From pat.uwe-bristol.ac.uk!kp_sudlo@netcom.com Fri Jul 2 09:05:57 1993 From: KP Sudlow Date: Fri, 2 Jul 93 12:30:36 BST To: hyperchem@autodesk.com Subject: bond lengths and angles Status: RO Does anyone know of a method of getting a list of bond lengths and angles from Hyperchem without having to laboriously go through the molecule and select each bond or (group of bonds) in turn? Thanks. Kevin Sudlow Faculty of Applied Sciences University of the West of England, Bristol Coldharbour Lane Bristol BS16 1QY UK email: kp_sudlo@uk.ac.uwe-bristol.pat tel: (0272) 656261 ext 2493 ________________________________________________________________________ From pat.uwe-bristol.ac.uk!kp_sudlo@netcom.com Fri Jul 2 10:56:58 1993 From: KP Sudlow Date: Fri, 2 Jul 93 15:21:57 BST To: hyperchem@autodesk.com Subject: bond lengths and angles Status: RO Apologies if you recieve this twice but I seem to be having trouble at my end and I am not sure if this got through. Does anyone know of a method of getting a list of bond lengths and angles from Hyperchem without having to laboriously go through the molecule and select each bond or (group of bonds) in turn? Thanks. Kevin Sudlow Faculty of Applied Sciences University of the West of England, Bristol Coldharbour Lane Bristol BS16 1QY UK email: kp_sudlo@uk.ac.uwe-bristol.pat tel: (0272) 656261 ext 2493 ________________________________________________________________________ From hyper!slee@autodesk.com Fri Jul 2 12:01:35 1993 From: hyper!slee@autodesk.com (Thomas Slee) Subject: Re: bond lengths and angles To: autodesk!kp_sudlo%pat.uwe-bristol.ac.uk@netcom.com (KP Sudlow) Date: Fri, 2 Jul 93 11:38:58 EDT Cc: autodesk!hyperchem@netcom.com (HyperChem e-mail group) Status: RO KP Sudlow writes... | | Does anyone know of a method of getting a list of bond lengths and | angles from Hyperchem without having to laboriously go through the molecule | and select each bond or (group of bonds) in turn? | Hardly an elegant solution, but if you carry out an MM+ calculation with the print level set to 1, and log the results, the log file will contain the coordinate data, the bond length data, the bond angle data, as well as the torsion and non-bonded (electrostatic as well as van der Waals) data. The non-bonded data can take up a lot of space for a big molecule, so if you want to suppress this set a short cutoff (say .1 to .2 A). Here is a script that does the relevant operations. :----------------------------------------------------------------- ; STRUCT.SCR ; script to generate structural data ; in a log file named "struct.log ; in the current directory. calculation-method molecular-mechanics molecular-mechanics-method mm+ cutoff-type switched cutoff-inner-radius .1 cutoff-outer-radius .2 mechanics-print-level 1 start-logging struct.log no do-single-point stop-logging ; reset cutoff values to HyperChem factory settings ; for next time a cutoff is chosen cutoff-inner-radius 10 cutoff-outer-radius 14 ; reset to no cutoffs. cutoff-type none :----------------------------------------------------------------- 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 Mon Jul 5 20:27:16 1993 From: hyper!slee@autodesk.com (Thomas Slee) Subject: Re: bond lengths from HyperChem To: autodesk!hyperchem@netcom.com (HyperChem e-mail group) Date: Mon, 5 Jul 93 14:58:20 EDT Status: RO Apologies if you have received this already: we had mailer problems, so I am resending in case... Tom KP Sudlow writes... | | Does anyone know of a method of getting a list of bond lengths and | angles from Hyperchem without having to laboriously go through the molecule | and select each bond or (group of bonds) in turn? | Hardly an elegant solution, but if you carry out an MM+ calculation with the print level set to 1, and log the results, the log file will contain the coordinate data, the bond length data, the bond angle data, as well as the torsion and non-bonded (electrostatic as well as van der Waals) data. The non-bonded data can take up a lot of space for a big molecule, so if you want to suppress this set a short cutoff (say .1 to .2 A). Here is a script that does the relevant operations. :----------------------------------------------------------------- ; STRUCT.SCR ; script to generate structural data ; in a log file named "struct.log ; in the current directory. calculation-method molecular-mechanics molecular-mechanics-method mm+ cutoff-type switched cutoff-inner-radius .1 cutoff-outer-radius .2 mechanics-print-level 1 start-logging struct.log no do-single-point stop-logging ; reset cutoff values to HyperChem factory settings ; for next time a cutoff is chosen cutoff-inner-radius 10 cutoff-outer-radius 14 ; reset to no cutoffs. cutoff-type none :----------------------------------------------------------------- Tom Slee ________________________________________________________________________ From UCBEH.SAN.UC.EDU!SHERTZHG@netcom.com Thu Jul 8 16:37:07 1993 Date: Thu, 08 Jul 1993 12:17:13 -0400 (EDT) From: SHERTZHG@UCBEH.SAN.UC.EDU Subject: OXIDATION POTENTIALS To: HYPERCHEM@autodesk.com Status: RO I AM INTERESTED IN CALCULATING OXIDATION POTENTIALS FOR INDOLE COMPOUNDS USING HYPERCHEM. THE REACTION IS : INDOLE = INDOLE NITROGEN RADICAL CATION + ELECTRON. IT IS NOT CLEAR HOW TO CONSTRUCT A RADICAL SPECIES (THAT IS, CONTAINING AN UNPAIRED ELECTRON SUCH AS WOULD EXIST ON THE INDOLIC NITROGEN ABOVE THE OXIDATION POTENTIAL). NOR IS IT CLEAR HOW TO CALCULATE MINIMUM ENERGIES FOR COMPOUNDS WITH AN UNPAIRED ELECTRON. IF ANYONE HAS ANY IDEAS, I WOULD BE MOST GRATEFUL. DR. HOWARD SHERTZER AT UNIVERSITY OF CINCINNATI, INTERNET SHERTZHG@UCBEH.SAN.UC.EDU BITNET SHERTZHG@UCBEH ________________________________________________________________________ From ncsc.org!kmoore@netcom.com Thu Jul 8 18:57:03 1993 Date: Thu, 8 Jul 93 17:09:53 EDT From: Kevin Moore To: hyperchem@autodesk.com Subject: pdb problem... Status: RO I sent this question in the other day, but I have heard no response and am wondering if there may have been a mailer glitch. Here goes again with a little more depth: I have two pdb files, one is nicotine free-base and the other is protonated. They were created by Gaussian 92's newzmat program and can be read into Tripos' SYBYL package without any problems. When I read the free-base pdb into hyperchem, everything is fine, but when I try to read the protonated version, I get the following error: ! Error opening file nic-prot.pdb In my previous post, I generalized this to protonated amines and since have realized that this was incorrect (nh4+ works fine). Any suggestions on how I can get this read in? Is it fixed in the new version of hyperchem (which I should be getting in the next month or so)? ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ || Kevin Moore North Carolina Supercomputing Center || || Scientific Support Analyst 3021 Cornwallis Rd. || || (919) 248-1179 Research Triangle Park, NC 27709 || ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ ________________________________________________________________________ From hyper!slee@autodesk.com Fri Jul 9 13:17:46 1993 From: hyper!slee@autodesk.com (Thomas Slee) Subject: Re: OXIDATION POTENTIALS To: autodesk!SHERTZHG%UCBEH.SAN.UC.EDU@netcom.com Date: Fri, 9 Jul 93 9:34:22 EDT Cc: autodesk!hyperchem@netcom.com (HyperChem e-mail group) Status: RO Dr. Howard Shertzer writes... | | I AM INTERESTED IN CALCULATING OXIDATION POTENTIALS FOR INDOLE COMPOUNDS USING | HYPERCHEM. THE REACTION IS : INDOLE = INDOLE NITROGEN RADICAL CATION + | ELECTRON. IT IS NOT CLEAR HOW TO CONSTRUCT A RADICAL SPECIES (THAT IS, | CONTAINING AN UNPAIRED ELECTRON SUCH AS WOULD EXIST ON THE INDOLIC NITROGEN | ABOVE THE OXIDATION POTENTIAL). NOR IS IT CLEAR HOW TO CALCULATE MINIMUM | ENERGIES FOR COMPOUNDS WITH AN UNPAIRED ELECTRON. IF ANYONE HAS ANY IDEAS, I | WOULD BE MOST GRATEFUL. DR. HOWARD SHERTZER AT UNIVERSITY OF CINCINNATI, | First, you must use one of the semi-empirical methods for these calculations. You can use the same initial screen representation for the indole and for the radical cation. In the semi-empirical options dialog box, you set the charge and multiplicity as appropriate for the species (charge = 0 and multiplicity = 1 for indole, charge = 1 and multiplicity = 2 for the radical cation.) You can optimize the neutral molecule using the regular RHF calculation. For the radical cation you have two choices: you can either use RHF or UHF. If you choose RHF you will get a warning, to the effect that the half-electron approximation being used means that the optimized structure may not be that of the minimum energy. This warning is because the energy function being minimized in this case is not quite the total energy of the system. However, the differences for the case of a doublet are very small, and you can carry out the optimization without worrying about it, in my opinion. If you choose UHF, the optimization will take a while longer, as each UHF calculation takes twice as long as the corresponding RHF. The geometry will be rigorously the minimum energy geometry for the method in this case. If you use AM1 or PM3, which are generally the most accurate methods, then I recommend that you compare the heats of formation rather than the energies given on the status line to get the answers you wish. These values are available in the log file (choose Start Log... under the Files menu), or alternatively by running a script containing the line heat-of-formation ? or, equivalently query-value heat-of-formation If you choose the log file option, I recommend that you carry out the optimization without logging, then turn on logging for a single point calculation at the final geometry, to avoid having lots of unnecessary information. Hope this helps.. 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 Fri Jul 9 13:42:39 1993 From: hyper!slee@autodesk.com (Thomas Slee) Subject: Re: pdb problem... To: autodesk!hyperchem@netcom.com (HyperChem e-mail group) Date: Fri, 9 Jul 93 8:57:05 EDT Status: RO Kevin Moore writes... | | I have two pdb files, one is nicotine free-base and the other is protonated. | They were created by Gaussian 92's newzmat program and can be read into Tripos' | SYBYL package without any problems. When I read the free-base pdb into | hyperchem, everything is fine, but when I try to read the protonated version, | I get the following error: | | ! Error opening file nic-prot.pdb | | In my previous post, I generalized this to protonated amines and since have | realized that this was incorrect (nh4+ works fine). Any suggestions on how | I can get this read in? Is it fixed in the new version of hyperchem (which | I should be getting in the next month or so)? | Without seeing the particular file, I cannot be sure, but one possibility is that the amine hydrogens are not named quite properly. There are a number of programs out there that use names such as "HN4A" for some hydrogens, while the pdb format rigorously requires the first two characters to be the element symbol, right justified: so this will get read as a nitrogen. If this is the case, then a fix is to run a script with the line non-standard-pdb-names true in it, then try reading the file again. If this doesn't work, please e-mail the file to me so that I can take a look at it. Tom -- Tom Slee Hypercube, Inc., #7-419 Phillip St., Waterloo, Ont. N2L 3X2 Internet: slee@hyper.com Tel. (519) 725-4040 ________________________________________________________________________ From uoft02.utoledo.edu!DSMITH@netcom.com Sun Jul 11 12:48:21 1993 Date: Sun, 11 Jul 1993 10:59:10 -0500 (EST) From: "DR. DOUGLAS A. SMITH, UNIVERSITY OF TOLEDO" Subject: hydrogen bonding - reviewers needed To: chemistry@osc.edu, mmodinfo@uoft02.utoledo.edu, hyperchem@autodesk.com Status: RO I am chairing a two-day symposium on Modeling the Hydrogen Bond at the ACS Chicago meeting, and the ACS has agreed to publish the procedings as part of their Symposia-in-Print series. I will edit the book, and will need to find reviewers for the articles to be included. So.... Anyone who is interested in possibly acting as a reviewer for one or more chapters in this book, which will be on theoretical and computational methods for modeling hydrogen bonding (primarily in non-biological systems), please send me your name, address, telephone and fax numbers, and your area of interest/expertise. The chapters will be sent for review right around the first of September, 1993, and will be due back within about 3-4 weeks. No chapter will be longer than 14 pages in the final, camera ready book. Doug Douglas A. Smith Assistant Professor of Chemistry The University of Toledo Toledo, OH 43606-3390 voice 419-537-2116 fax 419-537-4033 email dsmith@uoft02.utoledo.edu ________________________________________________________________________ From uidaho.edu!kellogg@netcom.com Mon Jul 12 16:02:18 1993 Date: Mon, 12 Jul 1993 12:44:50 +0800 (PST) From: Scott Kellogg Subject: Hyperchem Questions To: Hyperchem Status: RO I am sending this email message directly to the Hyperchem address and hope that I need not send it to Hyperchem-Request, as I am registered Hyperchem owner and somewhat knowledgeable about Internet Email. Basically, I have a simple question. In Hyperchem, when I want to print, I see only one printer come up. Isn't Hyperchem supposed to have a Select button or give one the choice whether I want a laser printer, 35 mm camera, etc?? Please advise me as there are several students in my lab that use Hyperchem and they are not sufficiently knowledgeable or privledged to use the Control panel. Thanks ________________________________________________________________________ From hyper!slee@autodesk.com Tue Jul 13 10:56:56 1993 From: hyper!slee@autodesk.com (Thomas Slee) Subject: Re: Hyperchem Questions To: autodesk!hyperchem@netcom.com (HyperChem e-mail group) Date: Tue, 13 Jul 93 9:41:21 EDT Status: RO Scott Kellogg writes... | | Basically, I have a simple question. In Hyperchem, when I want to print, | I see only one printer come up. Isn't Hyperchem supposed to have a Select | button or give one the choice whether I want a laser printer, 35 mm | camera, etc?? Please advise me as there are several students in my lab | that use Hyperchem and they are not sufficiently knowledgeable or | privledged to use the Control panel. Thanks | HyperChem uses the current Control Panel settings to determine the printer and setup to use. Our feeling was that including a printer dialog box duplicates this existing functionality, and so was not a high priority. Yours is the first time I have heard of a setup where this causes real problems, and I will ensure that this information goes into the pot for discussions about future releases. Tom -- Tom Slee Hypercube, Inc., #7-419 Phillip St., Waterloo, Ont. N2L 3X2 Internet: slee@hyper.com Tel. (519) 725-4040 ________________________________________________________________________ From autodesk!autodesk.com!uucp@netcom.com Tue Jul 13 12:30:46 1993 Date: Tue, 13 Jul 93 09:57:11 EDT From: SC18000 To: Subject: RE:Tale of woe @ intrigue Status: RO Hi All, I have a why-does-your-door-do-that? question. When optimizing toluene using HYPERCHM and MNDO I find that repeated optimizations always begin with a l;arge gradient no matter how many times we tell it to minimize. Yet after a single geometry minimization with AM1 i can get a reminimization is a matter of very few cycles, with a small gradient to begin with. This is no idle curiosity because I'll have to explain this to students in the Fall semester. Any reasons or ideas out there? Sincerely, Ken Fountain /sc18@nemomus ________________________________________________________________________ From uidaho.edu!kellogg@netcom.com Wed Jul 14 14:56:18 1993 Date: Wed, 14 Jul 1993 09:42:47 +0800 (PST) From: Scott Kellogg Subject: Printers & Hardcopy devices To: Hyperchem Status: RO As a new user of Hyperchem I find that it is difficult to select one of the 3 common hardcopy devices we use in Windows. Typically we would like to have a menu choice called something like Printer Select as we may be sending output to 35 mm cameras (Scodl format), laser printer, or color hardcopy units. The students that use my Hyperchem are not very facile with setting the default output device in the Control Panel, nor would I want them too. Have I missed something in Hyperchem? ________________________________________________________________________ From uidaho.edu!kellogg@netcom.com Wed Jul 14 23:57:12 1993 Date: Wed, 14 Jul 1993 20:07:42 +0800 (PST) From: Scott Kellogg Subject: Hyperchem Output To: Hyperchem Status: RO As a new user of Hyperchem I am perplexed by the Printer or output option. I may have missed something in the manual, but I seem to only be able to print to whatever the Windows default device is. How do I select different print devices within Hyperchem? In all my other windows programs there is a menu button for Printer select. This is important since we will be sending output to one of 3 devices, 35 mm camera system, laser printer, or color laser hardcopy. My students in the lab are are not facile with the Control Panel and setting default devices, nor do I want them to change that. I must have missed something and hopefully I can find out how to change devices within Hyperchem. WIndows and my other programs already know about those 3 devices and I use them quite easily, e.g., in Freelance, etc. By the way the University of Idaho as a great, free Windows device driver for 35 mm film output in SCODL format. Testing with a variety of programs easily generates 4K line great output. Thanks. ________________________________________________________________________ From CompuServe.COM!76702.531@netcom.com Thu Jul 15 19:38:47 1993 Date: 15 Jul 93 17:13:47 EDT From: Jeffrey Pike <76702.531@CompuServe.COM> To: "internet:hyperchem@autod" Subject: Hyperchem problems Status: RO ---------- Forwarded Message ---------- From: INTERNET:jumtow@technikum.chemie.uni-leipzig.d400.de, INTERNET:jumtow@technikum.chemie.uni-leipzig.d400.de TO: (unknown), 70761,3021 (unknown), 70453,21 Jeffrey Pike, 76702,531 DATE: 7/14/93 12:40 RE: Hyperchem problems Sender: jumtow@technikum.chemie.uni-leipzig.d400.de Received: from ixgate.gmd.de by iha.compuserve.com (5.67/5.930129sam) id AA18457; Wed, 14 Jul 93 15:38:22 -0400 X400-Received: by mta ixgate.GmD.de in /PRMD=GmD/ADMD=d400/C=de/; Relayed; Wed, 14 Jul 1993 21:31:13 +0200 X400-Received: by /PRMD=UNI-LEIPZIG/ADMD=D400/C=DE/; Relayed; Wed, 14 Jul 1993 21:31:29 +0200 Date: Wed, 14 Jul 1993 21:31:29 +0200 X400-Originator: jumtow@technikum.chemie.uni-leipzig.d400.de X400-Recipients: non-disclosure:; X400-Mts-Identifier: [/PRMD=UNI-LEIPZIG/ADMD=D400/C=DE/;ulmta1491930714213129-ISM] X400-Content-Type: P2-1984 (2) From: jumtow@technikum.chemie.uni-leipzig.d400.de Message-Id: <930714213128*/S=jumtow/OU=technikum/OU=chemie/PRMD=UNI-LEIPZIG/ADMD=D4 00/C=DE/@MHS> To: 70761.3021@Compuserve.com, 70453.21@Compuserve.com, 76702.531@Compuserve.com Subject: Hyperchem problems Hallo, Since a week Iom a new HYPERCHEM 3.0 user. I found your compuserv-mailadress in compuserve. I hope you can help me solving a few problems. Iom an analytical chemist at the university of Leipzig in Germany. We tried to use hyperchem for calculation of interactions between beta-cyclodextrin and some other molecules in solution. The first problem is that we didnot be able to move the small molecules without moving the cyclodextrin too. I also tried to use superposition but then we got error messages saying that 2 atoms are at the same place. Hyperchem moves the small molecule away from the cyclodextrin using the switch "add H-atoms and build structure". The MM+ algorithm moves the small molecule into the same plane as the cyclodextrin lies in but away from the cyclodextrin. I would be glad to get some information from you concerning my problems. I have also a suggestion: Why donot using the compuserve-forum or an ftp-server to interchange experiences concerning problems with hyperchem? One could also exchange *.hin files after simulation by hyperchem. I would recommand an ftp-server; it is easier to handle. With regards Frank Jumtow