From komatsu@bn.kubota.co.jp Wed Sep 7 07:51:02 1994 Date: Wed, 7 Sep 1994 03:51:02 -0400 From: bn.kubota.co.jp!komatsu@hyper.hyper.com (Katsuichiro Komatsu) To: hyperchem@HYPER.COM Subject: Back End Trouble Cc: komatsu@bn.kubota.co.jp Dear Sir I am working in Simulation Technology Inc. as one of HyperChem technical supports. I recived Ph. D. from School of Pharmaceutical Scienses, Kitasato University. I am studying QSAR and Protein Physical Chemistry. We recieved HyperChem Back End flopy disks from you last week. I installed Molecular Mechanics and Semi Empirical Back End programs to RS6000 530H today as I consulted HyperChem Installation Guide for Molecular Mechanics and Semi Empirical Back End Target: AIX/RS6000. But I can not make them run. How do I need to set up to HyperChem on PC ? I recieved the Guides and the flopy disks only. Is there a manual for the Back End ? Yours sincerely, Simulation Technology Inc. Katsuichiro Komatsu E-Mail: komatsu@kubota.co.jp ________________________________________________________________________ From komatsu@bn.kubota.co.jp Tue Sep 6 08:22:34 1994 Date: Tue, 6 Sep 1994 04:22:34 -0400 From: bn.kubota.co.jp!komatsu@hyper.hyper.com (Katsuichiro Komatsu) To: hyperchem%hyper.com@kpc.com Subject: Back End Trouble Cc: komatsu@bn.kubota.co.jp Dear Sir I am working in Simulation Technology Inc. as one of HyperChem technical supports. I recived Ph. D. from School of Pharmaceutical Scienses, Kitasato University. I am studying QSAR and Protein Physical Chemistry. We recieved HyperChem Back End flopy disks from you last week. I installed Molecular Mechanics and Semi Empirical Back End programs to RS6000 530H today as I consulted HyperChem Installation Guide for Molecular Mechanics and Semi Empirical Back End Target: AIX/RS6000. But I can not make them run. How do I need to set up to HyperChem on PC ? I recieved the Guides and the flopy disks only. Is there a manual for the Back End ? Yours sincerely, Simulation Technology Inc. Katsuichiro Komatsu E-Mail: komatsu%kubota.co.jp@kpc.com ________________________________________________________________________ From ASCHICK@chemserver.chem.vt.edu Sat Sep 17 20:51:57 1994 From: "ALAN SCHICK" To: hyperchem@HYPER.COM Date: Sat, 17 Sep 1994 16:51:57 -0400 Subject: Printing pop-up menus I recently upgraded from Release 3 to 4. I am now having trouble capturing the contents of pop-up menus, which now appear with gray backgrounds instead of the white (as in Release 3). I have been keeping track of my semi-emperical setup by clip-boarding a hyperchem screen which contains a diagram of the molecule and the pop-up menus of (i) method used, (ii) options, and (iii) CI info. I then copy the clip-board into a graphics file and print it. In release 3 this worked fine. However, in release 4, the menus all have gray backgrounds which copy as black, thereby obscurring the useful information. This appears also to be true for much of the UV spectrum window. I have hyperchem set for window background white. Anything I can do? ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ G. Alan Schick Asst. Professor Dept. of Chemistry Virginia Tech Blacksburg, VA 24061-0212 Voice: 703/231-8215 FAX: 703/231-3255 Internet: aschick@chemserver.chem.vt.edu ________________________________________________________________________ From J_RABER@ACAD.LVC.EDU Fri Sep 16 17:25:28 1994 Date: Fri, 16 Sep 1994 13:25:28 -0400 From: ACAD.LVC.EDU!J_RABER@hyper.hyper.com To: hyperchem@HYPER.COM Cc: J_RABER@ACAD.LVC.EDU Subject: Potential Energy Surface Hello Everyone: I am trying to generate a potenial energy surface, and graph it. The manuals explain how everything works, but they don't give the directions on how to do it. If there is anyone that can help me through this, I would greatly appreciate it. Thanks in advance. ******************************************************************************* Jeffrey Raber Tel: Home: (717)-274-9407 Work: (717)-867-6179 BioChemistry Major Fax: (717)-228-2453 ATTN: Jeff Raber Lebanon Valley College Annville, PA Mail: 24 Fox Chase Lane E-Mail: J_RABER@ACAD.LVC.EDU Lebanon, PA 17042 ________________________________________________________________________ From hurst@hyper.hyper.com Mon Sep 19 15:57:21 1994 Date: Mon, 19 Sep 1994 11:57:21 -0400 From: hurst@hyper.hyper.com (Graham Hurst) To: "ALAN SCHICK" , hyperchem@HYPER.COM Subject: Re: Printing pop-up menus Alan Schick writes: > I recently upgraded from Release 3 to 4. I am now having trouble > capturing the contents of pop-up menus, which now appear with gray > backgrounds instead of the white (as in Release 3). I have been > keeping track of my semi-emperical setup by clip-boarding a > hyperchem screen which contains a diagram of the molecule and the > pop-up menus of (i) method used, (ii) options, and (iii) CI info. I > then copy the clip-board into a graphics file and print it. In > release 3 this worked fine. However, in release 4, the menus all > have gray backgrounds which copy as black, thereby obscurring the > useful information. This appears also to be true for much of the UV > spectrum window. I have hyperchem set for window background white. > Anything I can do? Three possible solutions are: 1. Use a colour screen capture to avoid grey being converted to black. 2. Change colours in the Control Panel to use white text. 3. Use Look3D=No in your CHEM.INI (described in the first item in R4 README). Hope this helps, Graham ------------ Graham Hurst (hurst@hyper.com) Hypercube Inc, 7-419 Phillip St, Waterloo, Ont, Canada N2L 3X2 (519)725-4040 Info requests to: info@hyper.com Support questions to: support@hyper.com Email group: Send "subscribe hyperchem" to hyperchem-request@hyper.com ________________________________________________________________________ From rachel.vallance@stonebow.otago.ac.nz Tue Sep 20 07:25:02 1994 X-Sender: ou004692@brandywine.otago.ac.nz Date: Tue, 20 Sep 1994 03:25:02 -0400 To: hyperchem@uunet.ca From: stonebow.otago.ac.nz!rachel.vallance@hyper.hyper.com (Rachel Vallance) Subject: protein numbering Dear Hyperchemists, I've noticed that when one selects a portion of a protein and then deletes the rest of it hyperchem renumbers the selection with every 'loose end' resulting from the selection process being renumbered as '1'. Is there any way to keep the original numbering while only viewing a portion of the original protein? Thanks, Rachel Vallance Rachel Vallance ^ ^ School of Pharmacy ' ' University of Otago ' Dunedin, N.Z. \___/ Email: rachel.vallance@stonebow.otago.ac.nz ________________________________________________________________________ From hurst@hyper.hyper.com Tue Sep 20 14:03:05 1994 Date: Tue, 20 Sep 1994 10:03:05 -0400 From: hurst@hyper.hyper.com (Graham Hurst) To: rachel.vallance@stonebow.otago.ac.nz (Rachel Vallance), hyperchem@HYPER.COM Subject: Re: protein numbering Rachel Vallance writes: > I've noticed that when one selects a portion of a protein and then deletes > the rest of it hyperchem renumbers the selection with every 'loose end' > resulting from the selection process being renumbered as '1'. Is there any > way to keep the original numbering while only viewing a portion of the > original protein? Select the residues you don't want to see, use Display/Hide Selection and then clear the selection. Alternatively you could select what you want to see, use Display/Show Selection Only and then clear the selection. Hope this helps, Graham ------------ Graham Hurst (hurst@hyper.com) Hypercube Inc, 7-419 Phillip St, Waterloo, Ont, Canada N2L 3X2 (519)725-4040 Info requests to: info@hyper.com Support questions to: support@hyper.com Email group: Send "subscribe hyperchem" to hyperchem-request@hyper.com ________________________________________________________________________ From hurst@hyper.hyper.com Tue Sep 20 16:34:13 1994 Date: Tue, 20 Sep 1994 12:34:13 -0400 From: hurst@hyper.hyper.com (Graham Hurst) To: J_RABER@ACAD.LVC.EDU Subject: Re: Potential Energy Surface Cc: hyperchem@HYPER.COM Jeffrey Raber writes: > Hello Everyone: > I am trying to generate a potenial energy surface, and graph it. The > manuals explain how everything works, but they don't give the directions on > how to do it. If there is anyone that can help me through this, I would > greatly appreciate it. Thanks in advance. I know that lots of subscribers have tackled the generation of a PES with HyperChem - please share your knowledge with the rest of us! There are at least two ways to generate a PES. Once you have chosen one or more internal coordinates to vary (eg. interatomic distance, bond dihedral angle), you need to decide whether you want to keep the rest of the internal coordinates fixed or free. In the former you simply step the variable internal coordinates through a grid of values perform a single point calculation at each grid point to obtain the potential energy. The latter approach is generally preferred, and the usual algorithm is to step the variables through fixed increments and perform an optimization with the variables frozen and the rest of the system unconstrained. To do this in HyperChem you need to use restraining forces to "fix" the variables you are interested in (eg. two dihedral angles) for the optimizations then follow each optimization with a restraint-free single point (perhaps with the variables returned to their ideal values since restraints are not rigid). If you want to create a PES dependent on two dihedral angles, I'd recommend the Excel 4 macro that comes with ChemPlus. It allows either way of generating a potential surface and plots the results as a 3D surface in Excel. It's distributeed as source, so you could modify it. Cheers, Graham ------------ Graham Hurst (hurst@hyper.com) Hypercube Inc, 7-419 Phillip St, Waterloo, Ont, Canada N2L 3X2 (519)725-4040 Info requests to: info@hyper.com Support questions to: support@hyper.com Email group: Send "subscribe hyperchem" to hyperchem-request@hyper.com ________________________________________________________________________ From oberhols@mcis.messiah.edu Wed Sep 21 15:54:00 1994 From: mcis.messiah.edu!oberhols@hyper.hyper.com Date: Wed, 21 Sep 1994 11:54:00 -0400 Subject: Setting file format To: hyperchem@HYPER.COM The file-format message can be used to set the file format to hin, pdb, etc. Is there any way that the format can be set to scr by using a message? ....................................................................... Item Subject: Signature Karl M. Oberholser Internet: oberhols@mcis.messiah.edu Natural Science Dept. Voice: 717-766-2511 Messiah College Fax: 717-691-6002 Grantham, PA 17027 ________________________________________________________________________ From hurst@hyper.hyper.com Wed Sep 21 16:09:43 1994 Date: Wed, 21 Sep 1994 12:09:43 -0400 From: hurst@hyper.hyper.com (Graham Hurst) To: hyperchem@HYPER.COM Subject: HyperChem references Hyperchemists, We've been compiling a list of publications that have used or reviewed HyperChem, ChemPlus or HyperNMR. I include the list below. It's been straightforward to find papers that cite HyperChem in the list of references. Unfortunately some times its use just gets mentioned in the text without being referenced, and those cases are hard to find so I'd like your help! If you know of any publications that used or reviewed HyperChem, ChemPlus or HyperNMR that aren't in the list below, please send me (hurst@hyper.com) the details or even send a reprint. (The mail address is in my .signature at the bottom and our FAX number is +1 519 725 5193.) If you're the first one to send a reference that is not in the list below, I'll send you a genuine Hypercube sweatshirt! (Only available in large or extra large.) Hope to hear from you soon! Graham ************************************************************************* Papers that report using HyperChem ************************************************************************* Authors: Boere-RT Eng-JA Preuss-K Parvez-M Bryan-CD Cordes-AW Title: Alkene Adducts of Cyclic Thiazenes - Identification of Exo and Endo Addition of 1,3,2,4,6-Dithiatriazines to 1,5-Norbornadiene by 2-D NMR Methods and the Crystal-Structure of a Single-Molecule in Which Both Modes of Addition Are Displayed Source: CANADIAN JOURNAL OF CHEMISTRY-REVUE CANADIENNE DE CHIMIE 1994, Vol 72, Iss 4, pp 1171-1180 Language: English Document type: Article Authors: Neidle-S Goodwin-GH Title: A Homology-Based Molecular-Model of the Proline-Rich Homeodomain Protein Prh, from Hematopoietic-Cells Source: FEBS LETTERS 1994, Vol 345, Iss 2-3, pp 93-98 Language: English Document type: Article Authors: Jursic-BS Title: Spectroscopic and Molecular Mechanics Calculations of Discrimination Between Enantiomers Possessing an Electron-Rich Aromatic Group Directly Attached to the Chiral Carbon-Atom with Optically Pure Benzoyl Derivatives Source: JOURNAL OF THE CHEMICAL SOCIETY-PERKIN TRANSACTIONS 2 1994, Iss 5, pp 961-969 Language: English Document type: Article Authors: Arteca-GA Title: Shape-Analysis of Hydrogen-Bonded Networks in Solvation Clusters Source: JOURNAL OF COMPUTATIONAL CHEMISTRY 1994, Vol 15, Iss 6, pp 633-643 Language: English Document type: Article Authors: Barlow-D Satoh-T Title: The Design of Peptide Analogs for Improved Absorption Source: JOURNAL OF CONTROLLED RELEASE 1994, Vol 29, Iss 3, pp 283-291 Language: English Document type: Article Authors: Pola-J Cukanova-D Ponec-R Stanczyk-W Title: Laser Powered Homogeneous Decomposition of Tetramethylcyclotetrasiloxane - A Source for Hydroxy(Methyl) Silylene Source: JOURNAL OF ORGANOMETALLIC CHEMISTRY 1994, Vol 468, Iss 1-2, pp 49-53 Language: English Document type: Article Authors: Falter-J Medina-R Schmidt-HL Title: Concepts of Artificial Affinity Systems for Sensor Development Source: SENSORS AND ACTUATORS B-CHEMICAL 1994, Vol 19, Iss 1-3, pp 694-697 Language: English Document type: Article Authors: Patrick-DL Beebe-TP-Jr Title: Substrate Defects and Variations in Interfacial Ordering of Monolayer Films on Graphite Source: LANGMUIR 1994, Vol 10, Iss 1, pp 298-302 Language: English Document type: Article Authors: Schraml-J Jakoubkova-M Kvicalova-M Kasal-A Title: Steric Effects on NMR Chemical-Shifts Controlled by the Solvent Accessible Surface Source: JOURNAL OF THE CHEMICAL SOCIETY-PERKIN TRANSACTIONS 2 1994, Iss 1, pp 1-2 Language: English Document type: Note Authors: Keseru-GM Nogradi-M Title: Prediction of Antibacterial Activity of Some Diarylheptanoids Isolated from Garuga Species by Molecular Mechanics and Molecular-Orbital Calculations Source: THEOCHEM-JOURNAL OF MOLECULAR STRUCTURE 1993, Vol 105, Iss OCT, pp 259-265 Language: English Document type: Article Authors: Szantay-C Demeter-A Honty-K Kolonits-P Szantay-C Title: Structural Reinvestigation of 2 Diastereoisomeric Aspidosperma Eburnea Type bis-Indoles by NMR Methods - Detection of a Hidden Exchange Partner and Implications in Noe Analysis Source: MAGNETIC RESONANCE IN CHEMISTRY 1993, Vol 31, Iss 8, pp 773-785 Language: English Document type: Article ************************************************************************* Software reviews of HyperChem ************************************************************************* Authors: Pazun-JL Title: Hyperchem Release 3 for Windows Source: JOURNAL OF CHEMICAL INFORMATION AND COMPUTER SCIENCES 1993, Vol 33, Iss 6, pp 931-933 Language: English Document type: Software-Review Authors: Elissa-BD Janini-GM Title: Hyperchem for PC - Windows Version Source: JOURNAL OF LIQUID CHROMATOGRAPHY 1993, Vol 16, Iss 11, pp 2425-2426 Language: English Document type: Article Authors: Bures-M Title: Hyperchem, Software for Molecular Computer-Simulation Source: CHEMICKE LISTY 1993, Vol 87, Iss 5, pp 382-383 Language: Czech Document type: Letter Authors: Sklenak-S Pospichal-J Kvasnicka-V Title: Hyperchem, Software for Molecular Computer-Simulation Source: CHEMICKE LISTY 1993, Vol 87, Iss 5, pp 379-382 Language: Czech Document type: Software-Review Authors: Bearden-DW Title: Hyperchem Release-2 for the Silicon Graphics Workstation Source: JOURNAL OF CHEMICAL INFORMATION AND COMPUTER SCIENCES 1993, Vol 33, Iss 3, pp 525-528 Language: English Document type: Article Authors: Kingsbury-CA Title: Hyperchem for the PC or for the Silicon Graphics Iris Workstation Source: JOURNAL OF CHEMICAL EDUCATION 1993, Vol 70, Iss 5, pp A144-A145 Language: English Document type: Software-Review Authors: Goodman-J Title: Hyperchem Source: CHEMISTRY & INDUSTRY 1992, Iss 15, pp 572-573 Language: English Document type: Software-Review Authors: Winchester-WR Doyle-MP Title: Hyperchem Source: JOURNAL OF THE AMERICAN CHEMICAL SOCIETY 1992, Vol 114, Iss 23, pp 9243-9243 Language: English Document type: Software-Review Authors: Teppen-BJ Title: Hyperchem, Release .2. Molecular Modeling for the Personal-Computer Source: JOURNAL OF CHEMICAL INFORMATION AND COMPUTER SCIENCES 1992, Vol 32, Iss 6, pp 757-759 Language: English Document type: Software-Review Author: Simon-B Title: Hyperchem: Complex Chemistry in Windows Source: PC MAGAZINE, 1992, Vol 11, Iss 10, pp 56-56 Language: English Document type: Software-Review Author: Mock-G McClarin-J Smith-D Title: Molecular Design: Applications of PC-Driven Molecular Modeling and Analysis Source: SCIENTIFIC COMPUTING AND AUTOMATION, 1992, Vol 8, Iss 6, pp 29-32 Language: English Document type: Article Author: Studt-T Title: Models For Bench Chemists Source: R&D MAGAZINE, 1992, Iss JUL, pp 83-83 Language: English Document type: Software-Review Author: DuBose-RF Title: Molecular Modeling - Hyperchem Release 2 Source: BIOPHARM, 1992, Iss SEP, pp 52-52 Language: English Document type: Software-Review Author: Breeze-P Title: Up and Atom Source: PC USER, 1992, Iss 190, pp 44-45 Language: English Document type: Software-Review Author: Bernard-M Title: Hyperchem Release 2 for Windows Source: BIOTECHNOLOGY SOFTWARE, 1992, Vol 9, Iss 5, pp 24-29 Language: English Document type: Software-Review Author: Endres-M Title: Molecular Modeling: Is It Finally Ready for the Bench Chemist? Source: TODAY'S CHEMIST AT WORK, 1992, Vol 1, Iss 4, pp 31-44 Language: English Document type: Software-Review Author: Wong-M Title: Hyperchem Source: CHEMISTRY IN AUSTRALIA, 1992, Iss NOV Language: English Document type: Software-Review ------------ Graham Hurst (hurst@hyper.com) Hypercube Inc, 7-419 Phillip St, Waterloo, Ont, Canada N2L 3X2 (519)725-4040 Info requests to: info@hyper.com Support questions to: support@hyper.com Email group: Send "subscribe hyperchem" to hyperchem-request@hyper.com ________________________________________________________________________ From hurst@hyper.hyper.com Wed Sep 21 18:02:37 1994 Date: Wed, 21 Sep 1994 14:02:37 -0400 From: hurst@hyper.hyper.com (Graham Hurst) To: oberhols@mcis.messiah.edu, hyperchem@HYPER.COM Subject: Re: Setting file format Karl M. Oberholser writes: > The file-format message can be used to set the file format to hin, pdb, etc. > Is there any way that the format can be set to scr by using a message? Use the "read-script" command to open a script file. Cheers, Graham ------------ Graham Hurst (hurst@hyper.com) Hypercube Inc, 7-419 Phillip St, Waterloo, Ont, Canada N2L 3X2 (519)725-4040 Info requests to: info@hyper.com Support questions to: support@hyper.com Email group: Send "subscribe hyperchem" to hyperchem-request@hyper.com ________________________________________________________________________ From David_DeBerry@pc.radian.com Wed Sep 21 19:43:50 1994 Date: Wed, 21 Sep 1994 15:43:50 -0400 From: "David DeBerry" To: hyperchem@HYPER.COM Subject: nonaqueous bath What would be involved in creating a nonaqueous "box" for computationally solvating molecules, and could HyperChem be tricked into using this nonaqueous medium instead of the standard water box? Thanks, David ________________________________________________________________________ From hurst@hyper.hyper.com Wed Sep 21 21:58:42 1994 Date: Wed, 21 Sep 1994 17:58:42 -0400 From: hurst@hyper.hyper.com (Graham Hurst) To: "David DeBerry" Subject: Re: nonaqueous bath Cc: hyperchem@HYPER.COM "David DeBerry" writes: > What would be involved in creating a nonaqueous "box" for computationally > solvating molecules, and could HyperChem be tricked into using this > nonaqueous medium instead of the standard water box? The periodic box and the addition of solvent are linked for the HyperChem user interface, but you can work around it. ChemPlus includes a Crystal Builder module that can create crystals in boxes in HyperChem for instance. You can add a periodic box without adding solvent or re-orienting the molecule by adding a "box" line to a HIN file (see appendix D), being careful to center the system at the origin and have all atoms within the box dimensions. Actually atoms can start outside the box but they will mapped to the periodic images that are inside the box for calculations. When coordinates are sent back to the front end for display an atom with only one bond may be mapped outside the box to be displayed close to the atom that it is bonded to. This question has come up before - does anyone else out there have some experience they could share with the rest of us? Hope this helps, Graham ------------ Graham Hurst (hurst@hyper.com) Hypercube Inc, 7-419 Phillip St, Waterloo, Ont, Canada N2L 3X2 (519)725-4040 Info requests to: info@hyper.com Support questions to: support@hyper.com Email group: Send "subscribe hyperchem" to hyperchem-request@hyper.com ________________________________________________________________________ From michael.moller Wed Sep 21 23:21:12 1994 Date: Wed, 21 Sep 1994 19:21:12 -0400 From: BRI.NRC.CA!michael.moller@hyper.hyper.com (Michael Moller) To: hyperchem@HYPER.COM Subject: Re: nonaqueous bath "Graham Hurst" wrote: >"David DeBerry" writes: > >> What would be involved in creating a nonaqueous "box" for computationally >> solvating molecules, and could HyperChem be tricked into using this >> nonaqueous medium instead of the standard water box? > >The periodic box and the addition of solvent are linked for the >HyperChem user interface, but you can work around it. ChemPlus >includes a Crystal Builder module that can create crystals in >boxes in HyperChem for instance. You can add a periodic box >without adding solvent or re-orienting the molecule by adding a >"box" line to a HIN file (see appendix D), being careful to center >the system at the origin and have all atoms within the box dimensions. > >Actually atoms can start outside the box but they will mapped >to the periodic images that are inside the box for calculations. >When coordinates are sent back to the front end for display an atom >with only one bond may be mapped outside the box to be displayed close >to the atom that it is bonded to. > >This question has come up before - does anyone else out there >have some experience they could share with the rest of us? > >Hope this helps, > >Graham >------------ >Graham Hurst (hurst@hyper.com) >Hypercube Inc, 7-419 Phillip St, Waterloo, Ont, Canada N2L 3X2 (519)725-4040 >Info requests to: info@hyper.com Support questions to: support@hyper.com >Email group: Send "subscribe hyperchem" to hyperchem-request@hyper.com You can also create a periodix box around your molecule with no solvent by choosing a very large number for: Minimum distance between solvent and solute atoms: _______ in the Periodic Box Options dialog box (Menu Command: Setup/Periodic Box...), for example: 99999. Note that this will re-orient the molecule to best fit inside the box. Michael Moller ________________________________________________________________________ From ELEC!UNDERHILLR%MECH_STAFF@BANEE.rmc.ca Thu Sep 22 12:35:40 1994 From: BANEE.rmc.ca!UNDERHILLR%MECH_STAFF%ELEC@hyper.hyper.com Date: Thu, 22 Sep 1994 08:35:40 -0400 Subject: non-aqueous solvent To: hyperchem@HYPER.COM I've done this pretty well the way Graham has suggested. You start with one molecule and throught the magic of cut and paste or merge you can create a large crystal which can be placed in a periodic box with a large exclusion zone for water. Seemed to work OK. One problem I did encounter was that molecules that straddled the periodic box boundary got mapped so that half of them were on one side and the other half on the other side, with bonds drawn right across the box linking the two halves. Presumably there is a switch you can throw to stop this? The biggest problem I have is the size of the box you need and the number of molecules in the problem. I'm getting ready to try OPLS united atoms, at least during the equilibriation phase to get the time required down to a reasonable scale. Speaking of which I'm sending another e-mail on the whole topic of equilibriation times and equilibrium states that I could really use some comments on. ________________________________________________________________________ From ELEC!UNDERHILLR%MECH_STAFF@BANEE.rmc.ca Thu Sep 22 12:42:29 1994 Date: Thu, 22 Sep 1994 08:42:29 -0400 From: BANEE.rmc.ca!UNDERHILLR%MECH_STAFF%ELEC@hyper.hyper.com Subject: molec dyn., equilib. times and zero point vibrations To: hyperchem@HYPER.COM I've encountered a problem with MD that experienced modellers may be able to put my mind to rest about. Taking an isolated molecule (a mere 28 atoms)which had been loosely geometry optimized, I turned it loose in a molecular dynamics simulation using PM3 and monitored a few bond torsions and the potential energy. (1 fs time step and .1ps bath relaxation). The potential energy slowly drifted downward and after 20ps seemed to be assymptotically approaching a binding energy of -2542 kcal/mole. During this time the torsions which I was observing noticeably damped down substantially. Afterwards I optimized the molecule, getting an energy of about -2546 kcal/mole and started a new md run with the new structure with a heating period of 1 ps to 300C. The potential energy leaped up about 25 kcal/mole which seems about right (28 * 3/2 *(RT=.6kcal/mole)). The potential energy is slowly settling back down and presumably will approach -2542 kcal/mole again. Observing the damping out of the torsions and the small change in the mean potential energy (4kcal/mole) has lead to worry about where are the zero point vibrations. When the simulations are started the atoms are given randomn directions which basically excites all sorts of modes. As the molecule deexcites and the bath carts off the excess energy all the bond vibrations (bends, stretches and torsions) seem to be disappearing so that one is left with a molecule travelling through space and spinning but that's all. I dusted off my trusty old QM textbook and looked up 1-d harmonic oscillators. It pointed out that zero point energy (that 1/2h(nu)) is a quantum mechanical effect arising from the non-commutation of the positon and momentum operators (i.e. the Heisenberg uncertainty principle raises its ugly head). Now in a computer simulation of a molecule there is no such problem about commutation. I can know both the position and momentum of the nuclei to arbitrary accuracy. Does this mean that if I wait long enough the vibrations will all freeze out completely and I'll be left with a spinning molecule careening through space. One might also point out that it will be spinning and careening far too fast since the bath will make sure the overall kinetic energy, alot of which should be tied up in vibrations, is correct. Obviously in a liquid, inter-molecular interactions will cause randomization of some sort and pump energy back into vibrational modes. However, the whole thing leaves me a little concerned about these kind of calculations. Can someone out there reassure me? Ross Underhill underhil@me2.rmc.ca ________________________________________________________________________ From ELEC!UNDERHILLR%MECH_STAFF@BANEE.rmc.ca Thu Sep 22 18:41:24 1994 Date: Thu, 22 Sep 1994 14:41:24 -0400 From: BANEE.rmc.ca!UNDERHILLR%MECH_STAFF%ELEC@hyper.hyper.com Subject: md and equilibrium To: hyperchem@HYPER.COM I got a fair number of replies from the ccl. The gist of the matter is that md calculations do not have zero point vibrations. If you make it cold enough all motion will stop. At room T most of the energy will be in rotation and translation with a little bit in low energy internal motions. When you start up a md calculation the program puts energy randomly into atomic motion which excites all sorts of vibrations. It is to be expected that these will eventually cool down to the state just described. This can take a while!! In my case, with a 28 atom molecule, at least 20ps at 1fs/step, a long time using PM3. The real implication comes in when you want to create a solvent, where you need lots of molecules. The nice thing about the water in the periodic box is that this has already been done for you. You could save yourself A LOT of time if instead of assigning random velocities, you gave your molecule the right amount of angular energy, 3/2RT, and then assigned it a random translational velocity, another 3/2RT, while setting it into a liquid. It would be nice if this feature were built into hyperchem. The little nudges needed to keep a system at a given temperature could be done the way they are now with the bath, as this is a small perturbation. However the nudges should be put into the MOLECULAR translation energy only. Collisions will randomize this and distribute it very quickly. Scaling the atomic motions amounts to artificially pumpin the vibrational structure. ________________________________________________________________________ From DESJARDI.S@fs.sciences.WLU.EDU Thu Sep 22 19:47:55 1994 To: hyperchem@HYPER.COM From: "Dr. Steven Desjardins" Organization: Washington & Lee University Date: Thu, 22 Sep 1994 15:47:55 -0400 Subject: An unusual question. I know that hyperchem will generate ribbon pictures of proteins. I'm curious about the algorithm used. Is it some sort of spline, and could I get a reference? Steven G. Desjardins Department of Chemistry Washington and Lee University Lexington VA 24450 (703) 463-8873 ________________________________________________________________________ From MARTINN@VXC.OCIS.UNCWIL.EDU Thu Sep 22 19:32:49 1994 From: VXC.OCIS.UNCWIL.EDU!MARTINN@hyper.hyper.com Date: Thu, 22 Sep 1994 15:32:49 -0400 Subject: Availability of Excel Scripts for HyperChem To: hyperchem@HYPER.COM X-Envelope-To: hyperchem@hyper.com X-Vms-To: IN%"hyperchem@hyper.com" Mime-Version: 1.0 Content-Transfer-Encoding: 7BIT Hi, I am inquiring about the availability of scripts in Excel to drive HyperChem calculations such as rotation around a bond and measuring (recording in a spreadsheet) the energy as a function of the angle of rotation, or measuring energy as a function of the distance between two molecules as they approach one another. When I bought HyperChem (22 copies total, 5 of V. 2.0 and 17 of v. 3.0) I was told that as uswers created these scripts they would be distributed to other users, but I have heard nothing. I realize that there has been a change in ownership. Could you direct me to a source of such scripts? Would they be available on the User's group email system? Thanks in advance to any help you can be. Our students are enjoying using HyperChem in their Organic Chemistry assignments! Ned H. Martin Professor and Chair Department of CHemistry University of North Carolina at Wilmington Wilmington, NC 28403-3297 ________________________________________________________________________ From ELEC!UNDERHILLR%MECH_STAFF@BANEE.rmc.ca Fri Sep 23 14:50:48 1994 Date: Fri, 23 Sep 1994 10:50:48 -0400 From: BANEE.rmc.ca!UNDERHILLR%MECH_STAFF%ELEC@hyper.hyper.com Subject: lone pairs To: hyperchem@HYPER.COM I can't seem to find a whole lot in the reference section of Hyperchem on the use of lone pairs. I note that when they are put on an atom they take the place of one of the normal bonds, so, for example, you can't put them on O and expect to form water when you build. Presumably then they exist primarily for working with ions. How does the program decide where to put lone pairs? I was interested in them because I have a phosphate ester I'm trying to do an MM+ calculation on and it gets the bond torsion energies all wrong, primarily because the negative charge, which is sticking out the back of the oxygen as lone pairs doesn't like moving past nearby negatively polarized species. I can reparameterize to get the bond torsions right but was wondering if I could have used lone pairs to achieve the same thing. ________________________________________________________________________ From hurst@hyper.hyper.com Fri Sep 23 16:08:15 1994 Date: Fri, 23 Sep 1994 12:08:15 -0400 From: hurst@hyper.hyper.com (Graham Hurst) To: UNDERHILLR%MECH_STAFF%ELEC@BANEE.rmc.ca, hyperchem@HYPER.COM Subject: Re: md and equilibrium I think the crucial point is that molecular dyanmics is classical dynamics, though the PES may be quantum mechanically derived. Thus there is no zero point energy. Another thing worth noting is how HyperChem generates and scales velocities. This is described in "Molecular Dynamics on a Potential Energy Surface" section of the "Computational Options" chapter of Part 2 ("Theory and Methods") of the Computational Chemistry manual. The "Random Velocities or Restart Velocities" subsection describes the generation of velocities. One thing it omits is that if a random distribution is used, it is "shifted" to remove the overall translational momentum. Angular momentum is not zeroed. It is then scaled to give a kinetic energy of 3/2 kT. Thus any overall translation that one observes is either because random velocities weren't used (i.e. Restart was checked), the simulation was unstable or cumulative roundoff errors became noticable. The idea of temperature is poorly defined with few degrees of freedom (as with a single molecule). The extreme case is with a single degree of freedom as with a single harmonic oscillator (i.e. a molecular mechanics diatomic). The total energy Et is constant and is the sum of the fluctuating kinetic energy Ek and potential energy Ep. At the equilibrium distance Ep=0 and Et=Ek so T=2Et/(3k). At the extrema Ep=Et and Ek=0 so T=0. Thus the "temperature" oscillates from 0 to 2Et/3k. Thus I wouldn't use temperature scaling (except perhaps with a long bath relaxation time) for small systems. There are several guidelines for assessing equilibration given in the Practical Guidelines part of the Computational Chemistry manual. I would particularly recommend reading the "Simulation Periods" and "Strategies" sections of the "Molecular Dynamics" chapter. (Also note that a 0.5 fs timestep is recommended if your system has hydrogen stretches.) Hope this helps, Graham ------------ Graham Hurst (hurst@hyper.com) Hypercube Inc, 7-419 Phillip St, Waterloo, Ont, Canada N2L 3X2 (519)725-4040 Info requests to: info@hyper.com Support questions to: support@hyper.com Email group: Send "subscribe hyperchem" to hyperchem-request@hyper.com ________________________________________________________________________ From hurst@hyper.hyper.com Fri Sep 23 21:47:16 1994 Date: Fri, 23 Sep 1994 17:47:16 -0400 From: hurst@hyper.hyper.com (Graham Hurst) To: UNDERHILLR%MECH_STAFF%ELEC@BANEE.rmc.ca Subject: Re: lone pairs Cc: hyperchem@HYPER.COM Ross Underhill writes: > I can't seem to find a whole lot in the reference section of Hyperchem on the > use of lone pairs. I note that when they are put on an atom they take the > place of one of the normal bonds, so, for example, you can't put them on O > and expect to form water when you build. Presumably then they exist > primarily for working with ions. How does the program decide where to put > lone pairs? I was interested in them because I have a phosphate ester I'm > trying to do an MM+ calculation on and it gets the bond torsion energies all > wrong, primarily because the negative charge, which is sticking out the back > of the oxygen as lone pairs doesn't like moving past nearby negatively > polarized species. I can reparameterize to get the bond torsions right but > was wondering if I could have used lone pairs to achieve the same thing. The trick is add lone pairs after adding hydrogens. I will add this one to the bug list, because it should know that lone pairs don't count as atoms. The QCPE MM2 documentation recommends adding lone pairs on oxygens in alcohols and ethers (but not for carbonyl) and for amine nitrogen (but not amide). This seems to have been omitted from the HyperChem documentation and the program does not add them automatically (the automatic ones for AMBER on sulphur come from the templates). I'll add this to the bug list too! Hope this helps, Graham ------------ Graham Hurst (hurst@hyper.com) Hypercube Inc, 7-419 Phillip St, Waterloo, Ont, Canada N2L 3X2 (519)725-4040 Info requests to: info@hyper.com Support questions to: support@hyper.com Email group: Send "subscribe hyperchem" to hyperchem-request@hyper.com ________________________________________________________________________ From vvk@itsa.ucsf.EDU Mon Sep 26 19:54:52 1994 Date: Mon, 26 Sep 1994 15:54:52 -0400 From: itsa.ucsf.EDU!vvk@hyper.hyper.com (Jaeho Kim) To: hyperchem@HYPER.COM Subject: ? Selection by Residue Name Hello, everybody I have question about HyperChem Release 4 . Is it possible somehow to select residues or atoms in the protein by name. I mean something like this : > Select all His > Select all His + Ser > Select all CA in ALA > Select all H in MET May be somebody has script or program to do this. Any help will be greatly appriciated. My e.mail is vvk@itsa.ucsf.edu Vlad Kuusk. ________________________________________________________________________ From ipcal05@cc.csic.es Tue Sep 27 09:39:14 1994 Date: Tue, 27 Sep 1994 05:39:14 -0400 From: Angel Lozano Subject: Diedral angle To: hyperchem@HYPER.COM I have calculated the minimun energy conformation of benzanilide C6H5-CONH-C6H5 both by MM+ and by AM1 and I obtain very different results. AM1 results: Diedral angle O=C-Car-Car: 41.0 degrees Diedral angle H-N-C=O: -175.4 degrees Distance H(amide)-Har(orto): 2.36 Amstrongs MM+ results: diedral angle O=C-Car-Car: 1.3 degrees diedral angle H-N-C=O: -166.5 degrees Distance H(amide)-Har(orto): 1.82 Amstrongs According to my knowledge, the results from AM1 are much closer to the experimental results that the obtained by MM+. The interaction between the amide hydrogen and the orto aromatic hydrogen is very strong in the planar conformation and this forces the carbonyl group to separate from the plane of the aromatic ring. However, by MM+ it seems that it is easier to distort the amide bond that to separate the carbonyl group from the plane. In addition, when the minimization by MM+ starts, a message of: Default parameters being used for torsions, appears. As I have to make many minimizations where amide groups are involved, and I cannot make them by AM1, I would like to know if there is any parameterization for the aromatic amide groups that I could introduce in the parameters set of MM+. Sincerely yours. Jose Gonzalez de la Campa Instituto de Ciencia y Tecnologia de Polimeros Madrid, Spain. ________________________________________________________________________ From ipcal05@cc.csic.es Tue Sep 27 15:38:27 1994 Date: Tue, 27 Sep 1994 11:38:27 -0400 From: Angel Lozano Subject: aromatic amides To: hyperchem@HYPER.COM I have calculated the minimun energy conformation of benzanilide C6H5-CONH-C6H5 both by MM+ and by AM1 and I obtain very different results. AM1 results: Diedral angle O=C-Car-Car: 41.0 degrees Diedral angle H-N-C=O: -175.4 degrees Distance H(amide)-Har(orto): 2.36 Amstrongs MM+ results: diedral angle O=C-Car-Car: 1.3 degrees diedral angle H-N-C=O: -166.5 degrees Distance H(amide)-Har(orto): 1.82 Amstrongs According to my knowledge, the results from AM1 are much closer to the experime ntal results that the obtained by MM+. The interaction between the amide hydrog en and the orto aromatic hydrogen is very strong in the planar conformation and this forces the ca rbonyl group to separate from the plane of the aromatic ring. However, by MM+ i t seems that it is easier to distort the amide bond that to separate the carbon yl group from the plane. In addition, when the minimization by MM+ starts, a me ssage of: Default p arameters being used for torsions, appears. As I have to make many minimization s where amide groups are involved, and I cannot make them by AM1, I would like to know if there is any parameterization for the aromatic amide groups that I c ould introduce in t he parameters set of MM+. Sincerely yours. Jose Gonzalez de la Campa Instituto de Ciencia y Tecnologia de Polimeros Madrid, Spain. ________________________________________________________________________ From shafer@cgl.ucsf.EDU Tue Sep 27 17:37:36 1994 Date: Tue, 27 Sep 1994 13:37:36 -0400 From: cgl.ucsf.edu!shafer@hyper.hyper.com (Dick Shafer) To: hyperchem@HYPER.COM Subject: problem with pdb files I am using release 4 on Windows of hyperchem, and when reading in a pdb file for nucleic acids, the program insists on adding a 5' terminal phosphate group even though it is not present in the structure or pdb file. Does anyone know how to stop this from occurring? Dick Shafer shafer@cgl.ucsf.edu ________________________________________________________________________ From kellogg@uidaho.edu Tue Sep 27 17:32:42 1994 Date: Tue, 27 Sep 1994 13:32:42 -0400 From: Scott Kellogg Subject: Amino Acid Sequence Input? (fwd) To: Hyperchem ========================================= Scott T. Kellogg, Dept. of Microbiol., Mol. Biol. & Biochem. Univ. of Idaho, Moscow, ID 83843 Internet: kellogg@uidaho.edu Phone: 208-885-6966 Fax: 208-885-6518 ---------- Forwarded message ---------- Date: Mon, 26 Sep 1994 11:55:17 -0700 (PDT) From: Scott Kellogg To: Hyperchem Subject: Amino Acid Sequence Input? I have translated a DNA sequence into a protein sequence with the program PC Gene; however, the output format is in EMBL. Is there a program available to translate those residue abbreviations into HIN or ENT formats? Thanks. ========================================= Scott T. Kellogg, Dept. of Microbiol., Mol. Biol. & Biochem. Univ. of Idaho, Moscow, ID 83843 Internet: kellogg@uidaho.edu Phone: 208-885-6966 Fax: 208-885-6518 ________________________________________________________________________ From kellogg@raven.csrv.uidaho.edu Wed Sep 28 14:28:02 1994 Date: Wed, 28 Sep 1994 10:28:02 -0400 From: Scott Kellogg Subject: Amino Acid Residue Input To: Hyperchem I have output the amino acid sequence (single letter abbrevations) from PC Gene and would like to use them as input for Hyperchem. However, PC Gene only outputs AA sequences in EMBL format. Is there a program that will translate this format or do I need to write one myself using the AA template file in order to generate a HIN file? Thanks. ========================================= Scott T. Kellogg, Dept. of Microbiol., Mol. Biol. & Biochem. Univ. of Idaho, Moscow, ID 83843 Internet: kellogg@uidaho.edu Phone: 208-885-6966 Fax: 208-885-6518 ________________________________________________________________________ From hurst@hyper.hyper.com Wed Sep 28 16:35:12 1994 Date: Wed, 28 Sep 1994 12:35:12 -0400 From: hurst@hyper.hyper.com (Graham Hurst) To: vvk@itsa.ucsf.EDU (Jaeho Kim), hyperchem@HYPER.COM Subject: Re: ? Selection by Residue Name Jaeho Kim wrote: > Hello, everybody > I have question about HyperChem Release 4 . > Is it possible somehow to select residues or atoms in the protein > by name. I mean something like this : > > Select all His > > Select all His + Ser > > Select all CA in ALA > > Select all H in MET > May be somebody has script or program to do this. > Any help will be greatly appriciated. > My e.mail is vvk@itsa.ucsf.edu > Vlad Kuusk. This has been on our wishlist for some time, but is certainly possible from an add-on. If any of you know of such an add-on, please let us all know! Cheers, Graham ------------ Graham Hurst (hurst@hyper.com) Hypercube Inc, 7-419 Phillip St, Waterloo, Ont, Canada N2L 3X2 (519)725-4040 Info requests to: info@hyper.com Support questions to: support@hyper.com Email group: Send "subscribe hyperchem" to hyperchem-request@hyper.com ________________________________________________________________________ From hurst@hyper.hyper.com Wed Sep 28 17:10:04 1994 Date: Wed, 28 Sep 1994 13:10:04 -0400 From: hurst@hyper.hyper.com (Graham Hurst) To: hyperchem@HYPER.COM Subject: Duplicate messages There seem to be some duplicate messages on this list lately, caused by people sending the same message again. If you post to this list, please ignore any 'bounce' messages that you get. These are not supposed to be reflected back to the person who posts but unfortunately they do. They occur when machines or users go offline or change names. After a while we delete them from the list but sometimes the problems are only temporary... Please don't send the same message to this list twice. If you think it failed, send email to listserv@hyper.com. Cheers, Graham P.S. To unsubscribe send 'unsubscribe hyperchem' to hyperchem-request@hyper.com ------------ Graham Hurst (hurst@hyper.com) Hypercube Inc, 7-419 Phillip St, Waterloo, Ont, Canada N2L 3X2 (519)725-4040 Info requests to: info@hyper.com Support questions to: support@hyper.com Email group: Send "subscribe hyperchem" to hyperchem-request@hyper.com ________________________________________________________________________ From hurst@hyper.hyper.com Wed Sep 28 17:22:25 1994 Date: Wed, 28 Sep 1994 13:22:25 -0400 From: hurst@hyper.hyper.com (Graham Hurst) To: Angel Lozano Subject: Re: aromatic amides Cc: hyperchem@HYPER.COM Angel Lozano writes: >I have calculated the minimun energy conformation of benzanilide C6H5-CONH-C6H5 > both by MM+ and by AM1 and I obtain very different results. >AM1 results: >Diedral angle O=C-Car-Car: 41.0 degrees >Diedral angle H-N-C=O: -175.4 degrees >Distance H(amide)-Har(orto): 2.36 Amstrongs > >MM+ results: >diedral angle O=C-Car-Car: 1.3 degrees >diedral angle H-N-C=O: -166.5 degrees >Distance H(amide)-Har(orto): 1.82 Amstrongs > >According to my knowledge, the results from AM1 are much closer to the experime >ntal results that the obtained by MM+. The interaction between the amide hydrog >en and the orto aromatic hydrogen is very strong in the planar conformation and > this forces the ca >rbonyl group to separate from the plane of the aromatic ring. However, by MM+ i >t seems that it is easier to distort the amide bond that to separate the carbon >yl group from the plane. In addition, when the minimization by MM+ starts, a me >ssage of: Default p >arameters being used for torsions, appears. As I have to make many minimization >s where amide groups are involved, and I cannot make them by AM1, I would like >to know if there is any parameterization for the aromatic amide groups that I c >ould introduce in t >he parameters set of MM+. >Sincerely yours. >Jose Gonzalez de la Campa >Instituto de Ciencia y Tecnologia de Polimeros >Madrid, Spain. To see the parameters used in an MM+ calculation and all contributions to the energy, save a log file from a Single Point MM+ calculation with MechanicsPrintLevel=3 (or 0 to suppress printing of electrostatic and van der Waals contributions). If you set MechanicsPrintLevel=9 in CHEM.INI you will also see details of the assignment of default parameters when MM2(91) parameters are not available. See the Theory and Methods part of the Computational Chemistry manual for references for AM1 and MM2 and the details of the extensions to MM2 that comprise MM+. Hope this helps, Graham ------------ Graham Hurst (hurst@hyper.com) Hypercube Inc, 7-419 Phillip St, Waterloo, Ont, Canada N2L 3X2 (519)725-4040 Info requests to: info@hyper.com Support questions to: support@hyper.com Email group: Send "subscribe hyperchem" to hyperchem-request@hyper.com ________________________________________________________________________ From madura@moe.chem.usouthal.edu Wed Sep 28 17:00:23 1994 Date: Wed, 28 Sep 1994 13:00:23 -0400 From: "Jeffry D. Madura" Subject: Program to read a dynamics SNP file... To: hyperchem Dear Colleagues, Does anyone have a BASIC, C, or Fortran program they are willing to share that will read an binary SNP file a write out the different components in ASCII format? I would like to read the ASCII data into Excel or Mathcad and perform some addition data analysis. Best Regards, Jeffry D. Madura Address: Department of Chemistry University of South Alabama Mobile, AL 36688 Phone: (205) 460-7430 FAX: (205) 460-7359 e-mail: madura@moe.chem.usouthal.edu ________________________________________________________________________ From hurst@hyper.hyper.com Wed Sep 28 18:37:19 1994 Date: Wed, 28 Sep 1994 14:37:19 -0400 From: hurst@hyper.hyper.com (Graham Hurst) To: Scott Kellogg , Hyperchem Subject: Re: Amino Acid Sequence Input? (fwd) Scott Kellogg writes: > I have translated a DNA sequence into a protein sequence with the program > PC Gene; however, the output format is in EMBL. Is there a program > available to translate those residue abbreviations into HIN or ENT > formats? Thanks. I have sent Scott information on ChemPlus which has a Sequence Editor that can read sequences specified by one-letter amino acid abbreviations, but have left out the ChemPlus feature summary here to save bandwidth. One can assign secondary structure to regions of the sequence and then construct the sequence in HyperChem. Cheers, Graham ------------ Graham Hurst (hurst@hyper.com) Hypercube Inc, 7-419 Phillip St, Waterloo, Ont, Canada N2L 3X2 (519)725-4040 Info requests to: info@hyper.com Support questions to: support@hyper.com Email group: Send "subscribe hyperchem" to hyperchem-request@hyper.com ________________________________________________________________________ From usech592@ibmmail.IBMMAIL.COM Wed Sep 28 19:28:55 1994 Date: Wed, 28 Sep 1994 15:28:55 -0400 From: ibmmail.COM!usech592@hyper.hyper.com To: hyperchem@HYPER.COM Subject: force fields ----------------------- Mail item text follows --------------- To: INTERNET--IBMMAIL Internet Communica cc: U856601 --ECDVM1 HUBBS JOHN C From: John C. Hubbs, Chemistry Research Division, B-150B Subject: force fields Angel Lozano and Hyperchem users group, I cannot resist interjecting a comment with the intent of both helping with your problem and initiating a more general discussion. I noted that you were attempting to minimize benzanilide using mm+ and am1. Unless it has been fixed in version 4, the rendition of mm+ in Hyperchem will incorrectly assign a sp2-sp2 double bond distance to the sp2-sp2 single bond in O=C-C=C. This problem seems general to all conjugated non-aromatic systems. This accounts for roughly 0.1 angstroms of the error you observe for H(amide)-Har(ortho) distance. My guess is that this particular error could be easily dealt with as a constraint although I doubt that your mm+ answer will improve much. As a non-computational chemist who can barely find time to write notes such as this, I come to the following unfortunate conclusion: All molecular mechanics force fields (including mm2) rely on a ball and spring approximation to chemical bonding. This approximation is fundamentally wrong. I prefer to leave reparamaterization of force fields to Norman Allinger and the writing of computer code to computer specialists.... Thus, if the suitability of a parameterization for a force field comes into question, I reluctantly avoid using that force field for the problem at hand. This seems to me to be the source of much of the 'art' in molecular modeling-that is, knowing when a force field (or any level of approximation) is inappropriate to the problem at hand. John Hubbs ________________________________________________________________________ From hurst@hyper.hyper.com Wed Sep 28 21:03:44 1994 Date: Wed, 28 Sep 1994 17:03:44 -0400 From: hurst@hyper.hyper.com (Graham Hurst) To: usech592@ibmmail.COM, hyperchem@HYPER.COM Subject: Re: force fields John C. Hubbs writes: > Angel Lozano and Hyperchem users group, > > I cannot resist interjecting a comment with the intent of both > helping with your problem and initiating a more general > discussion. > > I noted that you were attempting to minimize benzanilide using > mm+ and am1. Unless it has been fixed in version 4, the > rendition of mm+ in Hyperchem will incorrectly assign a sp2-sp2 > double bond distance to the sp2-sp2 single bond in O=C-C=C. This > problem seems general to all conjugated non-aromatic systems. > This accounts for roughly 0.1 angstroms of the error you observe > for H(amide)-Har(ortho) distance. My guess is that this > particular error could be easily dealt with as a constraint > although I doubt that your mm+ answer will improve much. If you force HyperChem to use the default scheme rather than MM2(91) parameters by making the atoms in question have type **, MM+ *will* look at bond orders to determine default parameters! The trick is changing the types to ** via the Build/Set Type menu (after selecting the atoms you want to change). This has been in HyperChem's MM+ since release 2, but didn't get documented very well until release 4 (and is admittedly still rather hard to find...). I'm sorry that I didn't twig to this when answering Angel Lozano's original question, as he should try it before embarking on reparameterization. Cheers, Graham Hurst ------------ Graham Hurst (hurst@hyper.com) Hypercube Inc, 7-419 Phillip St, Waterloo, Ont, Canada N2L 3X2 (519)725-4040 Info requests to: info@hyper.com Support questions to: support@hyper.com Email group: Send "subscribe hyperchem" to hyperchem-request@hyper.com ________________________________________________________________________ From emcgoran@ewu.edu Thu Sep 29 23:54:09 1994 Date: Thu, 29 Sep 1994 19:54:09 -0400 From: ewu.edu!emcgoran@hyper.hyper.com (Ernie McGoran) Subject: Default setting for Labels? To: hyperchem@HYPER.COM I have four different copies of HyperChem 3.0 for Windows running and three of them open up a tetrapeptide without the amino acid residue labels showing. The fourth gives students a set of answers, the aa sequence through the labels, that I would prefer them to determine without help from the program. I can't seem to find a way to change the default settings so that labels will not appear. Can you help? Thanks. Ernie McGoran | Phone: (509) 359-7931 Dept. of Chem./Biochem.MS 74 | FAX: (509) 359-6937 Eastern Washington University | email: emcgoran@eagle.ewu.edu Cheney, WA 99004 ________________________________________________________________________ From ML@mmf.ruc.dk Fri Sep 30 11:15:38 1994 From: "MORTEN LANGGaaRD - BIOKEM" Organization: Roskilde Universitetscenter To: hyperchem@HYPER.COM Date: Fri, 30 Sep 1994 07:15:38 -0400 Subject: MM2, MM+ or MM? Hello In the last week there have been some discussions about HyperChemAEs MM+ forcefield in terms of parameters and precision. This has encourage me to write a little note about MM? Beside the fact that HyperChem is a really powerful package of hard proven computational methods, I guess, it is fair to say that especially the implementation of Allinger's MM2 force field is less successful. The manual says "HyperChem's MM+ force field uses the latest MM2 (1991) parameters and atom types (provided directly by Dr. Allinger) with the 1977 functional form." This is completely right, but it leaves you with the impression (intended or not) that you are dealing with something comparable to MM2(91), which are definitely wrong. It is well know to all "MM people" (incl. the team at hypercube), that conjugated pi systems not are treated well by MM2(77) (the latest public domain version) e.g. as mentioned by John Hubbs - all sp2-sp2 carbon carbon distances are the same. These problems were recognized (MM1) even before the 1977 version, and since MM2(85), a SCF- scheme for dealing with pi systems, has been a part of the standard procedure. For these obvious reasons, it is unfortunately not a good idea to use HyperChem for such systems - just as Angel Lozano expired last week. I really donAEt understand, why MM+ is implemented without a SCF-scheme, when it can be done - even without having a license from Allinger. Make new mistakes - not old ones! I hope that the team at hypercube will do something about this situation in the future (or by making a implementation of MM3 instead). HyperChem deserves it. Sincerely, Morten Langgaard, Dept. of Chemistry, Roskilde University, Denmark ________________________________________________________________________ From hurst@hyper.hyper.com Fri Sep 30 14:40:22 1994 Date: Fri, 30 Sep 1994 10:40:22 -0400 From: hurst@hyper.hyper.com (Graham Hurst) To: emcgoran@ewu.edu (Ernie McGoran) Subject: Re: Default setting for Labels? Cc: hyper!hyperchem@uunet.ca Hi Ernie, > I have four different copies of HyperChem 3.0 for Windows > running and three of them open up a tetrapeptide without > the amino acid residue labels showing. The fourth gives students > a set of answers, the aa sequence through the labels, that I > would prefer them to determine without help from the program. > I can't seem to find a way to change the default settings so that > labels will not appear. Can you help? The last type of atom and residue labels are saved in the CHEM.INI file so that these settings are restored when you next run the program. The respective entries are DefaultAtomLabels and DefaultResidueLabels (described in Appendix F of the Reference manual). Bring up the Labels dialog, choose None for Atoms and Residues, choose OK and then close HyperChem. This should leave labels turned off when you next start the program (though students could still turn it on or select residues to see their names). Or you could edit the CHEM.INI lines when HyperChem wasn't running. You could completely prevent residue labels if you use a specific set of HIN files - just delete the 'res' and 'endres' lines of the HIN files, or change the residue names in the 'res' lines (see Appendix D of the Reference Manual for the HIN file format). Hope this helps, Graham ------------ Graham Hurst (hurst@hyper.com) Hypercube Inc, 7-419 Phillip St, Waterloo, Ont, Canada N2L 3X2 (519)725-4040 Info requests to: info@hyper.com Support questions to: support@hyper.com Email group: Send "subscribe hyperchem" to hyperchem-request@hyper.com