From owner-chemistry@ccl.net Mon Aug 7 05:48:21 1995 Received: from sangam.ncst.ernet.in for vrc@ncl.ernet.in by www.ccl.net (8.6.10/930601.1506) id FAA16971; Mon, 7 Aug 1995 05:45:39 -0400 From: Received: from ncl.UUCP (uucp@localhost) by sangam.ncst.ernet.in (8.6.12/8.6.6) with UUCP id PAA20275 for chemistry@ccl.net; Mon, 7 Aug 1995 15:16:02 +0530 Received: from ncl.UUCP by iucaa (4.1/SMI-4.1) id AA21594; Mon, 7 Aug 95 15:12:05+050 Date: Mon, 7 Aug 95 15:12:05+050 Message-Id: <9508071012.AA21594@iucaa> To: chemistry@ccl.net Subject: Can someone help on STARBASE ON HP UNIX To: chemistry@ccl.net Subject: Can Someone help me on Starbase routines on HP 4 aug . 1995 Dear Netters I would like to know if you could help me out with a problem I am facing. I have a Hewlett Packard 9000/712 workstation. The unit has come in without the set of Manuals required to run the graphics library routines using HP - STARBASE. The version of UNIX on the system is 9.03. Can anybody help me with a STARBASE program written with FORTRAN calls [A[Band also indicate to me how I should compile it to run the program using HP-FORTRAN. I am particularly interested in getting some scientific plotting programs both 2D and 3D. in X-WINDOWS ? Thanking you in anticipation Sincerely SIVADINARAYANA.C NCL Pune India e-mail: vrc@ncl.erent.in ----------- End Forwarded Message ----------- From owner-chemistry@ccl.net Mon Aug 7 06:32:08 1995 Received: from romeo.ic.ac.uk for o.casher@ic.ac.uk by www.ccl.net (8.6.10/930601.1506) id GAA17509; Mon, 7 Aug 1995 06:22:06 -0400 Received: from cscmgb.cc.ic.ac.uk (actually sg1.cc.ic.ac.uk) by romeo.ic.ac.uk with SMTP (PP); Mon, 7 Aug 1995 11:21:42 +0100 Received: from [155.198.224.115] by cscmgb.cc.ic.ac.uk (940816.SGI.8.6.9/4.0) id LAA04337; Mon, 7 Aug 1995 11:21:38 +0100 X-Sender: hoc@sg1.cc.ic.ac.uk Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Mon, 7 Aug 1995 11:18:09 +0200 To: chemistry@ccl.net From: o.casher@ic.ac.uk (Omer Casher) Subject: Explorer Cambridge FDAT reader for SGI machines I've just written an Explorer module that reads Cambridge FDAT files. Of course, I want to believe that we cracked that ubiquitous file format. Soooo... if you work with FDAT files, have an SGI running Explorer, and would like to have a copy of this module to test against your files, please let me know. Thanks! Omer From owner-chemistry@ccl.net Mon Aug 7 10:03:39 1995 Received: from ailab.ia.ac.cn for zhy@ailab.ia.ac.cn by www.ccl.net (8.6.10/930601.1506) id JAA20386; Mon, 7 Aug 1995 09:50:39 -0400 Received: by ailab.ia.ac.cn id AA00478 (5.67b/IDA-1.5 for chemistry@ccl.net); Mon, 7 Aug 1995 22:51:57 +0900 Date: Mon, 7 Aug 1995 22:51:57 +0900 From: Zhang HongYu Message-Id: <199508071351.AA00478@ailab.ia.ac.cn> To: chemistry@ccl.net Subject: Summary of "conformation of glycoprotein" Dear CCL'ers, Here is the summary of my post a month ago named "conformation of glycoprotein". Thanks to all the reponses and I am sorry for the deplaying of this summary for a excursion. yours Henry The original question is: >Does anyone know any works and references about modeling of conformation >of carbohydrate part of glycoprotein? I've searched CA between 1986 and >1993, but got little result. From shaomeng@helix.nih.gov Tue Jul 11 08:38:32 1995 Received: from sunserver (sunserver.ia.ac.cn) by ailab.ia.ac.cn with SMTP id AA00175 (5.67b/IDA-1.5 for ); Tue, 11 Jul 1995 08:38:31 +0900 Received: from helix.nih.gov by sunserver (5.x/SMI-SVR4) id AA03179; Mon, 10 Jul 1995 23:32:31 +0900 Received: by helix.nih.gov (940715.SGI.52/1.35(m-sg-1.0)) id AA03659; Mon, 10 Jul 95 11:34:33 -0400 Date: Mon, 10 Jul 95 11:34:33 -0400 From: shaomeng@helix.nih.gov (Shaomeng Wang) Message-Id: <9507101534.AA03659@helix.nih.gov> To: Zhang HongYu Subject: Re: CCL:conformation of glycoprotein Status: RO X-Status: Hello, Henry, There is a recent paper in J. Medicinal Chemistry (1994, 37, 616-624) entitled " Molecular Modeling Studies on Ligand Binding to Sialidase from Influenza Virus and the Mechanism of Catalysis" by Neil R. Taylor and Mark von Itzstein that might be helpful. -Shaomeng Wang, Ph.D. National Cancer Institute National Institutes of Health Bethesda, MD 20892, USA From nauss@ucmod2.che.uc.EDU Tue Jul 11 08:38:37 1995 Received: from sunserver (sunserver.ia.ac.cn) by ailab.ia.ac.cn with SMTP id AA00185 (5.67b/IDA-1.5 for ); Tue, 11 Jul 1995 08:38:34 +0900 Received: from CUNYVM.CUNY.EDU by sunserver (5.x/SMI-SVR4) id AA03133; Mon, 10 Jul 1995 21:40:37 +0900 Received: from UCBEH.SAN.UC.EDU by CUNYVM.CUNY.EDU (IBM VM SMTP V2R2) with BSMTP id 8558; Mon, 10 Jul 95 09:39:58 EDT Received: from ucmod2.che.uc.edu by UCBEH.SAN.UC.EDU (PMDF V5.0-4 #7238) id <01HSP83ZFGIGHV1SUR@UCBEH.SAN.UC.EDU> for zhy@ailab.ia.ac.cn; Mon, 10 Jul 1995 09:31:51 -0500 (EST) Received: by ucmod2.che.uc.edu (920330.SGI/920502.SGI.AUTO) for @uc.edu:zhy@ailab.ia.ac.cn id AA00357; Mon, 10 Jul 1995 09:37:24 -0400 Date: Mon, 10 Jul 1995 09:37:24 -0400 From: nauss@ucmod2.che.uc.EDU (Jeffrey L. Nauss) Subject: Re: CCL:conformation of glycoprotein To: Zhang HongYu Reply-To: nauss@ucmod2.che.uc.EDU Message-Id: <9507101337.AA00357@ucmod2.che.uc.EDU> Content-Transfer-Encoding: 7BIT Status: RO X-Status: A >From: Zhang HongYu >Does anyone know any works and references about modeling of conformation >of carbohydrate part of glycoprotein? I've searched CA between 1986 and >1993, but got little result. I am not aware of any. However, you might want to post the question to the newsgroup bionet.glycosci. Please post a summary of your responses to CCL. 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 http://www.che.uc.edu/~nauss * **************************************************************************** From reimerk@unbc.edu Wed Jul 12 08:38:42 1995 Received: from sunserver (sunserver.ia.ac.cn) by ailab.ia.ac.cn with SMTP id AA00186 (5.67b/IDA-1.5 for ); Wed, 12 Jul 1995 08:38:41 +0900 Received: from unbc.edu by sunserver (5.x/SMI-SVR4) id AA04788; Wed, 12 Jul 1995 00:44:49 +0900 Received: by unbc.edu id m0sViSZ-00NslAC for zhy@ailab.ia.ac.cn ; Tue, 11 Jul 95 09:46 PDT Date: Tue, 11 Jul 1995 09:46:59 -0700 (PDT) From: Kerry Reimer To: zhy@ailab.ia.ac.cn Subject: modelling of carbohydrates Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Status: RO X-Status: R. Stuike-Prill and B. Meyer developed a program to do this sort of calculation using Monte Carlo type calculations. The reference to this paper is: Stuike-Prill, R. and Meyer, B. A new force-field program for the calculation of glycopeptides and its application to a heptacosapeptide-decasaccharide of immynoglobulin G1. Eur.J.Biochem. 194:903-919, 1990. Some other work that has been done that I am aware of follows: Stuike-Prill, R. and Meyer, B. A new force-field program for the calculation of glycopeptides and its application to a heptacosapeptide-decasaccharide of immynoglobulin G1. Eur.J.Biochem. 194:903-919, 1990. Poppe, L., Stuike-Prill, R., Meyer, B., and van Halbeek, H. The solution conformation of sialyl-a(2-6)-lactose studied by modern NMR techniques and Monte Carlo simulations. J.Biomolecular NMR 2:109-136, 1992. Pollexkruger, A., Meyer, B., Stuikeprill, R., Sinnwell, V., Matta, K.L., and Brockhausen, I. Preferred Conformations and Dynamics of Five Core Structures of Mucin Type O-Glycans Determined by NMR Spectroscopy and Force Field Calculations. Glycoconjugate J. 10:365-380, 1993. Hope this is of some help to You. Kerry ---------------------------------------------------------------------- Kerry Reimer Phone: 604-960-6675 Chemistry Department FAX: 604-960-5545 University of Northern B.C. E-Mail: reimerk@unbc.edu 3333 University Way Prince George, British Columbia CANADA, V2N 4Z9 ---------------------------------------------------------------------- From kzhao@biovx1.biology.ucla.edu Wed Jul 12 08:38:44 1995 Received: from sunserver (sunserver.ia.ac.cn) by ailab.ia.ac.cn with SMTP id AA00196 (5.67b/IDA-1.5 for ); Wed, 12 Jul 1995 08:38:43 +0900 Received: from biovx1 (biovx1.biology.ucla.edu) by sunserver (5.x/SMI-SVR4) id AA04776; Wed, 12 Jul 1995 00:00:33 +0900 Date: Tue, 11 Jul 1995 09:01:25 -0700 Message-Id: <95071109012544@biovx1.biology.ucla.edu> From: kzhao@biovx1.biology.ucla.edu To: zhy@ailab.ia.ac.cn Subject: sugar chain modeling X-Vms-To: SMTP%"zhy@ailab.ia.ac.cn" Status: RO X-Status: I sent my message to your old address, and am pasting it again to this address. Hi Henry: A couple of reviews from Reimond Dwek's group published some carbo- hydrate modeling pictures (colored), especially for IgG: Dwek RA: Glycobiology: "towards understanding the function of sugars" Biochem Soc Trans 23:1-25, 1995 Rudd PM et al: The effects of variable glycosylation on the functional activi- ties of ribonuclease, plasminogen and tissue plasminogen activator. Biochim Biophys Acta 1248: 1-10, 1995 I hope this would be of some help to you. Ke-Wei Zhao, Ph.D. Department of Biological Chemistry UCLA School of Medicine, CHS 33-257 10833 Le Conte Avenue Los Angeles, CA 90095-1737 Phone: (310)825-8722 Fax: (310)206-5272 From teoulf@garm.teokem.lu.se Tue Jul 11 20:38:24 1995 Received: from sunserver (sunserver.ia.ac.cn) by ailab.ia.ac.cn with SMTP id AA00171 (5.67b/IDA-1.5 for ); Tue, 11 Jul 1995 20:38:23 +0900 Received: from prldec4.ia.ac.cn (prlsgi1.ia.ac.cn) by sunserver (5.x/SMI-SVR4) id AA04489; Tue, 11 Jul 1995 17:00:59 +0900 Received: by prldec4.ia.ac.cn (5.65/DEC-Ultrix/4.3) id AA14198; Tue, 11 Jul 1995 17:03:46 -0800 Received: by garm.teokem.lu.se (AIX 3.2/UCB 5.64/4.03) id AA40863; Tue, 11 Jul 1995 10:20:39 +0200 Date: Tue, 11 Jul 1995 10:20:39 +0200 From: teoulf@garm.teokem.lu.se (Ulf Ryde) Message-Id: <9507110820.AA40863@garm.teokem.lu.se> To: zhy@ailab.ia.ac.cn Subject: RE: CCL:conformation of glycoprotein Status: RO X-Status: Dear Henry, here are three references about carbohydrate force fields: Homans SW: Biochem. 29(1990)9110 Glennon TM, et al.: J. Comput. Chem. 15(1994)1019 Woods RJ, et al.: J. Phys. Chem. 99(1995)3832 The last one is included in the Amber41 force field. Ulf Ryde Dep. Theoretical Chemistry University of Lund POB 124 S-221 00 Lund Sweden teoulf@garm.teokem.lu.se Fax: 46-46-2224543 Phone: 46-46-2224502 From cmeyer@tripos.fr Mon Jul 24 22:51:40 1995 Received: from relay1.fnet.fr by pchsgi25.IPC.PKU.EDU.CN via SMTP (911016.SGI/911001.SGI) for zhy id AA21876; Mon, 24 Jul 95 22:51:40 +0800 Received: from triposf.UUCP by relay1.fnet.fr (5.65c8d/92.02.29) via Fnet/EUnet-France id AA01963; Mon, 24 Jul 1995 16:57:35 +0200 (MET) Received: by triposf (931110.SGI/930416.SGI.AUTO) for relay1!pchsgi25.ipc.pku.edu.cn!zhy id AA01043; Mon, 24 Jul 95 16:53:39 +0200 Date: Mon, 24 Jul 95 16:53:39 +0200 From: cmeyer@tripos.fr (Christophe MEYER) Message-Id: <9507241453.AA01043@triposf> To: zhy Subject: Carbohydrate parameters Status: RO X-Status: Dear Dr Zhang, As a response to your request of carbohydrate parameters and information on glycoprotein modeling, I tried to send you a fax with usefull with the desired information but unfortunately it did not go through. I tried the following number : 861-2501725 Is this correct ? If not could you correct ? Best regards, Dr Chris MEYER ============================================================= | Dr. Christophe MEYER Phone : 33 1 69 19 16 70 | | Support scientist Fax : 33 1 69 32 09 47 | | E-Mail : cmeyer@tripos.fr | | Tripos Associates | | 3, Allee des Garays | | 91124 PALAISEAU | ============================================================= From owner-chemistry@ccl.net Mon Aug 7 10:17:13 1995 Received: from VMS.HUJI.AC.IL for ALEXK@vms.huji.ac.il by www.ccl.net (8.6.10/930601.1506) id KAA21225; Mon, 7 Aug 1995 10:14:55 -0400 Received: by HUJIVMS (HUyMail-V7b); Mon, 07 Aug 95 17:14:59 +0200 Received: by HUJIVMS (HUyMail-V7b); Mon, 07 Aug 95 17:07:09 +0200 Date: Mon, 7 Aug 95 17:06 +0200 Message-id: <07080095170658@HUJIVMS> From: To: chemistry@ccl.net MIME-version: 1.0 Content-type: Text/plain; charset=US-ASCII Content-Transfer-Encoding: 7BIT Subject: summary of responses about esff hi, This is the summary of answers i got about the esff force field. Dear Alexandra Kilshtain, I am sorry that version 235 is a very first beta release for ESFF that can only handle systems where there are no more than 25 molecules and each molecule has no more than 200 atoms. However, the later versions, 236, 237, 940 and 950 could handle a systems having no more than 15000 atoms. Please try the new versions and let me know if you have any questions. Best wishes, shenghua ************************************************************************** Hi, I have been using both the cvff and cff91 forcefields in discover and discover 94 on a solvated protein (~15,000) atoms including a Zn cation. I modified the cvff and cff91 forcefields to include my parameters for Zn. The Zn cation is treated totally as a nonbonded entity. If this is suitable for your problem, I can provide you with the necessary changes to cvff or cff91. Lee Bartolotti -- -------------------------------------------------------------------------------- Lee Bartolotti North Carolina Supercomputing Center Computational Scientist 3021 Cornwallis Rd. Research Institute Research Triangle Park, NC 27709 bartolot@ncsc.org (919) 248-1185 -------------------------------------------------------------------------------- *************************************************************************************** Dear Alexandra: As you experienced, only 200 atoms in each molecule and 15 molecules per crystal cell are allowed using ESFF force field with Biosym release 2.3.5. This limitation will be lifted in our upcoming release 95.0 and ESFF force field will be able to treat molecular systems up to 10,000 atoms. Lisa Yan Biosym Technologies, Inc. Tel (619)546-5547 9685 Scranton Road email lly@biosym.com San Diego, CA 92121 ************************************************************************************** Hi Alexandra, I'm sorry for not beeing able to give you any help. There's just a comment, I want to make: I'm doing MM for transition metals with insight/discover. I tried to use the ESFF because Biosym told me, it should be better than UFF of A. Rappe and so forth. They told me, that I should help them in testing ESFF. But I wanted to have a description , what ESFF actually does and how the parameters are generated from the atomic parameters (which is all published for UFF). But they didn't tell me. So I couldn't say, why some calculations gave reasonable result and others not. I can't publish all that and so I stopped the project. I really have to say, that I lost all (I don't know a better word) trust in Biosym. My suggestion: the advantage of ESFF would be to model your zinc environement (probably !!!!) reasonable. All the rest is calculated well by cff91, I guess. Why don't you use cff91 together with discover 94.0 (discover_3) and use some BTCL restraints to model just your zinc environement. Maybe you can overcome the 200 atom limit by that. Good luck, Greetings from Munich, Rochus -- ******************************************************************************** Rochus Schmid Technische Universitaet Muenchen Tel. ++49 89 3209 3140 Anorganisch Chemisches Institut 1 Fax. ++49 89 3209 3473 Prof. W. A. Herrmann E-mail: Lichtenbergstrasse 4 rochus@felix.anorg.chemie.tu-muenchen.de 85747 Garching ******************************************************************************** ************************************************************************************* Shalom Alexandra! I just want to worn you about using the esff seriously. First of all it has no parameters for Zn ion ( Look at the parameter table Page 3-23 Discover 2.9.5/94 Users Guide). Secondly, this ff, as I understand the things, is just under development. I even have an impression that the BIOSYM people themselves are not exactly aware of what they want this ff to work for - they write in the same Users guide that it is being designed for organic and organometallic compounds. I tested it for our organic compounds ( crown ether like mols) and it was completely wrong. I had a possibility to speak it over with BIOSYM people and they said that it was not at all a surprise for them because they design the esff for inorganics! So, use maybe AMBER or some other known ff (obligatory test them before for your comds!) and keep in touch with BIOSYM . I think your experience could help them. Yours, Lara. ________________________________________________________________________ / \ | Dr.Larisa Golender tel. +972-3-6408437 | | School of Chemistry fax: +972-3-6409293 | | Tel Aviv University e-mail: lara@chemdc1.tau.ac.il | | Ramat Aviv, Tel Aviv 69978 | | ISRAEL | \________________________________________________________________________ **************************************************************************************** Dear Alexandra Kilshtain, re: support request #45580 >1. Is their a version of discover that can deal with >more than 200 atoms and have esff potentials ? In the upcoming release, which should be out Mid-September, ESFF will have a 10,000 atom limit. >2. Is there any reference or manual section that you could send me >that will explain how to use the esff force field potentials for zinc? I don't know what you have received previously, below is a release note for ESFF for Insight235. Also, if you want to know what the atom type names refer to you can look in the esff.frc file in $BIOSYM/iris405/irix405_r3/biosym_lib For example the Zn atom types are: 1.0 1 Zn 65.390000 Zn 10 Zinc atom with s orbitals involved in bonding 1.0 1 Zn+ 65.390000 Zn 10 Zinc +1 free ion 1.0 1 Zn+2 65.390000 Zn 10 Zinc +2 free ion 1.0 1 Zn022 65.390000 Zn 10 Zinc with 2 coordinations 1.0 1 Zn023 65.390000 Zn 10 Zinc with 3 coordinations 1.0 1 Zn024 65.390000 Zn 10 Zinc with 4 coordinations 1.0 1 Zn025 65.390000 Zn 10 Zinc with 5 coordinations 1.0 1 Zn025s 65.390000 Zn 10 Zinc with 5 coordinations, D4h symmetry 1.0 1 Zn025t 65.390000 Zn 10 Zinc with 5 coordinations, D3h symmetry 1.0 1 Zn026 65.390000 Zn 10 Zinc with 6 coordinations 1.0 1 Zn026o 65.390000 Zn 10 Zinc with 6 coordinations, oh symmetry If you still have questions after reading this note, you can always send us your .car and .mdf files and we can take a look at them. The ESFF Forcefield-Release Note -------------------------------- The Discover 94.1 release of ESFF a new rule-based forcefield. The initial goal of ESFF was to provide the widest possible coverage of the periodic table at a level of accuracy capable of producing reasonable structures. The limit for the total number of atoms in a system is 200 (for 235 release) and 10,000 (for 950 release). Setting up ESFF: - In the 235 release, before starting up the Insight program, esff_setup must be entered at the UNIX prompt: > esff_setup This command sets the appropriate environmental variables to access the ESFF data sets. It is not possible to select ESFF within the Insight environment with the Forcefield/Select command. The reason for this is the elements.dat file, which defines the properties of the elements, differs (in ESFF) from that of other forcefields and the Select command does not change the variable which reads the elements.dat. It is still possible to switch from ESFF to one of the other forcefields using this command. However, the elements.dat file will remain as the one associated with the ESFF forcefield. Because of this, you must exit the Insight program, unset the INSIGHT_DATA environmental variable by running cvff_setup and restart the Insight program. Building Pi Bonded Systems: - pi bonds are created by first defining a pseudoatom as the center of a set of ligand atoms and then bonding this pseudo atom to the metal. What appears are bonds between the metal and each atom that defines the pseudo atom. For an example see the tutorial below. Assigning Atom Types, Partial Charges and Formal Charges: - The procedure for assigning atom types and charges in ESFF differs from that of other forcefields. With ESFF the total charge of a molecule is used to determine the oxidation state of the metal which in turn is used in determining the atom types. - The oxidation number of the metal is given by the following expression: Nox = Qt - Sum(Fqi)/Nm - Sum(Fqj/Nb) where Qt is the total charge on the complex, and the sums over Fqi and Fqj are the sums of formal charges on atoms not bonded to metals and bonded to metals, respectively. Nm is the number of metal atoms in the complex, and Nb is the number of metal atoms bonded to the jth ligand atom. - Once you have built a molecule, the first step in assigning the atom types is to set the total charge of the molecule. Insight will sum all partial charges on the molecule and consider this the total charge. Therefore, the simplest way to set the total charge is to change the partial charge of an arbitrary atom to the value of the total charge and zero all other partial charges. This step can be carried out using an existing BCL macro, initialize_charge.bcl. To do so enter: source $BIOSYM/data/discover/esff/initialize_charge.bcl This will insert the command Set_Molec_Chg into the Forcefield pulldown. Choosing this command results in a prompt for the name of the molecule. The macro then zeros all partial charges and sums the formal charges in the molecule. The resulting sum is reported as a suggested total molecular charge. You may either accept this or specify a different value. When the Set_Molec_Chg command is executed, the macro places this charge on the first atom in the molecule and zeros all other partial charges. If the total charge on your molecule is zero and you have checked that all partial charges are zero or if all the partial charges add up to the desired total charge, you will not need to use this command. However, it is important to verify this before continuing (non-zero partial charges can result from previous calculations with other forcefields or from fragment libraries). The next step is to derive formal charges and assign the atom types using the Forcefield/Potentials command. - In the 235 release the fix partial charges action has been disabled. The reason for this is that ESFF calculates charges on the fly based on atom type as well as other topological considerations (see the Discover User Guide ). The charges used in the calculation can be displayed in the Insight program after the calculation has completed and the structure has been updated. The charges are also written to the .cor and .mdf files. - The atom types for metals are based on the symmetry of the metal complex as well as the oxidation state and coordination number of the metal. For example, Ag024t specifies that Ag has an oxidation level of 2+, is 4-coordinated and has a tetrahedral symmetry. The following table describes the atom type suffixes: Symbol Symmetry Coordination Description ================================================================================ d Dip 2 Linear (ligands are pseudo atoms) t Dih 2 Linear (ligands are real atoms) C2v 2 Bent -------------------------------------------------------------------------------- l C2v 3 T-shaped D3h 3 Planar C3v 3 Pyramide -------------------------------------------------------------------------------- t Td 4 Tetrahedral s D4h 4 Square Planar l C2v 4 Trigonal Bipyramide less an equatorial -------------------------------------------------------------------------------- t D3h 5 Trigonal Bipyramide s,l D4h 5 Square Pyramide l C2v 5 Tetragonal Octahedral less an equatorial -------------------------------------------------------------------------------- D2h 6 Rhombic Octahedral D4h 6 Tetragonal Octahedral o Oh 6 Octahedral -------------------------------------------------------------------------------- p D5h 7 Pentagonal Bipyrimide l C2v 7 Hexagonal Bipyrimide less an equatorial -------------------------------------------------------------------------------- h D6h 8 Hexagonal Bipyrimide -------------------------------------------------------------------------------- Note, that there are several combinations that do not have a symbol for the symmetry in these cases only the oxidation number and coordination are specified in the atom type name. Some metals with differing oxidation numbers may be treated with the same parameters. In these cases, the atom type is a generic atom type associated with the metal. ESFF Forcefield Editor Option (only available in the 236 release): You may modify the explicit parameters of the ESFF forcefield for a particular molecular system. To do so, first run a job for that system in the default mode. An explicit parameter file, run_name.epa, is output when the job (run_name) is finished. You can then edit run_name.epa to modify the explicit parameters; force constants, alphas and reference values. To rerun the job with the modified parameters, you must add the following line to the command input file (run_name.inp) after the "begin" command: set esffOverrideParameters 1 When this flag is set to 1 (the default is 0), only the parameters contained in the file run_name.epa are used. Tutorial on Use of the ESFF Forcefield -------------------------------------- The following tutorial is given as an example of how to use the organometallic builder. It is strongly recommended that you run through this example before using the Builder. This tutorial is written in outline form and assumes that you already have some familiarity with the Insight molecular modelling program and its Discover_3 module. Tutorial -Creating and Minimizing Dichloro(Dicyclopentadienyl) Titanium (IV), (C5H5)2TiCl2, with ESFF Before starting the Insight program, enter the following at the UNIX prompt: > esff_setup 1. Start the Insight program by entering insightII at the UNIX prompt. 2. Add the Set_Molec_Chg command to the Forcefield pulldown by entering on the Insight command line (near the bottom of the Insight screen): source $BIOSYM/data/discover/esff/initialize_charge.bcl 3. The Builder module is automatically accessed. 4. Select the Fragment/Get command and set Type Of Fragment to Metal_Templates. Click any atom in the Coord4-Td fragment (set Scroll to Next until you see it near the top of the Insight window) and select Execute. *Note, be sure to select the template that best represents the symmetry of the structure you wish to build, subsequent atom type assignments will depend on it. 5. Select the Atom/Replace command, choose Ti (scroll to find it by using the scrollbar to the right of the Element Type list), and then click the Mx (central atom) of the molecule in the display area. *Note that the central atom should be replaced by a metal before adding any ligands. This is to ensure that the metal-ligand bond lengths are correct. 6. In the same way, replace two of the ligand atoms with Cl. 7. Select the Fragment/Get command and set Type Of Fragment to Metal_Ligands. Toggle the To_Modify_Bond parameter off and click the Lg_pentadien fragment twice (followed by selecting Execute) to retrieve two cyclopentadienyl rings. 8. Connect to each of the rings in turn and move it so it is near the unbound ligand positions of the metal complex. 9. Define a pseudoatom at the center of one of the rings by using the Pseudo_Atom/Define command and specifying the ring carbons. 10. Bond the pseudoatom to one of the ligand atoms (use the Modify/Bond command with Bond Operation set to Create) 11. Repeat Steps 9 and 10 with the other cyclopentadienyl ring, bonding it to the last ligand atom. 12. You will see that the pseudoatom associated with the first ring bound disappears when the second ring is bound. Create a new pseudoatom for this ring. 13. Select the Forcefield/Set_Molec_Chg command and choose the molecule name from the value-aid. After a short time, a recommended charge based on the molecule's formal charges appears in the Charge parameter box. In this example there are no formal charges, so zero will appear. Accept this charge by selecting Execute. In this case this step is not necessary however if you would want to place a net charge on the molecule you woulddo so here. 14. Select the Forcefield/Potentials command. Assure that Potential Action is set to Fix, Partial Chg Action to Accept, and Formal Chg Action to Fix. Select Execute. 15. Go to the Discover_3 module (by clicking the Biosym logo). 16. Select the Setup/System command and click the Ti complex. 17. Select the Commands/Minimize command and select Execute (this accepts the default parameter values). 18. Select the D_Run/Run command and select Execute. 19. Quit the Insight interface by entering quit on on the command line. I hope that you find this helpful. Please let us know if you have any further questions. Jodi ++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Jodi Shaulsky BIOSYM Technologies jodi@biosym.com 619-546-5542 end From owner-chemistry@ccl.net Mon Aug 7 13:03:30 1995 Received: from axp1.acc.georgetown.edu for CHOICH@guvax.acc.georgetown.edu by www.ccl.net (8.6.10/930601.1506) id MAA25890; Mon, 7 Aug 1995 12:55:39 -0400 From: Received: from guvax.acc.georgetown.edu by guvax.acc.georgetown.edu (PMDF V4.3-9 #7802) id <01HTSEVFSUKW90PQ8N@guvax.acc.georgetown.edu>; Mon, 07 Aug 1995 10:53:14 -0400 (EDT) Date: Mon, 07 Aug 1995 10:53:14 -0400 (EDT) Subject: electron position? To: chemistry@ccl.net Message-id: <01HTSEVFVD0290PQ8N@guvax.acc.georgetown.edu> X-VMS-To: IN%"chemistry@ccl.net" MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Content-transfer-encoding: 7BIT Dear CCLers Most ab initio program give us dipole moment of a molecule. To get dipole moment , one should calculate the expectation position of electron(s) . Is it possible to get these values from Gaussian or Gamess output? Thanks in advance. Cheolho Choi. Georgetown Univ. From owner-chemistry@ccl.net Mon Aug 7 17:02:15 1995 Received: from midway.uchicago.edu for cmartin@rainbow.uchicago.edu by www.ccl.net (8.6.10/930601.1506) id QAA04553; Mon, 7 Aug 1995 16:58:43 -0400 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 PAA28401 for <@midway.uchicago.edu:chemistry@ccl.net>; Mon, 7 Aug 1995 15:58:38 -0500 Received: by rainbow.uchicago.edu (931110.SGI/930416.SGI) for @midway.uchicago.edu:chemistry@ccl.net id AA01759; Mon, 7 Aug 95 15:58:15 -0500 From: cmartin@rainbow.uchicago.edu (Charles Martin) Message-Id: <9508072058.AA01759@rainbow.uchicago.edu> Subject: Comparisons between MD and Experiment To: chemistry@ccl.net Date: Mon, 7 Aug 1995 15:58:13 -0500 (CDT) X-Mailer: ELM [version 2.4 PL24] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Length: 1088 Dear list members, I am attempting to track down research on molecular dynamics simulations of proteins and small peptides which provide detailed comparisons between experiment and theory, such as the accuracy of computed relaxation times and/or time correlation functions in NMR, floursence deopolarization, or whatever. One example I know of is "Polypeptide dynamics: Experimental tests of an optimized Rouse-Zimm type model" by Yi Hu, Jean M. MacInnis, Binny J. Cherayil, Graham R. Flemming, Karl F. Freed, and Angelo Perico, JCP 93 (1), 1 July 1990 page 822, as well as some of their later work. I am, of course, aware of the chapter in the volume LXXI Advances in Chemical Physics, Brooks, Karplus, and Petit (1988). I am looking for more recent studies. I am trying to determine to what extent MD simulations can reproduce experiment correctly, and if the current MD forcefields do accurately describe dymanics in addition to static structures. I will summarize the responses accordingly. Chuck Martin Beckman Institute The University of Illinois at Urbana-Champaign From owner-chemistry@ccl.net Mon Aug 7 18:02:16 1995 Received: from SLVAXA.umsl.edu for C1790@SLVAXA.UMSL.EDU by www.ccl.net (8.6.10/930601.1506) id SAA05572; Mon, 7 Aug 1995 18:00:46 -0400 Received: from SLVAXA.UMSL.EDU by SLVAXA.UMSL.EDU (PMDF V4.3-7 #2503) id <01HTSS0NWDFS9OCV28@SLVAXA.UMSL.EDU>; Mon, 7 Aug 1995 17:02:43 CDT Date: Mon, 07 Aug 1995 17:02:43 -0500 (CDT) From: BILL WELSH Subject: effects of side-chain bulk on polymer spatial configurations To: chemistry@ccl.net Message-id: <01HTSS0NWN2Y9OCV28@SLVAXA.UMSL.EDU> X-VMS-To: in%"chemistry@ccl.net" MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Content-transfer-encoding: 7BIT Dear Netters, I am looking for published examples of cases in which the strong steric interactions between the side-chain and main-chain produces a large influence on the spatial configuration of polymer molecules. I understand that examples are found among the polyolefins, poly(vinyl ethers), poly(alkylene oxides), poly(methyl acrylates), poly(chloral), and polysaccharides, but I am looking for cited references in the literature. I appreciate any suggestions. Bill Welsh Dept of Chem. Univ. of Missouri-St. Louis From owner-chemistry@ccl.net Mon Aug 7 21:02:18 1995 Received: from utsc.s.u-tokyo.ac.jp for smori@chem.s.u-tokyo.ac.jp by www.ccl.net (8.6.10/930601.1506) id UAA07072; Mon, 7 Aug 1995 20:58:48 -0400 Received: from [133.11.6.102] (nakaquadra.chem.s.u-tokyo.ac.jp) by utsc.s.u-tokyo.ac.jp (5.67+1.6W/TISN-1.3/R2) id AA07253; Tue, 8 Aug 95 09:54:38 JST Message-Id: <9508080054.AA07253@utsc.s.u-tokyo.ac.jp> Date: Tue, 8 Aug 1995 09:57:40 +0900 To: chemistry@ccl.net From: smori@chem.s.u-tokyo.ac.jp (Mori Seiji) X-Sender: smori@chem.s.u-tokyo.ac.jp (Unverified) Subject: thank you for replys of the optimization problem with G94. Cc: smori@utsc.s.u-tokyo.ac.jp Mime-Version: 1.0 Content-Type: text/plain; charset=iso-2022-jp X-Mailer: Eudora-J(1.3.8.5-J13) Dear Netters; In July 26th, I sent my question to CCL. The subject is "Converge problem in the optimization on G94". and I am happy there are many responses. Spatial thanks to: Eric V. Patterson Anthony P Scott Sang-Yeon Lee Magan Govender Hsing Lee Karl Irikura Wolfram Koch Jing Kong Kui Zhang Karl F. Moschner (with Doug Fox) Fernando Vila Craig Wilson Frank Jensen E. Lewars Akinori Murakami Brian Salter-Duke ---question-- Dear Netters; I use the gaussian 92 and g94 programs. I have a problem about the geometry optimization and frequency analysis. After the geometry optimization completed ,I performed the frequency calculation analysis. However, from the output of frequency analysis , sometimes Optimization is not completed because values about displacement exceed the thresholds. How should I resolved it and wolud you tell me your thought about this problem ? --end-- The summary of my question is following. Difference of the displacement between optimization and frequency calculation are due to the difference of hessian approximation. The former is determined by update and the latter is by analytical calculation. 1. Restart with opt=(readfc,tight), opt=(calcfc,tight) or opt=(calcall,tight). 2. When the PES is flat, it is difficult to converge the displacement criteria. then, we can ignore this. In this case, in the frequency calculation, it is difficult to fit the PES by second order approximation. Regards. Seiji Mori ******************************* 森　聖治 東京大学理学部化学科 物理有機化学講座　中村研究室　D1 TEL:03-3812-2111内線4367 *******************************