13:26:03 1999 Received: from euch4e.chem.emory.edu (euch4e.chem.emory.edu [170.140.59.12]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id NAA01694 for ; Thu, 23 Sep 1999 13:26:03 -0400 Received: (from dima@localhost) by euch4e.chem.emory.edu (AIX4.2/UCB 8.7/8.7) id NAA36942; Thu, 23 Sep 1999 13:20:12 -0400 (EDT) From: Dmitry Khoroshun Message-Id: <199909231720.NAA36942@euch4e.chem.emory.edu> Subject: Re: CCL:Freezing Bond Angles To: jamal@chemie.uni-marburg.de (Jamal Uddin) Date: Thu, 23 Sep 1999 13:20:11 -0400 (EDT) Cc: bmoritz@chem10.idbsu.edu (Benny Moritz), chemistry@ccl.net In-Reply-To: <37EA3B65.144DB9EC@chemie.uni-marburg.de> from "Jamal Uddin" at Sep 23, 1999 04:38:29 PM X-Mailer: ELM [version 2.5 PL0b1] MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hello! It may be better to use opt=(AddRedund) and adding 1 2 3 F, where 1, 2 and 3 are the numbers of the atoms defining the angle, to the Modredund section (right after the molecule specification). This way the optimization would still be performed in redundand internal coordinates system, which is superior to z-matrix optimization. Sincerely, Dmitry Khoroshun dima@euch4e.chem.emory.edu According to Jamal Uddin: > > Dear Morits, > > You have to specify opt=Z-Matrix in the command line and in the geometry section > you have to specify frozen angle as a constant. > > Cheers, > > > Jamal Uddin > > > Benny Moritz wrote: > > > Dear Netters, > > > > I have recently been working on perfluoro-2-azopropene (CF3-N=CF2) > > trying to locate a transition state about the N=CF2 bond. I'm having > > trouble freezing the angle made by the C-N=C bond trying to keep it at 120 > > degrees. I've been setting the value of the angle in the Z-Matrix as a > > value and not a variable, but when optimized Gaussian 98 treats it as a > > variable. Is there anyway that I can restrict this angle from moving? > > > > Ben Moritz > > bmoritz@chem.boisestate.edu > > > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > > From chemistry-request@server.ccl.net Thu Sep 23 20:46:11 1999 Received: from condor.coastalnet.com (condor.coastalnet.com [204.183.40.7]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id UAA04203 for ; Thu, 23 Sep 1999 20:46:04 -0400 Received: from pavilion (pm-jax5-172.coastalnet.com [205.245.112.172]) by condor.coastalnet.com (8.9.3/8.9.3) with SMTP id UAA20446 for ; Thu, 23 Sep 1999 20:40:41 -0400 (EDT) Message-ID: <000c01bf0625$8e9d66e0$456cfea9@pavilion> Reply-To: "R D Brown" From: "R D Brown" To: Subject: Hyperchem 5.1 Date: Thu, 23 Sep 1999 20:37:58 -0400 I am a relatively new user of Hyperchem 5.1. I have been trying to = overlay PM3-optimized tricyclic thiamin onto omeprazole, a close = structural analog. I have followed the examples in the reference books = accompanying the program, but am unable to get the "Display-->Overlay" = menu command to work with this system. =20 Q: Does the program allow one to overlay dissimilar molecules, or only = alternative conformers of the same compound? Must I do ab initio = calculations for it to work? Thanx, Robert D. Brown Pelorus Research Laboratory From chemistry-request@server.ccl.net Fri Sep 24 07:54:32 1999 Received: from wirehead.arqule.com (email.arqule.com [207.252.12.140]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id HAA07591 for ; Fri, 24 Sep 1999 07:54:30 -0400 Received: by WIREHEAD with Internet Mail Service (5.5.2650.10) id ; Fri, 24 Sep 1999 07:46:10 -0400 Message-ID: <6B00FB949906D211A88800104B8AE520F419F8@WIREHEAD> From: "Czerminski, Ryszard" To: "'chemistry@ccl.net'" Subject: combinations Date: Fri, 24 Sep 1999 07:46:09 -0400 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2650.10) Content-Type: text/plain; charset="iso-8859-1" I am looking for a function which could compute combinations given lexicographical index e.g. C(1;3,2) -> 1,2 C(2;3,2) -> 1,3 C(3;3,2) -> 2,3 I have found function which does this ( http://math.nist.gov/GAMS.html ) but it is limited to small numbers since it is using regular 4 bytes representation for integers and therefore index range is severly limited ( < 2^32 ). Any pointers to the software which does this for integers of arbitrary length would be very much appreciated. Ryszard Czerminski phone: (781)395-1269 x 479 ArQule, Inc. e-mail: ryszard@arqule.com 200 Boston Avenue http://www.arqule.com Medford, MA 02155 From chemistry-request@server.ccl.net Fri Sep 24 10:57:48 1999 Received: from eros.iqm.unicamp.br (eros.iqm.unicamp.br [143.106.51.200]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id KAA08220 for ; Fri, 24 Sep 1999 10:57:47 -0400 Received: (from hermes@localhost) by eros.iqm.unicamp.br (8.9.2/8.8.8) id LAA76396 for CHEMISTRY@ccl.net; Fri, 24 Sep 1999 11:52:41 -0300 (EST) (envelope-from hermes) Date: Fri, 24 Sep 1999 11:52:41 -0300 From: Hermes Fernandes de Souza To: CHEMISTRY@ccl.net Subject: Extended Huckel Message-ID: <19990924115241.A76335@eros.iqm.unicamp.br> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii X-Mailer: Mutt 0.95.5i Hi CClers, I would like to thanks for all sugestions with Extended Huckel. I have dowload both Icon and YAeMOP programs. The firist one is in fortran, for me it is more easy, but I am studing the input file. The second is in C, well, I have tudy more. For more one time, Thanks. Hermes From chemistry-request@server.ccl.net Fri Sep 24 13:41:44 1999 Received: from mailserv.mta.ca (root@mailserv.mta.ca [138.73.101.5]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id NAA08870 for ; Fri, 24 Sep 1999 13:41:44 -0400 Received: from m0612.mta.ca (host-22-237.mta.ca [138.73.22.237]) by mailserv.mta.ca (8.9.3/8.9.3) with SMTP id OAA05120 for ; Fri, 24 Sep 1999 14:36:28 -0300 (ADT) Message-Id: <3.0.5.32.19990924144123.007e21c0@mailserv.mta.ca> X-Sender: mculf@mailserv.mta.ca X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.5 (32) Date: Fri, 24 Sep 1999 14:41:23 -0300 To: chemistry@ccl.net From: Miroslava Culf Subject: Lipid bilayer simulations Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Dear All, I would like to find out more about computer simulations of lipid bilayer. Thus I would appreciate any information about RECENT review articles or books dealing with any aspect of computer simulation of lipid bilayer or behaviour of lipids in the bilayer. Thanks very much for you help, Miroslava P.S. I will summarize responses. ____________________________________________________________ Miroslava Culf, Ph.D. 65 York St. Computer Services Department/Chemistry Department Mount Allison University Sackville, NB E4L 1E4 Canada e-mail: mculf@mta.ca tel. 506-364-2411 http://www.mta.ca/faculty/science/chem/staff/mculf.htm ____________________________________________________________ From chemistry-request@server.ccl.net Fri Sep 24 13:45:27 1999 Received: from chem.idbsu.edu (chem10.idbsu.edu [132.178.136.31]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id NAA08919 for ; Fri, 24 Sep 1999 13:45:26 -0400 Received: from labasst (LABASST.boisestate.edu [132.178.213.224]) by chem.idbsu.edu (8.8.5/8.8.5) with SMTP id KAA18749 for ; Fri, 24 Sep 1999 10:52:03 -0600 Message-Id: <3.0.6.32.19990924113018.0093aa30@chem.boisestate.edu> X-Sender: bmoritz@chem.boisestate.edu X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.6 (32) Date: Fri, 24 Sep 1999 11:30:18 -0600 To: chemistry@ccl.net From: Benny Moritz Subject: Freezing Bond Angles Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" I would just like to thank all that responded to my e-mail on freezing bond angles in Gaussian. I was successful in obtaining the desired transition state for my molecule, and couldn't have done it without your help. So thank you very much Ben Moritz "Whom the Gods destroy, they first make mad." From chemistry-request@server.ccl.net Fri Sep 24 14:46:50 1999 Received: from omega.omrf.ouhsc.edu (omega.omrf.ouhsc.edu [157.142.200.207]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id OAA09184 for ; Fri, 24 Sep 1999 14:46:50 -0400 Received: from omega.omrf.ouhsc.edu (pcxt13.omrf.ouhsc.edu [157.142.200.245]) by omega.omrf.ouhsc.edu (980427.SGI.8.8.8/980728.SGI.AUTOCF) via ESMTP id NAA20474 for ; Fri, 24 Sep 1999 13:41:33 -0500 (CDT) Message-ID: <37EBC5B9.CF9B023E@omega.omrf.ouhsc.edu> Date: Fri, 24 Sep 1999 13:40:57 -0500 From: Elizabeth Yuriev Organization: OMRF X-Mailer: Mozilla 4.51 [en] (Win98; U) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: sulfonamide force field parameters Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear all, I am interested in force field parameters for sulfonamides, especially aryl derivatives. I know that this question has been asked, answered and summarized by David Chalmers in ca. '95 (can't check for sure since I have not been able to use CCL search recently for some reason). Therefore, I am after the papers or reviews on the subject appeared since then. I am thinking about using MM2 but pointers to other force fields are of interest as well. Thanks in advance, Elizabeth Yuriev -- Elizabeth Yuriev, Ph.D. Postdoctoral Fellow Oklahoma Medical Research Foundation Protein Crystallography 825 NE 13th Street Oklahoma City, OK 73104 Ph: 405 271 1672 Fax: 405 271 3980 Email: yurieve@omega.omrf.ouhsc.edu From chemistry-request@server.ccl.net Fri Sep 24 18:35:31 1999 Received: from wugate.wustl.edu (wugate.wustl.edu [128.252.120.1]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id SAA10314 for ; Fri, 24 Sep 1999 18:35:31 -0400 Received: from mirlink.wustl.edu (mirlink.wustl.edu [128.252.155.1]) by wugate.wustl.edu (8.8.8/8.8.5) with SMTP id RAA06970 for ; Fri, 24 Sep 1999 17:30:11 -0500 (CDT) Message-ID: Date: 24 Sep 1999 17:28:40 -0500 From: "David Reichert" Subject: DFT & frequency calculations To: "CCL post" X-Mailer: Mail*Link SMTP-MS 3.0.2 Mime-Version: 1.0 Content-Type: text/plain; charset="ISO-8859-1"; Name="Message Body" Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id SAA10315 Hi, I'm hoping that someone can provide some enlightenment. I've been running some DFT calculations on some copper - amine complexes which appear to end up having only C1 symmetry. In order to ensure that these are indeed minimum energy structures, I've run frequency calculations on them as well. My question is what should I really be seeing in the frequency calculations? I know that for a transition structure you look for one imaginary frequency, and that ideally the translational and rotational modes should drop out. But in real life with non-perfect calculations what do you want to see that says, "Yes, this is indeed a low energy fully converged struture". Any rules of thumb are more than welcome. thanks, dave reichert ____________________________________________ | David Reichert, Ph.D | | Mallinckrodt Institute of Radiology | | Washington University School of Medicine | | St. Louis, MO | | | | e-mail: reichertd@mirlink.wustl.edu | | voice: (314) 362-8461 | | fax: (314) 362-9940 | ____________________________________________ From chemistry-request@server.ccl.net Fri Sep 24 16:25:35 1999 Received: from cardinal.prod.itd.earthlink.net (cardinal.prod.itd.earthlink.net [207.217.121.154]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id QAA09869 for ; Fri, 24 Sep 1999 16:25:35 -0400 Received: from lrz.de (1Cust182.tnt1.rancho-cucamonga.ca.da.uu.net [208.251.225.182]) by cardinal.prod.itd.earthlink.net (8.9.3/8.9.3) with ESMTP id NAA18038 for ; Fri, 24 Sep 1999 13:20:12 -0700 (PDT) Received: (from eugene.leitl@localhost) by lrz.de (8.8.8/8.8.8) id NAA14275 for ; Fri, 24 Sep 1999 13:17:45 -0700 Resent-From: Eugene Leitl MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Resent-Message-ID: <14315.56425.461006.571048@lrz.de> Resent-Date: Fri, 24 Sep 1999 13:17:45 -0700 (PDT) Resent-To: Message-Id: <199909241342.PAxxxA18515@chinon.cnrs-orleans.fr> X-Authentication-Warning: chinon.cnrs-orleans.fr: hinsen set sender to hinsen@cnrs-orleans.fr using -f Precedence: bulk From: To: beowulf@beowulf.gsfc.nasa.gov Subject: Network performance Date: Fri, 24 Sep 1999 15:42:06 +0200 From: hinsen@dirac.cnrs-orleans.fr We are planning to build a Beowulf-type cluster, using either dual-processor Pentium III nodes or single-processor Alpha nodes (we'd prefer Pentium nodes, but administrative complications might force us to buy Alphas). The biggest open question is the type of network: - Fast Ethernet - 2x Fast Ethernet (channel bonding) - Myrinet - Gigabit Ethernet In view of the significant cost of Myrinet or Gigabit Ethernet, we'd like to have some information on what performance increase we can expect *for our applications*, which are Molecular Dynamics simulations of biomolecular systems. Has anyone ever done a comparison for this type of calculation between systems with identical nodes that differ only in networking performance? Or is there any way to estimate the performance difference? It doesn't have to be very precise, we just want to decide if it is better to invest into fast networks or into more nodes. -- ------------------------------------------------------------------------------- Konrad Hinsen | E-Mail: hinsen@cnrs-orleans.fr Centre de Biophysique Moleculaire (CNRS) | Tel.: +33-2.38.25.55.69 Rue Charles Sadron | Fax: +33-2.38.63.15.17 45071 Orleans Cedex 2 | Deutsch/Esperanto/English/ France | Nederlands/Francais ------------------------------------------------------------------------------- From chemistry-request@server.ccl.net Fri Sep 24 20:50:07 1999 Received: from bluejay.prod.itd.earthlink.net (bluejay.prod.itd.earthlink.net [207.217.120.108]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id UAA11093 for ; Fri, 24 Sep 1999 20:50:06 -0400 Received: from lrz.de (1Cust80.tnt1.rancho-cucamonga.ca.da.uu.net [208.251.225.80]) by bluejay.prod.itd.earthlink.net (8.9.3/8.9.3) with ESMTP id RAA13633 for ; Fri, 24 Sep 1999 17:44:43 -0700 (PDT) Received: (from eugene.leitl@localhost) by lrz.de (8.8.8/8.8.8) id RAA15747; Fri, 24 Sep 1999 17:42:14 -0700 From: Eugene Leitl MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Message-ID: <14316.6757.120970.769337@lrz.de> Date: Fri, 24 Sep 1999 17:42:13 -0700 (PDT) To: Subject: Cornell Theory Center Computational Biology Tools X-Mailer: VM 6.71 under 21.1 (patch 4) "Arches" XEmacs Lucid http://www.tc.cornell.edu/reports/NIH/resource/CompBiologyTools/ The NIH "Parallel Processing Resource for Biomedical Scientists" at the Cornell Theory Center announces a major release of computer programs for molecular and protein modeling. The code was developed by the groups of Ron Elber and Harold Scheraga and is released to the public domain. Although the code is not copyrighted, we expect you to reference the code to the extent that it helped you in your work. We further expect that this code will NOT be used as a whole or as a part of any commercial software. This release includes the following: - protein folding The ECEPPAK package. A set of programs based on the ECEPP/3 force field used to study the conformational properties of polypeptides and proteins. Among others, ECEPPAK includes computational tools to carry out global conformational searches at the all-atom level. A parallel version of the code using MPI is available for an IBM SP. - molecular dynamics The MOIL modeling package to simulate structure, dynamics, and function of biological molecules at the atomic level of detail. Note the availability of a Window version in the present release and a parallel version for stochastic path simulations. - protein recognition The LOOPP program (Linear Optimization Of Protein Potentials). A program for potential optimization and alignments. LOOPP aligns sequence to sequence, sequence to structure, and structure to structure. It further enables the optimization of potentials and scoring functions for the above mentioned applications. - process dihedral angle files The ANALYZE package to classify conformations obtained from a global search into families and compute conformational characteristics such as RMS deviations and interproton distances. It can also estimate the statistical weights of the conformations by fitting the theoretically calculated average NOE intensities and coupling constants to the respective experimental data. A workshop will be held on the Cornell University campus November 15-16, 1999 to provide an in-depth description and hands-on experience with the software packages that the resource just released to the public domain. See http://www.tc.cornell.edu/Events/1999/CompBiologyTools