From jianfent@chaph.usc.edu Sat Oct 2 02:06:30 1993 Date: Fri, 1 Oct 93 22:16:40 PDT From: Jianfen Tsai To: hyperchem@autodesk.com Subject: question I am using Hyperchem to simulate polymer chain scission by AM1(molecular dynamic simulation), I found that C-C bond in C8H18 or C8H17 broke at around 3000 K, which is much higher than the real decomposition temp. of 500-700 K in the real pyrolysis experiment of PE. why? ________________________________________________________________________ From jianfent@chaph.usc.edu Sun Oct 3 15:24:43 1993 Date: Sun, 3 Oct 93 10:41:29 PDT From: Jianfen Tsai To: hyperchem@autodesk.com Subject: question I am using Hyperchem to simulate polymer chain scission by AM1(molecular dynamic simulation), I found that C-C bond in C8H18 or C8H17 broke at around 3000 K, which is much higher than the real decomposition temp. of 500-700 K in the real pyrolysis experiment of PE. why? Besides, I need reference on hyperchem application to molecular simulation. ________________________________________________________________________ From hyper!slee@autodesk.com Mon Oct 4 15:46:40 1993 From: hyper!slee@autodesk.com (Thomas Slee) Subject: Re: question To: jianfent@scf.usc.edu (Jianfen Tsai) Date: Mon, 4 Oct 93 15:13:05 EDT Cc: autodesk!hyperchem@openlink.openlink.com (HyperChem e-mail group) Jianfen Tsai writes... | | I am using Hyperchem to simulate polymer chain scission by AM1(molecular | dynamic simulation), I found that C-C bond in C8H18 or C8H17 broke at around | 3000 K, which is much higher than the real decomposition temp. of 500-700 K | in the real pyrolysis experiment of PE. why? | I suspect you are using RHF to carry out the dynamics. Restricted Hartree Fock is incapable of properly simulating bond breaking (see most texts on MO theory for an explanation of this). The bond dissociation energies are always much too high, which is what you are seeing. If you use UHF you will get much better results. My single point calculations on ethane give the following numbers (rough: no optimization). RHF UHF 1.54 Angstoms -669 kcal/mol -669 kcal/mol 20.0 Angstoms -306 kcal/mol -572 kcal/mol Bond Dissociation 363 kcal/mol 97 kcal/mol Energy The UHF value is fairly realistic, I think, while the RHF is too high by a factor of four or so. Tom -- Tom Slee Hypercube, Inc., #7-419 Phillip St., Waterloo, Ont. N2L 3X2 Internet: slee@hyper.com Tel. (519) 725-4040 ________________________________________________________________________ From mschriver@kean.ucs.mun.ca Tue Oct 12 12:21:42 1993 Sender: mschriver@kean.ucs.mun.ca Date: Tue, 12 Oct 1993 13:30:59 -0230 From: mschriver@kean.ucs.mun.ca Reply-To: mschriver@kean.ucs.mun.ca To: hyperchem@autodesk.com Subject: Orbital Dialog Box Is there any way to generate hard copy MO structures from the orbital dialog box? Is it possible to change the background color from black to white so that a laser printer would give a reasonable figure? Am I missing something? Just asking, I am new to the users' group and would like to see how it works. Mel Schriver Chem. Dept. Memorial University of Newfoundland St. John's, NFLD mschriver@kean.ucs.mun.ca ________________________________________________________________________ From hyper!slee@autodesk.com Thu Oct 14 20:18:39 1993 From: hyper!slee@autodesk.com (Thomas Slee) Subject: Re: Orbital Dialog Box To: mschriver@kean.ucs.mun.ca Date: Thu, 14 Oct 93 10:04:50 EDT Cc: autodesk!hyperchem@openlink.openlink.com (HyperChem e-mail group) mschriver%kean.ucs.mun.ca writes... | |Is there any way to generate hard copy MO structures from the orbital |dialog box? Is it possible to change the background color from black to |white so that a laser printer would give a reasonable figure? |Am I missing something? | | Just asking, I am new to the users' group and would like to see how | it works. Well, no you are not missing anything, but there is a way of doing this. I can't find it in the documentation, unfortunately. However, the process is as follows: 1. Choose Preferences from the File Menu, and set Window to white and Bond to black. 2. Choose Setup Image from the Edit menu and make sure the Window is set to Top Level, the Color checkbox is empty (so that the image is black and white). You may have to play around with the other options, but I suspect Metafile will be better than Bitmap, and that going throught the clipboard is more convenient than a file for most applications. 3. Bring up your orbital dialog box. It should look as you want it: black lines on a white background, with the selected orbital dashed. 4. Press the F9 key. This is the keyboard shortcut for the Copy Image item under the Edit menu, and places the image into the clipboard. 5. Paste into some other application for printing and/or editing. I hope this gets you where you want to go. Tom Slee -- Tom Slee Hypercube, Inc., #7-419 Phillip St., Waterloo, Ont. N2L 3X2 Internet: slee@hyper.com Tel. (519) 725-4040 ________________________________________________________________________ From CHUCK@psipsy.uct.ac.za Fri Oct 15 05:01:53 1993 To: hyper!slee@autodesk.com (Thomas Slee), autodesk!hyperchem@openlink.openlink.com (HyperChem e-mail group) From: "Charles Marais" Date: 15 Oct 93 10:17:45 SAST-2 Subject: Re: Orbital Dialog Box *|dialog box? Is it possible to change the background color from black to *|white so that a laser printer would give a reasonable figure? *|Am I missing something? *| What's wrong with just choosing print from the file menu after the contour is drawn ? It still comes out with dotted lines... C Charles Marais Department of Chemistry University of Cape Town Private Bag Rondebosch chuck@uctvax.uct.ac.za South Africa 7700 chuck@psipsy.uct.ac.za ------------------------------------------------------------------ ________________________________________________________________________ From hyper!slee@autodesk.com Fri Oct 15 10:43:06 1993 From: hyper!slee@autodesk.com (Thomas Slee) Subject: Re: Orbital Dialog Box To: autodesk!hyperchem@openlink.openlink.com (HyperChem e-mail group) Date: Fri, 15 Oct 93 10:03:35 EDT Charles Marais writes... | |*|dialog box? Is it possible to change the background color from black to |*|white so that a laser printer would give a reasonable figure? |*|Am I missing something? |*| | |What's wrong with just choosing print from the file menu after the |contour is drawn ? It still comes out with dotted lines... | |Charles Marais I guess we are talking about two different things here: I was describing how to get a printout of the energy level diagram from the orbitals dialog box, you are describing how to get the orbital itself, and of course you are correct. Which did Mel Schriver want in his original message? I guess it doesn't really matter as long as the relevant reply works! Tom -- Tom Slee Hypercube, Inc., #7-419 Phillip St., Waterloo, Ont. N2L 3X2 Internet: slee@hyper.com Tel. (519) 725-4040 ________________________________________________________________________ From EWING@JCVAXA.JCU.EDU Fri Oct 15 11:43:47 1993 Date: Fri, 15 Oct 1993 10:31 EST From: "DAVID W. EWING (216) 397-4742" Subject: Cartesian coordinates To: autodesk!hyperchem@openlink.openlink.com I was told that HyperChem cannot take a cartesian coordinate file or a MOPAC coordinate file and convert it to a .hin file. I find this incredible that one cannot import a cartesian coordinate file and have HyperChem draw the structure!! Is there a way to do this in version 2? I don't see any reference to this in the manuals. Thanks, Dave Ewing John Carroll University ewing@jcvaxa.jcu.edu ________________________________________________________________________ From hyper!slee@autodesk.com Fri Oct 15 13:45:20 1993 From: hyper!slee@autodesk.com (Thomas Slee) Subject: Re: Cartesian coordinates To: autodesk!hyperchem@openlink.openlink.com (HyperChem e-mail group) Date: Fri, 15 Oct 93 12:22:16 EDT DAVID W. EWING writes... | | I was told that HyperChem cannot take a cartesian coordinate file or a | MOPAC coordinate file and convert it to a .hin file. I find this incredible | that one cannot import a cartesian coordinate file and have HyperChem draw | the structure!! Is there a way to do this in version 2? I don't see any | reference to this in the manuals. | HyperChem Release 3 reads in MOPAC Z-matrix files, but not coordinate files per se. There are different variations on the coordinate file theme: could you let me know exactly what you have? Actually, you can read in a cartesian coordinate file if you reformat it slightly, as a HIN file at its simplest is pretty much just that. Although there is a lot of other stuff in a HIN file, a minimal one can be built that looks like this (for ethylene, without the hydrogens): mol 1 atom 1 - C ** - 0.0 -0.67 0.0 0.0 0 atom 2 - C ** - 0.0 0.67 0.0 0.0 0 endmol 1 Here is a description of what you need: You need the mol 1 and endmol 1 lines at the beginning and end of the entire thing. Each line needs an atom number and element. You need to put in the dashes, but their column numbers are not important, just so long as there is white space (a space character or a TAB character) between the fields. The ** is the place for an atom type, and ** is just "unknown". The first 0.0 is the atomic charge (you can leave it zero). The next three fields are the x,y, z coordinates. (Here -0.67, 0, 0 and +0.67, 0, 0) The final column is the number of neighbours: zero here as we are not putting in any bonds yet. So after reading this in, one has a bunch of dots around the screen. The trick to making a guess at the bonding information is to save the system as a Z-matrix file, and then read it in again. The reason this less-than-obvious method works is that the Z-matrix file format has no room for explicit bonding information, and so we had to put a routine in to make a guess at the bonding whenever reading in such a file. Generally the guesses are quite good for organic molecules in regular geometries, but will be less good for inorganic systems or unusual geometries. Also, the user should check the valences after doing this: there is nothing explicit to stop 5-coordinate carbons, etc. If your coordinate file did not have the hydrogen coordinates in (as is commonly the case with X-ray data) then you can choose "Add hydrogens" from the Build menu to add them on without altering the coordinates of the heavier atoms. If your valences are correct this will work fine for organic systems. For other systems where valences are less well defined, you may need to add hydrogens yourself by drawing them in. If you select the hydrogen atoms and model build, then they alone will be fixed in position, again without altering the positions of the heavier atoms. Hope this is of use, Tom Slee -- Tom Slee Hypercube, Inc., #7-419 Phillip St., Waterloo, Ont. N2L 3X2 Internet: slee@hyper.com Tel. (519) 725-4040 ________________________________________________________________________ From jmeehan@bioch.utas.edu.au Tue Oct 19 02:51:51 1993 Date: Tue, 19 Oct 1993 16:23:43 +1100 To: hyperchem@autodesk.com From: jmeehan@bioch.utas.edu.au (John Meehan) Subject: Calcium parameters in hyperchem Dear netters, I was wondering if anyone has has any success with calcium salts in hyperchem. In particular, I am interested in modelling octa calcium phosphate. I have already converted the X-Ray data into cartesian coordinates but I'm having difficulty reading the file. I get the error message "Bad atom record at line 5 etc". This is due to the calcium atom type in mm+ . I've set it to atom 1 - Ca ** - 2 x y z etc Anyone know what it should be or what I can set it to??? Is there a better alternative.... is AMBER better?? Thanks in advance, John Meehan CH2-COOH Department of Biochemistry, O l University of Tasmania, HO-P-O-C-COOH G.P.O Box 252C Hobart 7001, OH l Tasmania, Australia. CH2-COOH email: jmeehan@bioch.utas.edu.au -- PHOSPHOCITRIC ACID -- A NATURAL, POWERFUL, NON-TOXIC INHIBITOR OF PATHOLOGICAL BIOMINERALIZATION.......WE'RE MAKING IT BETTER THAN EVER!!!!!!!! ________________________________________________________________________ From NMUELLER@edvz.uni-linz.ac.at Wed Oct 20 04:47:58 1993 Date: Wed, 20 Oct 1993 09:32:19 +0100 To: autodesk!hyperchem@openlink.openlink.com From: NMUELLER@EDVZ.UNI-LINZ.AC.AT (Norbert Mueller) Subject: ? HyperChem 3.0 for SGI ? When will HyperChem 3.0 for SGI be available. Its a groteque situation to have to run the inferior version 2.0 on the superior workstations. -- Norbert Mueller Institut fuer Chemie Johannes Kepler Universitaet A-4040 Linz Austria e-mail: NMUELLER@edvz.uni-linz.ac.at (preferred) norbert@soft.uni-linz.ac.at (MacPost) NorbertM (AMDA-Link Linz) <-FirstClass NorbertM@AMDA.UNI-LINZ.AC.AT ->FirstClass ________________________________________________________________________ From DESJARDI.S@fs.sciences.WLU.EDU Wed Oct 20 09:41:17 1993 To: hyperchem@autodesk.com From: "Dr. Steven Desjardins" Organization: Washington & Lee University Date: Wed, 20 Oct 1993 08:57:35 EDT Subject: student versions We have recently obtained copies of Hypercell (no relation, I realize) and I am intrigued by the way they handle licences. In particular, the university pays a flat yearly fee for a master copy (about $1000), and students pay $29 for a key disk and a manual. The student key is NOT a copy of hypercell. This approach has let us use hypercell in big classes. Hyperchem would be a wonderful educational tool, but we can hardly buy 50 copies to use it in a large genral or organic chemistry class. Just a suggestion. Steven G. Desjardins Department of Chemistry Washington and Lee University Lexington VA 24450 (703) 463-8873 ________________________________________________________________________ From hyper!slee@autodesk.com Wed Oct 20 16:48:43 1993 From: hyper!slee@autodesk.com (Thomas Slee) Subject: Re: Calcium parameters in hyperchem To: jmeehan@bioch.utas.edu.au (John Meehan) Date: Wed, 20 Oct 93 11:03:02 EDT Cc: autodesk!hyperchem@openlink.openlink.com (HyperChem e-mail group) John Meehan writes... | | Dear netters, | I was wondering if anyone has has any success with calcium salts in | hyperchem. In particular, I am interested in modelling octa calcium | phosphate. I have already converted the X-Ray data into cartesian | coordinates but I'm having difficulty reading the file. | I get the error message "Bad atom record at line 5 etc". | This is due to the calcium atom type in mm+ . I've set it to | atom 1 - Ca ** - 2 x y z etc | Anyone know what it should be or what I can set it to??? | Is there a better alternative.... is AMBER better?? | Thanks in advance, | John Meehan CH2-COOH Actually, I think the problem is not with the atom types: a ** should read in just fine. I think there must be some other problem in the atom line. If you could e-amil me your HIN file I'll take a look at it and let you know what I find out. As for whether AMBER would be better--I would doubt if it has the parameters for this system, so I would recommend sticking with MM+ (no guarantees on that kind of advice, I'm afraid!) 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 Wed Oct 20 16:48:43 1993 From: hyper!slee@autodesk.com (Thomas Slee) Subject: Re: SGI vs. PC To: PPANETH1@PLEARN.BITNET Date: Wed, 20 Oct 93 10:18:16 EDT Cc: autodesk!hyperchem@openlink.openlink.com (HyperChem e-mail group) PPANETH1%PLEARN.BITNET%SEARN.SUNET.SE@autodesk writes... |Hi netters, |I'd like to know if there are any differences in capabilities (other than |size of handled molecules, speed, and graphics) of codes running PC and SGI. |Particularily, is it possible to select on SGI everything within a given radius |from a given residue/molecule? My understanding is that this is not possible on |PC. And secondly, what are the plans for moving to other platforms. |Cheers, |Piotr | I'm afraid I can't say anything about plans for other platforms (company policy). However, I can say something about the SGI/PC differences. The current version of HyperChem on the SGI is Release 2. This is very similar to Release 2 for Windows, with the following exceptions: 1. Three of the four computational "back-ends" run in parallel, and so take advantage of the capabilities of machines with several processors. 2. Extra renderings are available on the SGI (ball and stick, tubes). 3. 3D isosurfaces of orbitals, densities, and electrostatic potentials are available on the SGI. 4. A few bugs that became known after the release of R2 for WIndows were fixed for the SGI. As for your specific question regarding selection within a sphere, the capabilities of both versions are the same: one can select all atoms, residues or molecules within a sphere from a specified atom. This is done as follows: - Make sure that "Select Sphere" under the select menu is checked. - set your selection target to atoms, residues or molecules, as desired, under the select menu. - click (left mouse button) on the central atom of interest, and keep the mouse key down. - click the right mouse key down also, and (holding both keys down), drag the mouse: the radius will be shown on the screen and in the status line. I hope this is of use. Tom -- Tom Slee Hypercube, Inc., #7-419 Phillip St., Waterloo, Ont. N2L 3X2 Internet: slee@hyper.com Tel. (519) 725-4040 ________________________________________________________________________ From jeg10@slc5.INS.CWRU.Edu Wed Oct 20 18:47:47 1993 Date: Wed, 20 Oct 93 18:11:05 -0400 From: jeg10@po.CWRU.Edu (Jennifer E. Grant) To: hyperchem@autodesk.com Subject: view all constraints??? Reply-To: jeg10@po.CWRU.Edu (Jennifer E. Grant) I was wondering if it is possible to ask hyperchem to highlight all angles or bonds that i have constrained in some fashion... can i tell hyperchem to flag all atoms or bonds that have been constrained, much in the same way that the O molecular modelling program paints atoms according to properties??? J. Grant -- I believe in the AIQ Wer denkt, theory of education... schafft. ASK INTELLIGENT QUESTIONS! ________________________________________________________________________ From anderson@biochemistry.BIOC.CWRU.Edu Thu Oct 21 08:35:34 1993 From: "Vernon Anderson" Date: Thu, 21 Oct 93 08:07:31 EST To: hyperchem@autodesk.com Subject: Re: student versions I would like to second Steven DesJardins motion for making this program available in a version that is not further distributable. -Vernon- 10900 Euclid Avenue 216-368-2599, fax 216-368-4544 Case Western Reserve University anderson@biochemistry.cwru.edu Cleveland, OH 44106-4935 ________________________________________________________________________ From CHUCK@psipsy.uct.ac.za Fri Oct 22 09:36:26 1993 To: hyperchem@autodesk.com From: "Marais, Charles F. " Date: Fri, 22 Oct 1993 14:03:09 SAST-2 Subject: SCF convergence criteria Hi All How dangerous is it to relax the SCF convergence criteria ? In Hyperchem (on the PC), the units are kcal/mole and I usually find that my jobs run within reasonable time if I use 1e-6 or 1e-5. Is this OK ? I've seen programs use 1e-10 ! c Charles Marais Department of Chemistry University of Cape Town Private Bag Rondebosch chuck@uctvax.uct.ac.za South Africa 7700 chuck@psipsy.uct.ac.za ------------------------------------------------------------------ ________________________________________________________________________ From autodesk!smtpcc2!rodgerp@hyper Fri Oct 22 11:51:55 1993 Date: Thu, 21 Oct 1993 19:41:10 -0400 To: hyperloo@unix2cc.uucp Cc: sandrasw@smtpcc2.uucp, kavana@anlphy.phy.anl.gov Subject: Converting HyperChem Geometry Dear folks, Two days ago at EDUCOM in Cincinnati, I met a professor of chemistry who teaches at Purdue University's Hammond, IN, campus. She also works at Argonne National Laboratory--which I deduced from her email address. She's heard of a conversion utility to convert HyperChem geometry into AutoCAD- or 3D-Studio-readable formats. Please forward to her any information your have on these utilities. Here is contact information for the professor: Dr. Karen Kavana Assistant Professor of Chemistry Department of Chemistry Purdue University Hammond, IN 46323 219/989-2327 (phone) kavana@anlphy.phy.anl.gov (email) Please keep me in the loop on replies to Dr. Kavana. Thanks, Rodger ________________________________________________________________________ From hyper!slee@autodesk.com Fri Oct 22 12:10:25 1993 From: hyper!slee@autodesk.com (Thomas Slee) Subject: Re: view all constraints??? To: autodesk!hyperchem@openlink.openlink.com (HyperChem e-mail group) Date: Fri, 22 Oct 93 9:56:39 EDT Jennifer E. Grant writes... | | I was wondering if it is possible to ask hyperchem | to highlight all angles or bonds that i have | constrained in some fashion... can i tell hyperchem | to flag all atoms or bonds that have been constrained, | much in the same way that the O molecular modelling | program paints atoms according to properties??? | | J. Grant I cannot think of a way this could be done in HyperChem. The only way to approach it that comes to mind is to save all your constrained atoms in a named selection. This selection can then be called up at any time, and coloured as you wish. Named selections are saved in the HIN file, and so are not lost between sessions. Tom Slee -- 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 Fri Oct 22 12:10:36 1993 From: hyper!slee@autodesk.com (Thomas Slee) Subject: HyperChem EMail Group Poll To: autodesk!hyperchem@openlink.openlink.com (HyperChem e-mail group) Date: Fri, 22 Oct 93 10:05:47 EDT Dear HyperChemists, The group has been going for a while now, and traffic, while moderate, is becoming steady. In general, though not always, I have been sending technical answers to the whole group, rather than just to the individual, under the assumption that the material would be of interest to you all. I thought this is about the right time to check that assumption. So, please could you check one of the following and send your replies to me (slee@hyper.com). I'll summarize to the group. As with all polls, this is consultative rather than binding! 1. I don't want to see answers to other people's questions. Keep my mailbox clean and just reply to the respondent. [ ] 2. The current balance is about right. [ ] 3. I don't want to miss anything: send all answers to the group. [ ] Thanks for your time. Tom -- Tom Slee Hypercube, Inc., #7-419 Phillip St., Waterloo, Ont. N2L 3X2 Internet: slee@hyper.com Tel. (519) 725-4040 ________________________________________________________________________ From creon@nas.nasa.gov Fri Oct 22 19:44:16 1993 Date: Fri, 22 Oct 93 10:03:55 -0700 From: creon@nas.nasa.gov (M. Creon Levit) To: hyper!slee@autodesk.com Cc: autodesk!hyperchem@openlink.openlink.com Subject: HyperChem EMail Group Poll Reply-To: creon@nas.nasa.gov 3. I don't want to miss anything: send all answers to the group. [x] The right thing would probably be to make a usenet newsgroup (sci.hyperchem, or some such). That way everyone could see as much as they want, when they want. ________________________________________________________________________ From chemistry-request@osc.edu Fri Oct 22 21:08:55 1993 Date: Fri, 22 Oct 1993 16:34:05 +0100 To: chemistry@osc.edu From: NMUELLER@edvz.uni-linz.ac.at (Norbert Mueller) Subject: HyperChem 3.0 for SGI Would anyone more knowledgeable than myself please comment on the rumour that AutoDesk will drop HyperChem for the SGI - meaning that there will not be a version 3.0 for SGI. -- Norbert Mueller Institut fuer Chemie Johannes Kepler Universitaet A-4040 Linz Austria e-mail: NMUELLER@edvz.uni-linz.ac.at (preferred) norbert@soft.uni-linz.ac.at (MacPost) NorbertM (AMDA-Link Linz) <-FirstClass NorbertM@AMDA.UNI-LINZ.AC.AT ->FirstClass --- Administrivia: This message is automatically appended by the mail exploder: CHEMISTRY@osc.edu --- everyone CHEMISTRY-REQUEST@osc.edu --- coordinator OSCPOST@osc.edu send help from chemistry Anon. ftp kekule.osc.edu CHEMISTRY-SEARCH@osc.edu --- search the archives, read help.search file first --- ________________________________________________________________________ From CHUCK@psipsy.uct.ac.za Mon Oct 25 11:56:13 1993 To: hyperchem@autodesk.com From: "Marais, Charles F. " Date: Mon, 25 Oct 1993 15:23:13 SAST-2 Subject: Hyperchem pricing in SA Hi all IN South Africa, I've just heard from the local distributor, Hyperchem for the PC now costs R5500, about US$1650. Is this in line with the USA price ? If not, can anyone recommend a dealer in the USA ? Thanks ! C Charles Marais Department of Chemistry University of Cape Town Private Bag Rondebosch chuck@uctvax.uct.ac.za South Africa 7700 chuck@psipsy.uct.ac.za ------------------------------------------------------------------ ________________________________________________________________________ From hyper!slee@autodesk.com Mon Oct 25 21:17:07 1993 From: hyper!slee@autodesk.com (Thomas Slee) Subject: Re: SCF convergence criteria To: autodesk!hyperchem@openlink.openlink.com (HyperChem e-mail group) Date: Mon, 25 Oct 93 17:37:35 EDT Marais, Charles F. writes... | | How dangerous is it to relax the SCF convergence criteria ? In | Hyperchem (on the PC), the units are kcal/mole and I usually find that | my jobs run within reasonable time if I use 1e-6 or 1e-5. | | Is this OK ? I've seen programs use 1e-10 ! There may well be others on this group who have more experience than I do on this question, but here is my two cents' worth. As usual, I think the answer is "it depends". If you are interested in single point calculations at reasonable geometries, in order to simply look at the orbitals and their ordering, then there is no problem with an even looser criterion than you indicate: even 0.01 or so will be fine. The figure of 1e-6 or 1e-5 is around the default value for MOPAC (their's is given in eV in the manual, so there is a conversion factor). I think it is fine for most quantitative work where the main concern is energies and/or heats of formation. The only place I think tighter criteria may be needed is if you are interested in accurate geometries of floppy systems. Here, where there are large regions of small gradient (eg, torsion angle changes) a loose SCF criterion can lead to inaccurate geometries. The error in the SCF energy gets reflected in an inaccurate gradient, and while this is not a problem for minima with steep sides, it can lead to quite inaccurate structures where torsion angles are important. This was, I believe, the reason MOPAC introduced a PRECISE keyword, which has a tighter criterion. The other place a strict convergence is required is in the vibrational calculation, to get the secodn derivative right. here, HyperChem automatically makes the convergence criterion 1e-5 * the value you enter in the SCF dialog box when computing the frequencies, so the problem is taken care of. 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 Oct 26 18:34:44 1993 Date: Tue, 26 Oct 93 8:27:05 PDT From: Jianfen Tsai To: hyperchem@autodesk.com Subject: error measages I was trying to run geometry optimization for structure: CH2Cl-(CH2-CHCl)5-CH3 using AM1, RMS criterior is 0.001. 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? ________________________________________________________________________ From uucp@autodesk.com Wed Oct 27 12:33:28 1993 From: Mr Andrew D Allen Subject: SG version of Hyperchem To: hyperchem@autodesk.com Date: Wed, 27 Oct 93 14:26:00 GMT I am new to this list, so pardon me if this question has already been raised. Q. Has the SG version of HyperChem been dropped? Andy. ________________________________________________________________________ From uucp@autodesk.com Wed Oct 27 16:37:19 1993 From: Jesse Salb To: hyperchem@autodesk.com Subject: PDB file residue numbering Date: Wed, 27 Oct 93 13:29:54 EST Organization: NovaLink, 800-274-2814 (voice) or 800-825-8852 (data) 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