From chimichi@risc1.chimorg.unifi.it Fri Jul 8 23:02:38 1994 Date: Fri, 8 Jul 1994 19:02:38 -0400 From: "stefano chimichi" Sender: risc1.chimorg.unifi.it!chimichi@hyper.hyper.com To: hyperchem@HYPER.COM Subject: problems with Nortondesktop Hello Netters, I'd like to know if somebody experienced problems running Hyperchem v. 3 or 4 under a 486 PC with Windows AND Norton Desktop INSTALLED. We noticed problems in 'Vibrations' where the program is unable to conclude(?) the calculus. In other words the computer do not hangs up but the program remain in phase of matrix calculation with only "Cancel" active in the Menu window. Are there problems with DDE or what?? ThanX for help and suggestions (possibly not 'Uninstall NortonDesktop'!!) Cheers Stefano ---------------------------------------------------------------------- Prof. Stefano Chimichi Phone: 39+55+2757631 Organic Chemistry Dept. Fax: 39+55+2476964 Via Gino Capponi, 9 I-50121 FIRENZE - Italy ---------------------------------------------------------------------- ________________________________________________________________________ From hurst@hyper.hyper.com Fri Jul 8 20:08:41 1994 Date: Fri, 8 Jul 1994 16:08:41 -0400 From: hurst@hyper.hyper.com (Graham Hurst) To: "stefano chimichi" , hyperchem@HYPER.COM Subject: Re: problems with Nortondesktop Prof. Stefano Chimichi asks: > I'd like to know if somebody experienced problems running Hyperchem v. 3 or > 4 under a 486 PC with Windows AND Norton Desktop INSTALLED. > We noticed problems in 'Vibrations' where the program is unable to > conclude(?) the calculus. In other words the computer do not hangs up but > the program remain in phase of matrix calculation with only "Cancel" active > in the Menu window. Are there problems with DDE or what?? > ThanX for help and suggestions (possibly not 'Uninstall NortonDesktop'!!) I bet this is with Release 3. Release 3 has a rather annoying bug that large calculations overflowed a 16-bit integer when trying to send back vibrations or UV results (often after days performing the calculation). This bug is fixed in Release 4 and should have nothing to do with Norton. If the calculation is okay without Norton, or coccurs with Release 4, please send more details to support@hyper.com. 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 CHROSEN@scifac.indstate.edu Sat Jul 9 19:17:03 1994 From: To: hyperchem@HYPER.COM Date: Sat, 9 Jul 1994 15:17:03 -0400 Subject: optimization weirdness Hi, I am just getting started on Hyperchem, and while I sometimes have gotten good results using the geometry optimization routine, it does not appear to work always for metal carbonyls. As a specific example, I tried cis-Fe(CO)4Cl2 using Zindo/1. The model builder gave a reasonable (octahedral) starting geometry. But during optimization, there is significant departure both from octahedral iron and linear metal-carbonyl bonds. After several sets of 11x15 cycles, the program did indeed indicate convergence, but to a structure like one never seen by man or nature. If the iron is the center of a sphere, it seemed like it wanted all the atoms directly bonded to it in a single hemisphere. Also, the Fe-C-O bond angles decreased to values as low as 133 deg. A similar problem exists for metal isocyanides, M-CNR. Suggestions? Larry Rosenhein Indiana State University (Terre Haute) CHROSEN@SCIFAC.INDSTATE.EDU ________________________________________________________________________ From hurst@hyper.hyper.com Mon Jul 11 16:04:09 1994 Date: Mon, 11 Jul 1994 12:04:09 -0400 From: hurst@hyper.hyper.com (Graham Hurst) To: Subject: Re: optimization weirdness Cc: hyperchem@HYPER.COM Larry Rosenhein writes: > Hi, > I am just getting started on Hyperchem, and while I sometimes > have gotten good results using the geometry optimization routine, it > does not appear to work always for metal carbonyls. As a specific > example, I tried cis-Fe(CO)4Cl2 using Zindo/1. The model builder > gave a reasonable (octahedral) starting geometry. But during > optimization, there is significant departure both from octahedral > iron and linear metal-carbonyl bonds. After several sets of 11x15 > cycles, the program did indeed indicate convergence, but to a > structure like one never seen by man or nature. If the iron is the > center of a sphere, it seemed like it wanted all the atoms directly > bonded to it in a single hemisphere. Also, the Fe-C-O bond angles > decreased to values as low as 133 deg. > A similar problem exists for metal isocyanides, M-CNR. > Suggestions? It turns out that ZINDO/1 often does a better job with 2nd row transition metals than 1st row transition metals. This seems to be a "feature" of Michael Zerner's INDO/1 method (called ZINDO/1 in HyperChem) that was originally implemented in the ZINDO program from Zerner's group. Some ZINDO experts use different sigma-sigma or pi-pi overlap weighting factors to get better results. One user has reported problems that are due to a poor initial guess for the wavefunction; he got a reasonable structure when he started from one with short bond lengths, but a subsequent single point did not converge. We are continuing to investigate this behaviour, but in general the ZINDO methods are not as robust for transition metals as AM1 or PM3 are for non-transition metal complexes. We have tried very hard (with lots of generous assitance from Tom Cundari and David Baker) to reproduce results of INDO/1 or INDO/S calculations that use Michael Zerner's ZINDO program (including the choice of the initial guess for the wavefunction). The optimization algorithms and wavefunction convergence acceleration options may differ from the ZINDO program, but we are confident that an INDO/1 (or INDO/S) potential surface will be same whether calculated from HyperChem, ZINDO or Argus (Mark Thompson's program). While not very satisfactory, I would advise caution when using ZINDO/1 for geometry optimization. In some cases the model builder, MM+, or even "hand-editing" will give better structures. ZINDO/S (INDO/S) was not developed for geometry optimization and should not be used for any geometry optimization. One should check, via a log file or by monitoring the status line, that all iterations in the optimization actually reached wavefunction convergence. Sometimes better results are observed by turning "Accelerate convergence" off (or on!). 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 l_wester@acad.lvc.edu Mon Jul 11 19:32:57 1994 To: hyperchem@HYPER.COM From: acad.lvc.edu!l_wester@hyper.hyper.com (Lance M. Westerhoff) Subject: Inhibitor docking Cc: l_wester@uunet.ca Date: Mon, 11 Jul 1994 15:32:57 -0400 Greetings everyone. In the protein that we're working with we want to substitute inhibitors (example: 6-phosphogluconate) for the already present ribulose 1,5-bisphosphate. This concept is sometimes refered to as inhibitor docking. What would be the best way to perform these substitutions with HyperChem 4? Thanks, Lance ____________________ Lance M. Westerhoff Biochemistry Lebanon Valley College of Pennsylvania Phone: (717)867-6179 E-mail: L_WESTER@acad.lvc.edu LANCEW@aol.com ________________________________________________________________________ From ASCHICK@chemserver.chem.vt.edu Wed Jul 13 18:39:57 1994 From: "ALAN SCHICK" To: hyperchem@HYPER.COM Date: Wed, 13 Jul 1994 14:39:57 -0400 Subject: Constraining entire molecules I would like to get a feel for possible aggregation geometries of solutes in solution. Nominally, my approach is to start with two molecules (porphyrins in this case) having reasonable, but not necessarily optimized geometries and optimizing their relative orientations and positions to give an energy-minimized dimer structure. I would like to start with rigid monomers, but I don't see how to constrain an entire molecular geometry in Hyperchem. The molecules I'm studying are substituted tetraphenylporphyrins, so there are a lot of bond, angles, and torsions to have to constrain individually. Any suggestions? Currently, I'm using Release 3, but I would consider upgrading to either or both Release 4 and ChemPlus. Would these upgrades help in this case? Thanks. ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 hurst@hyper.hyper.com Wed Jul 13 21:01:54 1994 Date: Wed, 13 Jul 1994 17:01:54 -0400 From: hurst@hyper.hyper.com (Graham Hurst) To: "ALAN SCHICK" , hyperchem@HYPER.COM Subject: Re: Constraining entire molecules Alan Schick writes: > I would like to get a feel for possible aggregation geometries of > solutes in solution. Nominally, my approach is to start with two > molecules (porphyrins in this case) having reasonable, but not > necessarily optimized geometries and optimizing their relative > orientations and positions to give an energy-minimized dimer > structure. I would like to start with rigid monomers, but I don't > see how to constrain an entire molecular geometry in Hyperchem. The > molecules I'm studying are substituted tetraphenylporphyrins, so > there are a lot of bond, angles, and torsions to have to constrain > individually. Any suggestions? If you want to keep them rigid to remove degrees of freedom (and speed calculation) then adding restraining forces would not make sense anyway. The closest you can come with HyperChem is to select one molecule and not the other so that the unselected one is kept rigid. For semi- empirical calculations this has the probably undesired side effect of treating only the selected molecule quantum mechanically. > Currently, I'm using Release 3, but I would consider upgrading to > either or both Release 4 and ChemPlus. Would these upgrades > help in this case? If you're after faster calculations, you should upgrade, but there is nothing new in ChemPlus or HyperChem 4 with respect to rigid constraints. 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 BERGIN@chem.surrey.ac.uk Thu Jul 14 11:30:15 1994 To: hyperchem@HYPER.COM From: Paul Organization: Chemistry Department, Uni of Surrey Date: Thu, 14 Jul 1994 07:30:15 -0400 Subject: script file problems Dear All, I am writing to see if people have had any experiences in solving hyperchem script file problems. I am trying to do a conformational search on a number of compounds about two specific torsions. The script I have written runs fine for the first 130 iterations but then for some unknown reason comes up with the an Abort Script error - if you choose the no button on the abort script message it then comes up with "Unknown name for selection psi" (psi being the name of one of my selected torsions). Ignoring this message causes the message - "selection is inappropriate for set torsion" to appear, ignoring this message brings back to the initial abort message and the cycle of warnings appears again. I can't explain why this keeps occuring because it all works fine for the first 130 cycles. I have checked for typing errors - and have found none. Not surprising since the script was built up from cutting and pasting from the first 36 cycles which I know work. My script file is as follows calculation-method molecularmechanics molecular-mecanics-method MM+ optim-max-cycles 30000 optim-convergence 0.1 optim-algorithm NewtonRaphson start-logging c:\xyz.log no open-file c:\xyz.hin select-name psi set-bond-torsion 0 select-name phi set-bond-torsion 0 select-name mini do-optimization open-file c:\xyz.hin select-name psi set-bond-torsion 0 select name phi set-bond-torsion 10 select-name mini do-optimization etc etc......... psi & phi are the two torsions to be varied in the search mini is the complement selection when both psi & phi are selected. psi, phi & mini have been named in the file xyz.hin. so I am doing 10 degree rotations of phi from 0 to 180 and -170 to -10 (36 cycles) when psi is set to 0. then psi is set to 10 and phi is moved in 10 degree increments again. and so on. As I say this works fine for the first 130 cycles, but then breaks down, all I am asking is has anyone else found this problem before and how did they solve it? Thanks in advance for any help Paul Bergin ________________________________________________________________________ From hurst@hyper.hyper.com Thu Jul 14 18:17:33 1994 Date: Thu, 14 Jul 1994 14:17:33 -0400 From: hurst@hyper.hyper.com (Graham Hurst) To: l_wester@acad.lvc.edu (Lance M. Westerhoff), hyperchem@HYPER.COM Subject: Re: Inhibitor docking Hi Lance and HyperChemists, > Greetings everyone. In the protein that we're working with we want to > substitute inhibitors (example: 6-phosphogluconate) for the already present > ribulose 1,5-bisphosphate. This concept is sometimes refered to as > inhibitor docking. What would be the best way to perform these > substitutions with HyperChem 4? > > Thanks, > > Lance > ____________________ > Lance M. Westerhoff > Biochemistry > Lebanon Valley College of Pennsylvania > Phone: (717)867-6179 > E-mail: L_WESTER@acad.lvc.edu > LANCEW@aol.com I'm not sure what the "best" way is, but here are some suggestions that I hope are useful. I assume that for your substitution you want to place the new inhibitor in the same place as the old one. You can do this by using the draw tool to make the minimum changes needed to change the old inhibitor to the new inhibitor. You can then select only the changed parts and model build (the unselected atoms will keep the same coordinates). If you are interested in semi-empirical calculations you could then start modelling. For molecular mechanics simulations you would first need to set the atom types and partial charges of the new inhibitor (you don't need charges for MM+ if you are using bond dipoles for non-bonded electrostatics). The types can be set by selecting the inhibitor and using Build/Calculate Types (checking that none are ** unless you are using MM+). The charges are trickier - you could enter "standard" values manually if have them, select the inhibitor and use ChemPlus QSAR Properties to calculate partial charges, or isolate the inhibitor and use a semi-empirical calculation. A feature that you might wish to use, particularly to "isolate the inhibitor" for charge calculations, is File/Merge once you have set it to not translate the merged-in molecule. By default, File/Merge and Edit/Paste translate the added part (in the viewer's X direction) so that it does not overlap with the current system. You can turn off this behaviour via a HyperChem script command. Perhaps the simplest way to do this is to use Script/Open Script to read in a text file that consists of the script command: translate-merged-systems no If you always want this behaviour, put this command in a CHEM.SCR file (in your ChemIniPath) so that the command is executed whenever you start HyperChem. Once you have turned off translate-merged-systems, you can save, delete and merge to work with parts of the system independently without losing relative position information. For instance, to get charges after model building the changed portions of the inhibitor, you could: 1. Save the total system, eg. as both.hin. 2. Select and cut (via Edit/Cut) the inhibitor, then save as protein.hin. 3. Use Edit/Paste, Select/Complement Selection, Edit/Delete and then save as inhibit.hin. 4. Now use a semi-empirical calculation (single point or optimization) to calculate charges (and perhaps a better geometry). 5. It's probably a good idea to save, perhaps overwriting inhibit.hin. 6. Use File/Merge to read protein.hin and save, perhaps overwriting both.hin. Now you should have a reasonable starting point for molecular mechanics calculations of the new inhibitor and the protein. When you don't already have an inhibitor or substrate to replace, HyperChem allows two methods of "docking" a small molecule (substrate) onto a larger molecule (receptor). These are manual docking, and restrained energy minimization. Manual docking is carried out purely through moving molecules around on the screen: no actual simulation is carried out. Any "docked" structure obtained in this way should then be optimized to remove bad contacts and other unrealistic aspects of the structure. Restrained minimization requires a docking hypothesis (atom A on the substrate is assumed to be close to atom B on the receptor) which is incorporated into a simulation using restraints. A combination of dynamics and optimization subject to these restraints allows you to force proximity of substrate and receptor atoms. After restrained optimizition you can turn off the restraints and use further optimization and dynamics to test the docking hypothesis. If you select only the substrate to freeze the receptor, you may prefer to use one-atom restraints to tether substrate atoms to points in space that you define to be in your proposed docking site. 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 Thu Jul 14 18:24:37 1994 Date: Thu, 14 Jul 1994 14:24:37 -0400 From: hurst@hyper.hyper.com (Graham Hurst) To: hyperchem@HYPER.COM Subject: How to get off this list Just a reminder (to stem the tide of "Please unsubscribe me" messages) - to unsubscribe send a message with the body unsubscribe hyperchem to hyperchem-request@hyper.com Please don't send it to hyperchem@hyper.com! 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 Thu Jul 14 20:05:03 1994 Date: Thu, 14 Jul 1994 16:05:03 -0400 From: hurst@hyper.hyper.com (Graham Hurst) To: Paul , hyperchem@HYPER.COM Subject: Re: script file problems Hi Paul , You wrote: > I am writing to see if people have had any experiences in > solving hyperchem script file problems. I am trying to do a > conformational search on a number of compounds about two specific > torsions. The script I have written runs fine for the first 130 iterations > but then for some unknown reason comes up with the an Abort Script > error [further description deleted for brevity] I'll try rebuilding your script to see if I can reproduce the results (thanks for not posting the whole script to the group, but you could have sent the whole script and HIN file to support@hyper.com). For conformational searches with HyperChem you might want to get ChemPlus. I've written an Excel macro for stepping through two torsion angles, with optional restrained optimization, which records the energies in a spreadsheet and plots a 3D potential surface at the end. It can optionally save the lowest energy structure found to a file. I've also written an add-on program that randomly varies an unlimited number of torsions and optimizes, saving unique low-energy conformers that can be loaded into HyperChem from a spreadsheet showing energies, dihedral angles, and search statistics. These are both included with ChemPlus (the Excel macro comes with source that you can modify). Both of those ChemPlus modules can do thousands of repetitions of selecting torsions, varying them and optimizing without problems, so I'm puzzled by the problem you are experiencing (I assume that your typing check looked for non-printing characters). Your inner loop is: > open-file c:\xyz.hin > select-name psi > set-bond-torsion 0 > select-name phi > set-bond-torsion 0 > select-name mini > do-optimization One thing different from my inner loops is that you are always re-reading your file. The Excel macro just uses the last structure found (which is already in the HyperChem workspace) and the Conformational Search module uses previous conformations from memory. Another thing different is that you are freezing the 5-8 atoms in the two torsions. This will constrain bond lengths and angles as well as the two torsion angles. The Excel macro uses restraints during optimization followed by a unrestrained single point (with optional resetting of the dihedral angles to the precise values). I'll get back to you after I've had a chance to re-generate and run your script. It would help if you could email the full script and HIN file to support@hyper.com. 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 Mon Jul 18 17:32:24 1994 Date: Mon, 18 Jul 1994 13:32:24 -0400 From: hurst@hyper.hyper.com (Graham Hurst) To: Paul , hyperchem@HYPER.COM Subject: Re: script file problems Hi Paul, > From: Paul > Date: Thu, 14 Jul 1994 07:30:15 -0400 > > Dear All, > > I am writing to see if people have had any experiences in > solving hyperchem script file problems. I am trying to do a > conformational search on a number of compounds about two specific > torsions. The script I have written runs fine for the first 130 iterations > but then for some unknown reason comes up with the an Abort Script > error - if you choose the no button on the abort script message it then > comes up with "Unknown name for selection psi" (psi being the name > of one of my selected torsions). Ignoring this message causes the > message - "selection is inappropriate for set torsion" to appear, > ignoring this message brings back to the initial abort message and > the cycle of warnings appears again. I can't explain why this keeps > occuring because it all works fine for the first 130 cycles. I have > checked for typing errors - and have found none. Not surprising since > the script was built up from cutting and pasting from the first 36 > cycles which I know work. I've rebuilt a version of your script and run 200 cycles without problems, so I assume that you have some typo that you haven't found yet. I also found some typos in what you emailed, and have also annotated some comments below that you might find helpful. > My script file is as follows > > calculation-method molecularmechanics > molecular-mecanics-method MM+ ^^^^^^^^ mechanics This HSV is set from a HIN file when you open it, so it serves no purpose here. > optim-max-cycles 30000 I think that this is also reset when you open a file. > optim-convergence 0.1 > optim-algorithm NewtonRaphson > start-logging c:\xyz.log no > > open-file c:\xyz.hin > select-name psi > set-bond-torsion 0 > select-name phi > set-bond-torsion 0 This will only work if multiple selections is turned off. > select-name mini > do-optimization > open-file c:\xyz.hin > select-name psi > set-bond-torsion 0 > select name phi ^^^^^^^^^^^ select-name (was missing the hyphen) > set-bond-torsion 10 > select-name mini > do-optimization > > etc etc......... > > psi & phi are the two torsions to be varied in the search > mini is the complement selection when both psi & phi are selected. > psi, phi & mini have been named in the file xyz.hin. If you still think there is a problem, please email the script and HIN file to support@hyper.com. 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 willsd@zardoz.chem.appstate.edu Tue Jul 19 14:34:10 1994 From: zardoz.chem.appstate.edu!willsd@hyper.hyper.com (Stephen D. Williams) Subject: annotation of chemplus To: hyperchem@HYPER.COM Date: Tue, 19 Jul 1994 10:34:10 -0400 I am interested in enhancing images produced by the molecule presentation module in chemplus. I'd like to be able to add labels to atoms, add an arrow and label to an MO isosurface, and similar sorts of things. I have found that when I paste such an image into the windows paintbrush program I can add any sort of annotations that I want, but the image file (in the .bmp format) that paintbrush saves is awful: most things turn completely black, shading vanishes.... I have another image manipulation program that reads and writes many kinds of image FILES, but it ignores the windows clipboard so I can't paste from chemplus into it. Has anyone out there in the ether had success with chemplus image manipulation? If so, what other programs did you use? BTW: I have the recently upgraded version of chemplus, usually use a 1024x768 256 color screen driver, and have no unusual windows programs. ********************************************************************* Steve Williams F F F Chemistry \ / \ / Appalachian State University Al Al Boone, NC 28608 / \ / \ USA F F F ________________________________________________________________________ From hurst@hyper.hyper.com Tue Jul 19 21:09:15 1994 Date: Tue, 19 Jul 1994 17:09:15 -0400 From: hurst@hyper.hyper.com (Graham Hurst) To: willsd@zardoz.chem.appstate.edu (Stephen D. Williams), hyperchem@HYPER.COM Subject: Re: annotation of chemplus Hi Steve, > I am interested in enhancing images produced by the molecule > presentation module in chemplus. I'd like to be able to add > labels to atoms, add an arrow and label to an MO isosurface, > and similar sorts of things. I have found that when I paste > such an image into the windows paintbrush program I can add > any sort of annotations that I want, but the image file (in > the .bmp format) that paintbrush saves is awful: most things > turn completely black, shading vanishes.... I have another > image manipulation program that reads and writes many kinds > of image FILES, but it ignores the windows clipboard so I can't > paste from chemplus into it. Has anyone out there in the ether > had success with chemplus image manipulation? If so, what > other programs did you use? 'Paint' programs deal with bitmaps - you need a 'drawing" program to deal with resolution-independent metafiles (sometimes called 'pictures' or 'drawings' as opposed to 'bitmaps'). We've had good success with Corel Draw 3 and 4 (haven't tried 5 yet). Some users have had good results with Lotus Freelance Graphics. Many word processors now have bundled drawing programs (at least Word and WordPerfect do - I'm not sure about Ami Pro), but the complexity of ChemPlus metafiles may be more than they can handle. I know that we've found mixed success with MS-Draw (bundled with Word) - it wouldn't work until we pasted into Write and then copied from there! Anyone else care to share their experiences? 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 ASCHICK@chemserver.chem.vt.edu Thu Jul 21 16:25:49 1994 From: "ALAN SCHICK" To: hyperchem@HYPER.COM Date: Thu, 21 Jul 1994 12:25:49 -0400 Subject: Aligning transition moments I am working with a porphyrin dication molecule -- planar D4h structure -- and am wanting to do some UV spectra calculations. The ZINDO/S seems to work ok, but I'm having trouble analyzing the results because the transition moment orientations within the molecules are not easily interpreted. I see three "Transition Dipole Components" listed in the .LOG file, which I presume are the x, y, and z components. For the porphyrin, the standard way of looking at the structure is such that the atoms all lie in the xy plane. The two lowest-lying singlet transitions are degenerate, so nominally one would want to see one transition with a non-zero component only along x and the other only along y. Yet my .LOG files have non-zero values for all three components. I can calculate that, in fact, the transition moments for a degenerate pair are orthogonal, but I am going to be changing the molecular structure slightly and wish to track how the moment orientations change. It seems as though the cartesian coordinates of the actual atoms dictates the printed moment orientations because I've tried to align the molecule in the x,y plane, and although I can't seem to get it aligned, I do change the atomic coordinates, which does change the logged values of the transition moment components. So my question is...how can I get the molecule aligned so that the degenerate transition moments print out as being along x and y? Actually, if I could just get them in the xy plane, that would help, but then I need to know how the components are oriented within the molecular structure. I've tried to align the molecule so that certain atoms lie along the x and y axes, but I have been unable to find the correct sequence of alignments and translations to be able to do this. I am currently using Release 3. Release 4 is already on order. ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 mcaffery@keller.clarke.edu Fri Jul 22 16:05:31 1994 Date: Fri, 22 Jul 1994 12:05:31 -0400 From: "S. Mary Lou Caffery" Subject: VDW parameters To: hyperchem@HYPER.COM I am using release 4 of Hyperchem. What is the relationship between the parameters in mmpnbd.txt and those shown in the "Computational Chemistry" manual(Ver 4) page 185-186. The manual show some that are not in the parameter set and the parameter set shows differences - Mg for example Parameter set RSTAR = 2.2000 and EPS = 0.15 chart(p 186) 2r* = 3.46 and eps is not given so default = 0.1 I am interested in developing such parameters for other alkali and alkaline earth metals but this is very confusing! ________________________________________________________________________ From imcvey@capricorn.kent.edu Fri Jul 22 16:08:13 1994 From: capricorn.kent.edu!imcvey@hyper.hyper.com id AA09853; Fri, 22 Jul 1994 12:08:13 -0400 Date: Fri, 22 Jul 1994 12:08:13 -0400 To: hyperchem@HYPER.COM Subject: Constraining central atoms Cc: mcundik@kentvms.kent.edu Greetings all A friend of mine is working with dithiocarbamate complexes of cobalt. The complexes are octahedral and the ligands are bidentate. We thought it would be interesting to see what zindo/am1/pm3 produced as the structure of the complexes. Since there is data on the positions of the CO and S atoms bonded to the central atom we want to fix the location of these atoms and simply minimze the geometry of the remaining parts of the ligands. I know there have been a lot of similar questions, but when tose answers were posted I didn't know I'd be interested in using them. Such is life. Any sugestions will be greatly appreciated. Thank in advance Iain McVey IMCVEY@SCORPIO.KENT.EDU ________________________________________________________________________ From hurst@hyper.hyper.com Mon Jul 25 15:23:03 1994 Date: Mon, 25 Jul 1994 11:23:03 -0400 From: hurst@hyper.hyper.com (Graham Hurst) To: "S. Mary Lou Caffery" , hyperchem@HYPER.COM Subject: Re: VDW parameters Hi Mary Lou, > I am using release 4 of Hyperchem. What is the relationship between the > parameters in mmpnbd.txt and those shown in the "Computational Chemistry" > manual(Ver 4) page 185-186. The manual show some that are not in the > parameter set and the parameter set shows differences - Mg for example > Parameter set RSTAR = 2.2000 and EPS = 0.15 > chart(p 186) 2r* = 3.46 and eps is not given so default = 0.1 > I am interested in developing such parameters for other alkali and > alkaline earth metals but this is very confusing! The values listed on pp 185-6 in the Comp Chem manual are for the *default scheme*, and are only used when values cannot be found from mmpnbd.txt. (See the description starting on p 177 for more details.) Thus if your magnesium has been defined to have the MM+ type "Mg", then the values from mmpnbd.txt will be used. If your magnesium has an atom type that does not appear in mmpnbd.txt, such as "**", then the values from p 186 are used. Saving a log file from an MM+ single point will show you the values of parameters used (setting MechanicsPrintLevel greater than 5 in CHEM.INI will show all the details of the assignment of default parameters). As far as the inconsistency for Mg, it is due to two different sources for the parameters (the references for default parms are given on p 186). Lou Allinger has a note (unplished as far as I know) called "Brief Guidelines for Obtaining Parameters for the MM2 System" that you might want to ask him for (he's at the U of Georgia). Kenny Lipkowitz wrote an excellent Brief Communication entitled "MM2 Parameters" in the Feb 1992 QCPE Bulletin (volume 12, number 1) that lists many sources for MM2 parameters. 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 J_RABER@ACAD.LVC.EDU Mon Jul 25 17:57:27 1994 Date: Mon, 25 Jul 1994 13:57:27 -0400 From: ACAD.LVC.EDU!J_RABER@hyper.hyper.com To: hyperchem@HYPER.COM Subject: Neighbour error Hello everybody, I am currently trying to induce a new inhibitor into the active site of the RuBisCo protein. I have "docked" the new inhibitor by using a translate statement to the coordinates of the old inhibitor. Everything looked good and it saved properly. When I selected the new inhibitor, the charge was even correct on it. I run into a problem when I try to open up the file after I have saved it. All of these files were saved and loaded as .ent files. When the file reaches the point of reading the connectivity statements, I get the error: Hyperchem does not handle atoms with greater than 12 neighbours. I then have to hit the return button numerous times before I can cancel the current operation. The reason this is such a problem is that I would prefer to be able to do all of my calculations through a script file. Thanks for all of your help, Jeffrey Raber BioChemistry Major Lebanon Valley College Annville, PA E-Mail J_RABER@ACAD.LVC.EDU ________________________________________________________________________ From hurst@hyper.hyper.com Wed Jul 27 13:58:13 1994 Date: Wed, 27 Jul 1994 09:58:13 -0400 From: hurst@hyper.hyper.com (Graham Hurst) To: imcvey@capricorn.kent.edu Subject: Re: Constraining central atoms Cc: hyperchem@HYPER.COM Hi Iain, > A friend of mine is working with dithiocarbamate complexes of cobalt. > The complexes are octahedral and the ligands are bidentate. We thought > it would be interesting to see what zindo/am1/pm3 produced as the > structure of the complexes. Since there is data on the positions of > the CO and S atoms bonded to the central atom we want to fix the location > of these atoms and simply minimze the geometry of the remaining parts of > the ligands. > > I know there have been a lot of similar questions, but when tose > answers were posted I didn't know I'd be interested in using them. Such > is life. > > Any sugestions will be greatly appreciated. > > Thank in advance > Iain McVey > IMCVEY@SCORPIO.KENT.EDU You can select the ligands to freeze the rest of the system. For semi-empirical calculations with HyperChem this will also have the effect of treating only the selected atoms quantum mechanically, with unselected atoms treated as charges. See the "Mixed Quantum/Classical Model" section of the HyperChem Computational Chemisty manual (starting on p. 215 for the Release 4 version) for further details and considerations. You can also use restraining forces to maintain internal coordinates, but these are not rigid and thus do not reduce the degrees of freedom for geometry optimization. See pp 201-205 of the Relase 4 Reference manual for details on restraints. For the calculations that you propose there are some problems. Neither AM1 nor PM3 can treat transition metals, ZINDO/S is unsuitable for geometry optimization, and ZINDO/1 often does not do a good job for first row transition metals! This isn't a problem specific to HyperChem, rather it is a reflection of established semi-empirical methodology. There is research going on to develop improved semi-empirical methods for transition metals, and as these methods become published and accepted by the community we will consider adding them to HyperChem. 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 imcvey@gemini.kent.edu Wed Jul 27 23:20:52 1994 From: gemini.kent.edu!imcvey@hyper.hyper.com Subject: Animating MOPAC FORCE results with hyperchem To: hyperchem@HYPER.COM Date: Wed, 27 Jul 1994 19:20:52 -0400 Hello All I am doing some work on larger molecules, and so I am using MOPAC on another machine, and since I am interested in the vibrational spectra of the systems I am studying I would like to animate the minimized systems using the MOPAC generated force matrix. I would like to use Hyperchem for this since I am already familiar with the software, and there is online suport etc.... Is there some way to construct a script to acheive this? Thanks in Advance Iain IMCVEY@SCORPIO.KENT.EDU ________________________________________________________________________ From hurst@hyper.hyper.com Thu Jul 28 19:17:33 1994 Date: Thu, 28 Jul 1994 15:17:33 -0400 From: hurst@hyper.hyper.com (Graham Hurst) To: David Gill Subject: Re: Cc: hyperchem@HYPER.COM Hi Zelig, > Date: Thu, 28 Jul 1994 03:44:00 -0400 > From: David Gill > >From : Zelig Chernia c/o David Gill > Dept. of Physics, Ben Gurion Univ. Be'er Sheva, Israel > > Dear Graham, > I have a beginner's question. During the execution of : > = EXECUTE (Channel,"[Calculation-method molecular mechanics]") in > EXCEL Macro, the hyperchem asks if I would like to keep the current > changes. Is there a simple way to answer YES ? ? ! ! Or, perhaps, to > make the Hyperchem stop asking this question and take the YES answer as > default ? This isn't a beginner's question! You have found something we overlooked. When we added the script/DDE interface to HyperChem we had to come up with non-interactive alternatives to everything you could do with the GUI that invoked a dialog box. Since you don't always get this message we missed providing a direct way to avoid it! I've added it to our bug list. One only gets this message when a system has residues with charges that don't match the template charges for that residue, so HyperChem doesn't know which charges you want to use. Possible ways to avoid it are: 1. Make the residues "dirty" somehow. This means changing the elements or bonding to no longer match the template, or change the template to not match the residue. Adding then deleting an atom or lone pair seems to leave the residue dirty (i.e. the residue label has an asterisk). 2. Delete or change the name of the residue template in the template files. 3. Don't change the charges from the standard values, or restore the standard values before changing to molecular mechanics. > Very truly yours Zelig Chernia > > P.S. Kindly distribute Q&A among Hyperchem subscribers. Okay, I've cc'ed it to the list. 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 J_RABER@ACAD.LVC.EDU Sat Jul 30 00:02:23 1994 Date: Fri, 29 Jul 1994 20:02:23 -0400 From: ACAD.LVC.EDU!J_RABER@hyper.hyper.com To: hyperchem@HYPER.COM Cc: J_RABER@ACAD.LVC.EDU Subject: Charges and Force Fields Hello Everyone, I am using a script file to load in hin files, and I am running into a problem. The problem is that I want to run a single point calculation, but I can't do it under the MM+ force field because I don't have enough memory. I tried using the command "molecular-mechanics-method amber" but it asks me if I want to keep the current atom charges or change them. This deffeats the purpose os a script file because it won't be fully automated like I would hope it to be. Is there any way of changing the text file that would allow me to get around this? Thanks for all of your help in advance, Jeffrey Raber BioChemistry Major Lebanon Valley College Annville, PA E-Mail: J_RABER@ACAD.LVC.EDU