From XIENING@MEENA.CC.UREGINA.CA Mon Jun 29 00:14:31 1998 Received: from veena.cc.uregina.ca (VEENA.CC.UREGINA.CA [142.3.100.19]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id AAA20619 Mon, 29 Jun 1998 00:14:26 -0400 (EDT) Received: from meena.cc.uregina.ca by meena.cc.uregina.ca (PMDF V5.1-10 #27364) id <01IYSAMLEGAOBFIWYQ@meena.cc.uregina.ca> for chemistry@www.ccl.net; Sun, 28 Jun 1998 22:14:13 CST Date: Sun, 28 Jun 1998 22:14:13 -0600 (CST) From: Ning Xie Subject: G94: frequency calculation To: chemistry@www.ccl.net Reply-to: Ning Xie Message-id: MIME-version: 1.0 Content-type: TEXT/PLAIN; charset=US-ASCII Hi, there, I'm wondering if the frequency calculation in g94 must be performed in the second step of the calculation. If I have the check point file, can I do a separate frequency calculation (without optimizing the structure again because it takes too long). I used the following lines in my .com file and the program stopped short after it started because of "Error termination in NtrErr: NtrErr called from FileIO": $ RunGauss %mem=8000000 %chk=chkfile # HF/LANL2DZ Freq=(ReadFC, ReadIsotopes) Geom=AllCheck Test Thank you for your time and help. ========================================================================= | NING XIE Tel: (306)721-0301 (O) | | Chemistry Department (306)585-2184 (H) | | University of Regina Fax: (306)721-4720 | | Regina, SK E-Mail: xiening@meena.cc.uregina.ca | | Canada S4S 0A2 | ========================================================================= From r.knegtel@organon.oss.akzonobel.nl Mon Jun 29 03:08:53 1998 Received: from gate2.akzonobel.nl (gate2.oss.akzonobel.nl [192.87.3.6]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id DAA21674 Mon, 29 Jun 1998 03:08:52 -0400 (EDT) Received: (from fwmaster@localhost) by gate2.akzonobel.nl (8.8.4/8.6.12) id JAA19849 for ; Mon, 29 Jun 1998 09:08:52 +0200 (MET DST) Received: by gate2.oss.akzonobel.nl via smap (V1.3) id sma019773; Mon, 29 Jun 98 09:08:19 +0200 Received: by apou01.akzonobel.nl id JAA07536; Mon, 29 Jun 1998 09:15:32 +0200 (MET DST) Received: from organon.oss.akzonobel.nl (orchid.oss.akzonobel.nl) by vesta.oss.akzonobel.nl (PMDF V5.1-7 #22904) with SMTP id <01IYSX7SEZRK9D7JQC@vesta.oss.akzonobel.nl> for chemistry@www.ccl.net; Mon, 29 Jun 1998 09:01:14 +0100 Received: (from knegtel@localhost) by organon.oss.akzonobel.nl (950413.SGI.8.6.12/8.6.12) id GAA12990 for chemistry@www.ccl.net; Mon, 29 Jun 1998 06:58:51 +0000 (GMT) Date: Mon, 29 Jun 1998 08:58:51 +0200 (WDT) From: Knegtel Ronald Subject: CCL:Programs that can perform MD only in torsional space To: chemistry@www.ccl.net Message-id: <199806290658.GAA12990@organon.oss.akzonobel.nl> MIME-version: 1.0 X-Mailer: ELM [version 2.4 PL24 ME8b] Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7bit Richard Gillilan wrote: > > I want to know if there exists one program that can perform Molecular > > Dynamics Simulation only in torsional space. > Check out Axel Bruenger's X-plor, they recently implemented torsion angle dynamics for protein structure refinement: Proteins 1994 Aug;19(4):277-290 Torsion angle dynamics: reduced variable conformational sampling enhances crystallographic structure refinement. Rice LM, Brunger AT Cheers, Ronald ------------------------------------------------------------------------------- Dr. Ronald M. A. Knegtel Research Scientist Dept. of Molecular Design and Informatics Phone : +31-412-661469 N.V. Organon, RK2340 Fax : +31-412-662539 P.O. Box 20 5340 BH Oss http://www.organon.nl/ The Netherlands E-Mail : r.knegtel@organon.oss.akzonobel.nl ------------------------------------------------------------------------------- From vkitzing@silia.mpimf-heidelberg.mpg.de Mon Jun 29 08:07:51 1998 Received: from sunny.mpimf-heidelberg.mpg.de (sunny.mpimf-heidelberg.mpg.de [149.217.50.30]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id IAA22712 Mon, 29 Jun 1998 08:07:33 -0400 (EDT) Received: from [149.217.50.47] (mac20 [149.217.50.47]) by sunny.mpimf-heidelberg.mpg.de (8.8.8/8.8.8) with ESMTP id NAA10627; Mon, 29 Jun 1998 13:58:18 +0200 (MET DST) Message-Id: In-Reply-To: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Mon, 29 Jun 1998 14:00:52 +0200 To: CHEMISTRY@www.ccl.net From: Eberhard von Kitzing Subject: Re: CCL:Counter-ions on AMBER calculations Cc: andre mauricio de oliveira Dear Andre Mauricio de Oliveira, At 17:36 Uhr -0300 25.06.1998, andre mauricio de oliveira wrote: >Can anyone tell me about simulation of counter-ions upon oligonucleotide >backbones, employing any model such as Condensation Theory to avoid the >use of explicit sodium, potassium or magnesium atoms in AMBER force field >calculations? To calculate the transtion point between B-DNA and Z-DNA as a function of ion concentration and ion size we used MSA theory. >I'm interessed in setting any correction on the distance-dependent >dieletric constant present in the coulombic term of AMBER forcefield wich >includes charged atoms in the enviroment. See: Reinhard Klement, Dikeos Mario Soumpasis, Eberhard v. Kitzing and Thomas M. Jovin (1990). "Inclusion of ionic interactions in force field calculations of charged biomolecules - DNA structural transitions." Biopolymers 29 1089-1103. ====================================================================== Eberhard von Kitzing Max-Planck-Institut fuer Medizinische Forschung Jahnstr. 29 D 69115 Heidelberg Germanny email: vkitzing@silia.mpimf-heidelberg.mpg.de WWW: http://sunny.mpimf-heidelberg.mpg.de/people/vkitzing/ From cjao@stanley.bio.purdue.edu Mon Jun 29 14:16:39 1998 Received: from stanley.bio.purdue.edu (stanley.bio.purdue.edu [128.210.18.40]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id OAA25146 Mon, 29 Jun 1998 14:16:27 -0400 (EDT) Received: (from cjao@localhost) by stanley.bio.purdue.edu (8.8.5/8.8.5) id NAA04864 for CHEMISTRY@www.ccl.net; Mon, 29 Jun 1998 13:16:12 -0500 Date: Mon, 29 Jun 1998 13:16:12 -0500 From: Chris Jao Message-Id: <199806291816.NAA04864@stanley.bio.purdue.edu> To: CHEMISTRY@www.ccl.net Subject: parameter for sulfoxide Hi, I am using CHARMm all hydrogen forcefield and need to know the parameters for sulfoxide, Can anyone kindly tell me where I can find it or how I can get it by doing ab initio calculation? Thank you very much. chris ps. I did an optimization of CH3CH2S(=O)CH3 calculation using g94 (HF/6-31G**) and I really don't know what to do with it. From boufer@cennas.nhmfl.gov Mon Jun 29 15:01:25 1998 Received: from physics.cennas.nhmfl.gov (physics.cennas.nhmfl.gov [146.201.220.3]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id PAA25506 Mon, 29 Jun 1998 15:01:25 -0400 (EDT) Received: from localhost (boufer@localhost) by physics.cennas.nhmfl.gov (8.8.5/8.8.5) with SMTP id QAA20192 for ; Mon, 29 Jun 1998 16:02:21 -0400 (EDT) Date: Mon, 29 Jun 1998 16:02:21 -0400 (EDT) From: Ahmed Bouferguene X-Sender: boufer@physics To: CHEMISTRY@www.ccl.net Subject: Program to read a Gaussian input basis Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Greetings all, I was wondering if anybody on this forum is aware of a routine that could read a Gaussian output file and reconstruct the basis set as represented by Gaussian internally. Thanks for your time -- Ahmed Bouferguene ----------------------------------------------------------------------- Ce n'est pas par ce que les choses sont difficiles que nous n'osons pas les faire. C'est parce que nous n'osons pas les faire qu'elles sont difficiles. From rvenable@deimos.cber.nih.gov Mon Jun 29 16:26:39 1998 Received: from deimos.cber.nih.gov (deimos.cber.nih.gov [128.231.52.2]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id QAA26492 Mon, 29 Jun 1998 16:26:38 -0400 (EDT) Received: from localhost by deimos.cber.nih.gov with SMTP (1.37.109.14/16.2) id AA277391928; Mon, 29 Jun 1998 16:25:28 -0400 Date: Mon, 29 Jun 1998 16:25:28 -0400 (EDT) From: Rick Venable Reply-To: Rick Venable To: Chris Jao Cc: CHEMISTRY@www.ccl.net Subject: Re: CCL:G:parameter for sulfoxide In-Reply-To: <199806291816.NAA04864@stanley.bio.purdue.edu> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Mon, 29 Jun 1998, Chris Jao wrote: > I am using CHARMm all hydrogen forcefield and need to know the > parameters for sulfoxide, Can anyone kindly tell me where I can find > it or how I can get it by doing ab initio calculation? > ps. I did an optimization of CH3CH2S(=O)CH3 calculation using g94 > (HF/6-31G**) and I really don't know what to do with it. In general, one uses experimental geometries, with bond and angle force constants from IR spectroscopy; ab initio calculations are used to derive partial charges, perhaps at several geometries, and can be used to refine the LJ parameters. Note that for sp2 hydridized carbon, one often uses an added improper torsion to enforce planarity. The results should be iteratively refined against e.g. a crystal structure at a minimum. There's the CHARMm force field distributed by MSI for use with the Quanta/CHARMm product; I don't know if their parameter development methodology has been published. Also, their force field has been "generalized" in order be used for a wider range of polymers, but I've done some carbohydrate simulations which suggest the parameters may not be as transferable as one would like. Check the MSI manuals, or contact someone from MSI for development details; perhaps a reader of CCL has some experiences to share... There's also the CHARMM force fields developed by Alex MacKerell and collaborators; these are the ones distributed with the academic version >from Harvard, and are specific for each biopolymer type. A couple papers on the methodology are: Pavelites JJ, Gao JL, Bash PA, et al. A molecular mechanics force field for NAD(+), NADH, and the pyrophosphate groups of nucleotides J COMPUT CHEM 18: (2) 221-239 JAN 30 1997 Yin DX, Mackerell AD Combined ab initio empirical approach for optimization of Lennard-Jones parameters J COMPUT CHEM 19: (3) 334-348 FEB 1998 -- Rick Venable =====\ |=| "Eschew Obfuscation" FDA/CBER Biophysics Lab |____/ |=| Bethesda, MD U.S.A. | \ / |=| ( Not an official statement or rvenable@deimos.cber.nih.gov | \ / |=| position of the FDA; for that, http://nmr1.cber.nih.gov/ \/ |=| see http://www.fda.gov ) http://www.erols.com/rvenable From ijbarani@syr.edu Mon Jun 29 17:03:02 1998 Received: from mailbox.syr.edu (root@mailbox.syr.edu [128.230.1.5]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id RAA26996 Mon, 29 Jun 1998 17:03:02 -0400 (EDT) Received: from syr.edu (casehead.cat.syr.edu [128.230.59.14]) by mailbox.syr.edu (8.9.0/8.9.0) with ESMTP id RAA20446; Mon, 29 Jun 1998 17:03:02 -0400 (EDT) Message-ID: <35980059.8D72E97A@syr.edu> Date: Mon, 29 Jun 1998 17:00:09 -0400 From: "Igor J. Barani" X-Mailer: Mozilla 4.05 [en] (Win95; I) MIME-Version: 1.0 To: Rick Venable CC: CHEMISTRY@www.ccl.net Subject: MM3/MM2 Input files References: Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hello, I am looking for a rapid way of creating MM2/MM3 input files. Can anyone recommend how I can do this by using either Chem3D or some other shareware program? Thank you. Sincerely, Igor Barani From DEERFIELD@a.psc.edu Mon Jun 29 19:21:30 1998 Received: from CPWSCA.PSC.EDU (a.psc.edu [128.182.66.105]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id TAA28142 Mon, 29 Jun 1998 19:21:30 -0400 (EDT) Received: by B.PSC.EDU for chemistry@www.ccl.net; Mon, 29 Jun 1998 19:21:30 -0400 Date: Mon, 29 Jun 1998 19:21:30 -0400 From: DEERFIELD@B.PSC.EDU To: chemistry@www.ccl.net CC: DEERFIELD@B.PSC.EDU Message-Id: <980629192130.2080be9c@B.PSC.EDU> Subject: Workshop on "Methods and Applications of Molecular Mechanics and Dynamics to Molecules of Biological Interest" TITLE: METHODS AND APPLICATIONS OF MOLECULAR MECHANICS AND DYNAMICS TO MOLECULES OF BIOLOGICAL INTEREST INSTRUCTORS: Dr. Peter A. Kollkman (UCSF) Dr. David A. Case (Scripps) Dr. David A Pearlman (Vertex Pharmaceutical) Dr. Thomas Cheatham III (NIH) Dr. Carlos L. Simmerling (UCSF) SITE: Pittsburgh Supercomputing Center DATE: August 5-8 Mellon Institute, Pittsburgh, PA SPONSOR: Pittsburgh Supercomputing Center's Biomedical Supercomputing Initiative - an NIH Resource Center DESCRIPTION: The Pittsburgh Supercomputing Center will be hosting a workshop on the "Methods and Applications of Molecular Mechanics and Dynamics to Molecules of Biological Interest." The workshop will familiarize biomedical researchers with computational methods and provided practice in applying supercomputing resources to problems of concern in molecular mechanics. The workshop will consist of lectures and extensive hands-on sessions. General aspects of molecular mechanics software will be discussed. The program AMBER will be discussed in detail. Participants are encouraged to work on the examples provided or on their own experimental data. No prior supercomputing experience is necessary. EXPENSES: Partcipants must pay their own travel. Tuition, hotel, supercomputing time and workshop materials are provided for US academic partcipants by the PSC's NIH Research Resource grant. ELIGIBLE: There will be 20 openings for individuals from US academic insitutions and potentially a limited number of openings for industrial and others who would like to take this course. SEE: http://www.psc.edu/biomed/biomed.html APPLICATION July 3 DEADLINE: David W. Deerfield II, Ph.D. email: deerfiel@psc.edu Manager, Biomedical Applications Group phone: (412) 268-4960 Pittsburgh Supercomputing Center fax: (412) 268-8200 4400 Fifth Avenue; Room 218B www.psc.edu/biomed/biomed.html Pittsburgh, PA 15213 www.psc.edu/~deerfiel/ ** PSC's Biomedical Supercomputing Initiative is an NIH Resource Center **