From hyper!slee@autodesk.com Mon Nov 1 10:06:27 1993 From: hyper!slee@autodesk.com (Thomas Slee) Subject: Re: PDB File residue numbering To: autodesk!hyperchem@openlink.openlink.com (HyperChem e-mail group) Date: Mon, 1 Nov 93 9:52:11 EST Cc: uscience@nic.cerf.net (U.S. Science) Jesse Salb writes... | | Certain PDB files (.ENT) have undetermined residues marked "UNK" for | unknown. When a file containing UNKs is loaded into Hyperchem, the | numbering of all the known residues is disrupted. Other programs such as | Kinemage seem to handle UNKs well while preserving the residue numbering | from beginning to end of the protein. Does anyone know of a workaround | to this problem in Hyperchem? | jsalb@novalink.com | Dear Dr. Salb, I am having trouble reproducing this behaviour. Please could you send me (slee@hyper.com) a file that exhibits this behaviouir and describe what numbering you should get, and what you do get? Also, please could you tell me what version of HyperChem you are using? Tom -- Tom Slee Hypercube, Inc., #7-419 Phillip St., Waterloo, Ont. N2L 3X2 Internet: slee@hyper.com Tel. (519) 725-4040 ________________________________________________________________________ From hyper!slee@autodesk.com Mon Nov 1 13:33:52 1993 From: hyper!slee@autodesk.com (Thomas Slee) Subject: HyperChem EMail Group Poll Results To: autodesk!hyperchem@openlink.openlink.com (HyperChem e-mail group) Date: Mon, 1 Nov 93 10:36:56 EST Thanks to the 56 of you who replied to the E-Mail group survey. The results are as follows: | 1. I don't want to see answers to other people's questions. | Keep my mailbox clean and just reply to the respondent. 2 | | 2. The current balance is about right. 26 | | 3. I don't want to miss anything: send all answers to the group. 28 So, I'll continue sending most replies to the group. One exception is if extra information is needed concerning a problem I'll generally just e-mail that person, until we get the problem sorted out, whereupon I'll send the solution (or lack of one!) to the group as a whole. Thanks to those of you who said how useful they find the group. Two other issues came up in the responses. One was a suggestion for a News group. This is not something that can be initiated by Autodesk as a service: there is a whole protocol to go through to set up a new News group, including calls for discussion and calls for votes. Currently the most applicable group is sci.chem: we do keep an eye on that group, but certainly don't commit to answering questions there at the moment. The other issue was some kind of an archive of previous messages. As you will know, we don't currently have an ftp site or any of this capability. The input is useful, but I can't commit to acting on it in the near future. Anybody wanting to know if we have had previous messages on a given subject, please send your mail to hyperchem-request@autodesk.com, and we'll do this manually. Tom -- Tom Slee Hypercube, Inc., #7-419 Phillip St., Waterloo, Ont. N2L 3X2 Internet: slee@hyper.com Tel. (519) 725-4040 ________________________________________________________________________ From uucp@autodesk.com Mon Nov 1 17:49:23 1993 Date: Mon, 01 Nov 93 17:22:56 BD2 From: CCATF@BRLNCC.BITNET To: hyperchem@autodesk.com hyperchem: how do you freeze torsion angles and optimize geometries. thank you. Dr. C. A. Taft ________________________________________________________________________ From hyper!hurst@autodesk.com Mon Nov 1 23:14:31 1993 Date: Mon, 1 Nov 93 18:35:27 -0500 From: hyper!hurst@autodesk.com (Graham Hurst) To: CCATF@BRLNCC.BITNET, autodesk!hyperchem@openlink.openlink.com Subject: Freezing torisons during optimization Dr. C. A. Taft asked: > hyperchem: how do you freeze torsion angles and optimize > geometries. thank you. This can be done by applying restraining forces to the torsion angles that you wish to freeze. 1. Select a dihedral angle and name it with Select/Name Selection. Repeat for all dihedral angles that you wish to freeze. 2. Use Setup/Restraints to add harmonic restoring forces. You must specify the desired value for each dihedral angle (use Computed to set it to the angle that the system currently has) and a force constant which dictates how strongly the dihedral angle will be "held" at the desired angle. A force constant around 1000 should be strong enough to hold the dihedral close to the desired value, and values a lot larger can make the optimizers job more difficult. Although these do not perfectly "freeze" the angle, they can be used to "steer" an optimiztion to a desired conformation. Just remember to do a single point afterwards with the restraining forces turned off to get a potential energy without the restoring force. This is covered in the reference manual on pages 175-177 and pages 48-50 of Part II of the Computational Chemistry Guide, though note that the name changed from "Constraints" to "Restraints" in release 3 and it is now in the Setup menu since they are available now for semi-empirical as well as molecular mechanics calculations. Hope this helps, Graham ------------ Graham Hurst Hypercube Inc, 7-419 Phillip St, Waterloo, Ont, Canada N2L 3X2 (519)725-4040 internet: hurst@hyper.com ________________________________________________________________________ From apa@pop.cc.adfa.oz.au Wed Nov 3 12:13:14 1993 Date: Wed, 3 Nov 1993 16:16:48 +1100 To: hyperchem@autodesk.com From: apa@pop.cc.adfa.oz.au (Alan Arnold) Subject: Printing orbital energy diagram from HC rel3 for Windows. This seems a very simple Q and I hope the answer is not in the manual (because I couldn't find it) but: How do you print the orbital energy diagram that you create with Compute:Orbitals? I'm using Hyperchem release 3 for Windows. ---- Alan Arnold | e-mail: apa@pop.cc.adfa.oz.au Chem. Department,University College | voice : +61 6 268 8080 Australian Defence Force Academy | fax : +61 6 268 8002 CANBERRA ACT 2601 Australia | ________________________________________________________________________ From jeg10@slc8.INS.CWRU.Edu Wed Nov 3 13:59:28 1993 Date: Wed, 3 Nov 93 12:28:17 -0500 From: jeg10@po.CWRU.Edu (Jennifer E. Grant) To: hyperchem@autodesk.com Subject: printing vibrational spectra Reply-To: jeg10@po.CWRU.Edu (Jennifer E. Grant) This may also be a simple question, but how does one print out the vibrational spectrum using Hyperchem 3.0??? -- Jennifer Grant Wer denkt, Department of Biochemistry schafft. Case Western Reserve University ________________________________________________________________________ From uucp@autodesk.com Wed Nov 3 15:45:27 1993 Date: Wed, 03 Nov 93 16:51:36 BD2 From: CCATF@BRLNCC.BITNET To: hyperchem@autodesk.com try copying orbitals to clipboard, you can use corel-draw or other graphic program to print how you want. dr. c. a. taft centro brasileiro de pesquisas fisicas,Rio de Janeiro, BraSIL also HELP: I have been promised final release rel 3 HC from KaRYN Kambur, Autodesk, and so far have not received, i have been unable to establish bitnet/internet contact with her. I am interested in obtaininG the last release. ________________________________________________________________________ From uucp@autodesk.com Thu Nov 4 17:13:26 1993 Date: Thu, 04 Nov 93 11:49:47 BD2 From: CCATF@BRLNCC.BITNET To: hyperchem@autodesk.com I imagine any thing can be printed on screen using print command or copying to clipboard then copying from any windows program. dr. c. taft, centro brasileiro de pesquisas fisicas rio de janeiro, brasil help: unable to contact karyn kambur at autodesk to get my copy of release 3. c. a. taft ________________________________________________________________________ From jeg10@slc5.INS.CWRU.Edu Thu Nov 4 17:13:40 1993 Date: Thu, 4 Nov 93 09:08:12 -0500 From: jeg10@po.CWRU.Edu (Jennifer E. Grant) To: hyperchem@autodesk.com Subject: when opening HINfile, Hyperchem cant find HIN keywords Reply-To: jeg10@po.CWRU.Edu (Jennifer E. Grant) We recently created a file containing an organic molecule of interest, and one water molecule. having optimized the system (geometry optimization) i saved it in its appropriate HINfile. When i try and recall that particular file, the program prints the error message: does this mean that my file was garbled when it was saved? Perhaps the HIN-file can be edited, i.e. a keyword inserted, that will allow me to open this file? much obliged -- Jennifer Grant Wer denkt, Department of Biochemistry schafft. Case Western Reserve University ________________________________________________________________________ From mschriver@kean.ucs.mun.ca Thu Nov 4 17:20:47 1993 Sender: mschriver@kean.ucs.mun.ca Date: Thu, 04 Nov 1993 10:55:32 -0230 From: mschriver@kean.ucs.mun.ca Reply-To: mschriver@kean.ucs.mun.ca To: hyperchem@autodesk.com Subject: Printing Orbital Diagrams and Vibrational Spectra Hyperchemists, A few weeks ago I asked a question that is very similar to Alan Arnolds concerning the printing of orbital energy diagrams. Most of the answers I got concerned the printing of the contour plots of orbitals in the main view screen not the printing of the energy level diagrams that Alan and I are generating INSIDE the Orgitals box. I Have tried most of the suggestions that came my way without sucess. There is one suggestion left that I am still working on. A secondary problem is that the background colour is black and the options do not seem to allow one to change the colour of the backgrounds in the secondary screens (MO energy level diagrams and the vibrational spectra). If Alan or Jennifer get simple answers to their questions could you please put them on the net? Most of the replies I got were to me personally and I think that there may be others out there lurking on the net with the same problem(s). I really appreciate the net and I would be interested in hearing of publications that have used HYPERCHEM for semi-empirical calclations. keep your hardware locks dry Mel Schriver Memorial Univ. Newfoundland Canada ________________________________________________________________________ From hyper!hurst@autodesk.com Fri Nov 5 00:42:51 1993 Date: Thu, 4 Nov 93 18:56:34 -0500 From: hyper!hurst@autodesk.com (Graham Hurst) To: autodesk!hyperchem@openlink.openlink.com Subject: Printing orbital energy levels and spectra It may not be well documented, and it isn't ideal, but you *can* print the orbital dialog box and the spectra dialog boxes from HyperChem as long as you have another application to print the contents of the Windows clipboard (such as Write or Paintbrush that come with Windows). The procedure: 1. If you want black lines on white background, the secret incantation is to change Window colour to White and Bond colour to Black under File/Preferences. 2. Under Edit/Setup image, change Window to Top Level. This sets Chem up to capture the topmost window on the screen. Check at least one of Bitmap and Metafile and also check clipboard. 3. Get the dialog box you want on the screen (i.e. IR, UV or Orbitals). 4. Press the F9 key. 5. Bring up Paintbrush, Write, or another application and use Edit/Paste (or equivalent). Crop, resize, annotate, etc. if the application supports it and you want to, and then Print. If you have any trouble, use the clipboard viewer to make sure the image is getting into the clipboard. All the data used to generate these graphs is available via scripts, so if you have a spreadsheet or plotting program, you might want to use scripts to put the numbers into a text file that you can import into that program for plotting. Hope this helps! Graham ------------ Graham Hurst Hypercube Inc, 7-419 Phillip St, Waterloo, Ont, Canada N2L 3X2 (519)725-4040 internet: hurst@hyper.com ________________________________________________________________________ From hyper!hurst@autodesk.com Fri Nov 5 00:46:04 1993 Date: Thu, 4 Nov 93 19:15:57 -0500 From: hyper!hurst@autodesk.com (Graham Hurst) To: jeg10@po.CWRU.Edu (Jennifer E. Grant) Subject: Re: when opening HINfile, Hyperchem cant find HIN keywords Cc: autodesk!hyperchem@openlink.openlink.com Jennifer E. Grant asks: > We recently created a file containing an organic molecule > of interest, and one water molecule. having optimized the > system (geometry optimization) i saved it in its appropriate > HINfile. When i try and recall that particular file, the > program prints the error message: > > HIN keywords.> > > does this mean that my file was garbled when it was saved? > Perhaps the HIN-file can be edited, i.e. a keyword inserted, > that will allow me to open this file? What this means is that none of the file was recognizable as a HIN file. The most common reason for seeing this is that the file was inadvertently opened with a word processor, that changed it from a text file to its own format. Try opening the file in NotePad (if it's small enough) or the MS-DOS editor (or emaccs or vi or ...) but *not* WordPerfect, Word, Ami, etc. If there are nonsense characters interspersed with recognizable text then this is probably what happened. If so, try opening it in the word processor that corrupted it and saving it again (to a different name!) in text or ASCII format. If you're lucky it will be restored. If this isn't the problem, read Appendix D of the Reference manual and compare the HIN spec with the actual contents of your file. Hope this helps, Graham ------------ Graham Hurst Hypercube Inc, 7-419 Phillip St, Waterloo, Ont, Canada N2L 3X2 (519)725-4040 internet: hurst@hyper.com ________________________________________________________________________ From hyper!hurst@autodesk.com Fri Nov 5 00:46:21 1993 Date: Thu, 4 Nov 93 19:34:09 -0500 From: hyper!hurst@autodesk.com (Graham Hurst) To: Jesse Salb , autodesk!hyperchem@openlink.openlink.com Subject: Re: PDB file residue numbering Jesse Salb wrote: > Certain PDB files (.ENT) have undetermined residues marked "UNK" for > unknown. When a file containing UNKs is loaded into Hyperchem, the > numbering of all the known residues is disrupted. Other programs such as > Kinemage seem to handle UNKs well while preserving the residue numbering > from beginning to end of the protein. Does anyone know of a workaround > to this problem in Hyperchem? > jsalb@novalink.com We've already told Jesse the following, but I'm posting here for the benefit of any others interested. It turns out the the PDB file did not specify CONECT records for at least some of the non-standard residue's backbone. When HyperChem encounters a residue in a PDB that it does not have a template for, it relies on CONECT records to determine where bonds are since the PDB spec says that residues not in their standard list have to have CONECT records. If a has no CONECT records, i.e. no bonds, then HyperChem makes it a seperate molecule and restarts the residue numbering. There are two solutions to this problem. Either create a template entry to tell HyperChem where the bonds are (see the end of Appendix E of the Reference Manual for step-by-step instructions) or edit the PDB to add the missing CONECT records. Cheers, Graham ------------ Graham Hurst Hypercube Inc, 7-419 Phillip St, Waterloo, Ont, Canada N2L 3X2 (519)725-4040 internet: hurst@hyper.com ________________________________________________________________________ From jianfent@chaph.usc.edu Fri Nov 5 14:28:45 1993 Date: Fri, 5 Nov 93 10:37:02 PST From: Jianfen Tsai To: hyperchem@autodesk.com Cc: jianfent@scf.usc.edu Subject: heat of formation when we calculate heat of formation using Hyperchem am1 method, as you pointed out that the value are experimentally fited for each molecular geometry. as we optimize a specific strcture say CH3-CH3, by different force field for instance MM+ or AM1, the resulting value of heat of formation is quite different. Why?, How the AM1 method calculates the heat of formation? ________________________________________________________________________ From berger@wuchem.wustl.edu Mon Nov 8 17:18:05 1993 Date: Mon, 8 Nov 1993 14:55:25 -0600 To: "hyperchem@autodesk.com"@WUGATE.wustl.edu Subject: MO representations in HyperChem Release 3 for DOS Does anyone know of a simple program or macro which allows one to make 3D MO pictures in HyperChem Release 3? It would be even better if they were rotatable in real time... Thanks! Dan Berger ________________________________________________________________________ From jianfent@chaph.usc.edu Mon Nov 8 19:57:36 1993 Date: Mon, 8 Nov 93 13:33:54 PST From: Jianfen Tsai To: hyperchem@autodesk.com Subject: heat of formation 5-Nov-93 18:37:11-GMT,831;000000000001 Return-Path: Received: from sal-sun43.usc.edu by chaph.usc.edu (4.1/SMI-4.1+ucs-3.0) id AA12448; Fri, 5 Nov 93 10:37:08 PST Received: by sal-sun43.usc.edu (4.1/SMI-4.1+ucs-3.6) id AA15706; Fri, 5 Nov 93 10:37:04 PST Date: Fri, 5 Nov 93 10:37:02 PST From: Jianfen Tsai To: hyperchem@autodesk.com. Cc: jianfent@scf.usc.edu Subject: heat of formation Message-Id: when we calculate heat of formation using Hyperchem am1 method, as you pointed out that the value are experimentally fited for each molecular geometry. as we optimize a specific strcture say CH3-CH3, by different force field for instance MM+ or AM1, the resulting value of heat of formation is quite different. Why?, How the AM1 method calculates the heat of formation? ________________________________________________________________________ From hyper!slee@autodesk.com Tue Nov 9 11:51:01 1993 From: hyper!slee@autodesk.com (Thomas Slee) Subject: Re: heat of formation To: autodesk!hyperchem@openlink.openlink.com (HyperChem e-mail group) Date: Tue, 9 Nov 93 9:10:27 EST Jianfen Tsai writes... | | when we calculate heat of formation using Hyperchem am1 method, as you | pointed out that the value are experimentally fited for each molecular | geometry. as we optimize a specific strcture say CH3-CH3, by different force | field for instance MM+ or AM1, the resulting value of heat of formation is | quite different. Why?, How the AM1 method calculates the heat of formation? | If the total electronic binding energy of the molecule is E, then the the AM1 heat of formation is Heat of formation = E - Sum(H_atom) where H_atom is a correction for each atom, and is given in column 13 of the AM1_1.abp parameter file (see the Theory and Methods section of the documentation, p 178 for this). The total electronic binding energy depends on the geometry, so the heat of formation is dependent on this too. The method was parametrized to reproduce heats of formation at geometries optimized using the method itself, I believe, so for most molecules the AM1 geometry would be the appropriate one to use. Tom -- Tom Slee Hypercube, Inc., #7-419 Phillip St., Waterloo, Ont. N2L 3X2 Internet: slee@hyper.com Tel. (519) 725-4040 ________________________________________________________________________ From jianfent@chaph.usc.edu Tue Nov 9 14:31:48 1993 Date: Tue, 9 Nov 93 8:45:50 PST From: Jianfen Tsai To: hyperchem@autodesk.com Cc: jianfent@scf.usc.edu Subject: heat capacity can we calculate heat capacity, Cp, for both organic molecules and radical species like CH3-CH3 or CH3-CH2., by AM1 method in HyperChem, as we do for heat of formation? ________________________________________________________________________ From hyper!slee@autodesk.com Thu Nov 11 10:26:43 1993 From: hyper!slee@autodesk.com (Thomas Slee) Subject: Re: heat capacity To: autodesk!hyperchem@openlink.openlink.com (HyperChem e-mail group) Date: Thu, 11 Nov 93 10:09:37 EST Jianfen Tsai writes... | | can we calculate heat capacity, Cp, for both organic molecules and radical | species like CH3-CH3 or CH3-CH2., by AM1 method in HyperChem, as we do for | heat of formation? | You cannot get the heat capacity out as a straightforward number from HyperChem. HyperChem can provide some information that can help in this evaluation, however. If you are using statistical mechanics to calculate the heat capacity as the sum of contributions from vibrations, rotations, and translations, then the following information may be of use in calculating the partition functions you need (I am reaching back a few years here, so check the relevance with your favourite Phys Chem book). With your molecule on the screen, choose Display/Inertial axes. The moments of inertia are displayed on the status line, and these can be used in the calculation of the rotational partition function. The vibrational partition function is governed by the frequency of the normal modes, which can be obtained from a "vibrations" calculation. For radical species I guess there may be an electronic component, in which case the electronic energy levels produced by a UV spectrum calculation (use ZINDO/S at the AM1 geometry) would enable you to evaluate the electronic partition function. So, far from a straightforward task, but I hope this helps. Tom Slee -- Tom Slee Hypercube, Inc., #7-419 Phillip St., Waterloo, Ont. N2L 3X2 Internet: slee@hyper.com Tel. (519) 725-4040 ________________________________________________________________________ From jianfent@chaph.usc.edu Fri Nov 12 05:48:59 1993 Date: Fri, 12 Nov 93 2:08:41 PST From: Jianfen Tsai To: hyperchem@autodesk.com Cc: jianfent@scf.usc.edu Subject: error mesage I was trying to run geometry optimization for structure: CH2Cl-CH2-CHCl-CH2-CHCl-CH2-CHCl-CH3 using AM1, the following conditions were put: setup: AM1 option: conv. limit 0.01 iteration limit 50 total charge 0 spin multiplicity 1 spin pair UHF state lowest compute: algorithm polak-ribiere(conjugate gradient) options RMS gradient of 0.01 or 390 max. In vacuo HyperChem version 2.0 is installed on a PC 486 VLB DX2 66MHz made by Intel Corp., default of MS windows is used. Error measages always came after the simulation ran for several hours. and it has to be stoped without being saved. is there anybody having the same experience? the error mesage said: Chem caused a general protection fault in module USER.EXE at 0006:030B ________________________________________________________________________ From roth@organik.uni-erlangen.de Fri Nov 12 09:28:00 1993 From: Henryette Roth Subject: Printing Orbital Diagrams and Vibrational Spectra To: hyperchem@autodesk.com Date: Fri, 12 Nov 93 14:59:10 MET Hyperchemists, Concerning the mail from Mel Schriver, maybe this will help a little bit: ... the printing of the energy level diagrams that Alan and I are generating INSIDE the Orgitals box. The printing of the Orbital box is only possible with the help of screen capture programms working under Windows, a good one comes with Coreldraw 3.0, but there are some on ftp-servers too. ... A secondary problem is that the background colour is black and the options do not seem to allow one to change the colour of the backgrounds in the secondary screens (MO energy level diagrams and the vibrational spectra). If you change the background in "user preferences" to white and the bonds to black, you will get the Orbitals box in black and white too. Take care because some of the colours depend on the Windows settings, when I'm doing screen snap- shots, I always use the default White Windows screen. I hope this will help ... Henryette Roth ******************************************************************************** * Henryette Roth * * * Inst. f. Org. Chemie I * * * Universitaet Erlangen * * * Henkestr. 42 * * * 91051 Erlangen * * ******************************************************************************** * roth@organik.uni-erlangen.de * ******************************************************************************** ________________________________________________________________________ From NEELY@DUCVAX.AUBURN.EDU Mon Nov 22 21:08:14 1993 Date: Mon, 22 Nov 1993 17:02 CST Subject: energies To: hyperchem@autodesk.com The energy values that come up in the information bar as an opti- mization progresses seem to have very little relation to those obtained from stand-alone MOPAC: for example, formaldehyde should converge to -31.xx kcal/mol, but the values seen in Hyperchem are on the order of -200. (Needless to say, we've selected the AM1 Hamiltonian). What is going on? We're running Hyperchem on an 80386/80387 machine with 8Mb RAM... Thanks! Irene Newhouse ________________________________________________________________________ From hyper!slee@autodesk.com Wed Nov 24 00:42:18 1993 From: hyper!slee@autodesk.com (Thomas Slee) Subject: Re: energies To: autodesk!hyperchem@openlink.openlink.com (HyperChem e-mail group) Date: Tue, 23 Nov 93 9:26:57 EST Irene Newhouse writes... | | The energy values that come up in the information bar as an opti- | mization progresses seem to have very little relation to those | obtained from stand-alone MOPAC: for example, formaldehyde should | converge to -31.xx kcal/mol, but the values seen in Hyperchem are | on the order of -200. (Needless to say, we've selected the AM1 | Hamiltonian). What is going on? We're running Hyperchem | on an 80386/80387 machine with 8Mb RAM... | Thanks! | Irene Newhouse | The "energies" reported by MOPAC are actually heats of formation. These are obtained from binding energies by subtracting a fixed increment for each atom in the system. In HyperChem, the heat of formation is reported along with other stuff in a log file. I would recommend carrying out a single point calculation at the end of the optimization rather than logging for the whole calculation, to avoid huge log files, and you will see the heat of formation along with other stuff (e.g., dipole moment) listed there, so that is where your -31.xx kcal/mol will be found. The status line energy in HyperChem is somewhat unorthodox for semi-empirical calculations, but the only difference is in the origin -- all differences are the same as yoouo are used to. We decided to print all our status line energies in kcal/mol, which is pretty standard in molecular mechanics packages. The total binding energy of a semi-empirical calculation in kcal/mol is a pretty huge number, so we take away an increment for each atom: again, this is just a shift of origin. Hope this is clear. Tom Slee -- Tom Slee Hypercube, Inc., #7-419 Phillip St., Waterloo, Ont. N2L 3X2 Internet: slee@hyper.com Tel. (519) 725-4040