From owner-hyperchem@hyper.com Fri Nov 1 18:06:58 1996 Date: Fri, 1 Nov 1996 11:26:07 -0900 (AKST) From: KELLER JOHN W To: Joel Polowin Cc: Michael Neuber , hyperchem@hyper.com Subject: Other solvents possible? Hi Joel, Perhaps others have wondered whether one can use other solvents for periodic box calculations. HyperChem is set up to do water solvent automatically, but of course if you wanted to say solvate a lithium enolate ion pair water would not be an appropriate solvent. Perhaps dimethyl ether could be substituted to make a reasonable solvent for this species. (This can be done in Sybyl.) Thanks, John Keller _______________________________________________________________________________ From owner-hyperchem@hyper.com Fri Nov 1 18:34:22 1996 Date: Fri, 1 Nov 96 16:47:46 -0500 From: polowin (Joel Polowin) To: hyperchem@hyper.com Subject: Re: Other solvents possible? > Date: Fri, 1 Nov 1996 11:26:07 -0900 (AKST) > From: KELLER JOHN W > > Perhaps others have wondered whether one can use other solvents for > periodic box calculations. HyperChem is set up to do water solvent > automatically, but of course if you wanted to say solvate a lithium > enolate ion pair water would not be an appropriate solvent. Perhaps > dimethyl ether could be substituted to make a reasonable solvent for this > species. (This can be done in Sybyl.) There is no intrinsic way of doing it, no way of getting HyperChem to automatically set up a solvent box with anything but water. What you would need to do is to set up a periodic box of the appropriate size, add the number of solvent molecules appropriate to the size, temperature, solvent density, etc., do something to randomize the molecular orientations (especially with large molecules -- for example, use a macro to rotate each molecule randomly about each axis), and then do optimization and/or dyamics to equilibrate the system. Then you could save that for repeated later use. Then you load up the solvent box that you want, and merge in the solute structure -- probably after deleting a couple of solvent molecules to make room. I have got a brief description on file of how to calculate the proper number of molecules, if anyone wants it. I have had an entry on our development wish list for some time now for some way of automating this stuff -- if we cannot make the system more flexible to allow HyperChem to read something other than the water-box files, we should have some kind of add-on module that would generate periodic boxes with other solvents. If anyone would care to write it, we would be happy to put it on our WWW site... Regards, Joel ------------ Joel Polowin, Ph.D. Manager, Scientific Support Email to: polowin@hyper.com Hypercube Inc, 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 WWW: http://www.hyper.com/ _______________________________________________________________________________ From owner-hyperchem@hyper.com Mon Nov 4 17:23:09 1996 Date: Mon, 4 Nov 96 15:05:28 -0500 From: polowin (Joel Polowin) To: Jose Gonzalez de la Campa , hyperchem@hyper.com Subject: HyperChem direct SCF > Date: Mon, 4 Nov 1996 09:28:23 +0100 (MET) > From: Jose Gonzalez de la Campa > >> The work-around is to specify a small buffer size -- say, 100 words -- if >> one is doing a direct SCF calculation. We will probably do a patch for >> GAUSS.EXE to correct this problem after HyperChem 5 for NT has been >> completed. (HyperChem 5 for Windows 95 went for manufacturing last week, >> and it should be starting to ship in another week or so.) > > We have made several calculations on water, in a Silicon Graphics Indigo > 2, using Hyperchem, version 4.5. > When we use STO-3G we obtain the same results that George Mei obtained in > the case of H3O+. However, when other basis sets are used we obtain the > same values for direct and non direct SCF calculations. We have tried > 3-21G, 6-31G* and 6-31G** and all of them seem to give correct values. > Then, the question is: > Is the bug you are comenting only in the Windows version of Hyperchem?0 > Does it appear only when you use STO-3G? The bug should be in all versions of HyperChem that do _ab initio_ calculations. The effect of the basis set is that the smaller basis sets would have smaller storage requirements, and therefore would be within the buffer size limits; the larger basis sets require more storage. The storage requirement is 16 bytes (two double-precision words) per integral, and the number of integrals is (m^4 + 2m^3 + 3m^2 + 2m)/8 where m is the number of basis functions. Basis set # basis functions # words storage STO-3G 8 1332 3-21G 15 14520 6-31G* 21 53592 6-31G** 30 216690 So if you use the default buffer size of 3200 words, the integrals for STO-3G will be smaller than the buffer size, and the integrals for the other basis sets will be larger. Joel ------------ Joel Polowin, Ph.D. Manager, Scientific Support Email to: polowin@hyper.com WWW: http://www.hyper.com/ Hypercube Inc, 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" (or "unsubscribe hyperchem") to hyperchem-request@hyper.com; please do not send such administrative messages to the group itself. _______________________________________________________________________________ From owner-hyperchem@hyper.com Tue Nov 5 12:42:46 1996 Sender: neuber@exp.bessy.de Date: Tue, 05 Nov 1996 15:14:05 MET From: Michael Neuber To: hyperchem@hyper.com Subject: pi-pi-interaction ? Dear all, in "Semiempirical Molecular Orbital Methods" (Rev.Comp.Chem. 2(1990)pp 45-81) J.J.P. Stewart describes 'strong and weak points of NDDO semiempirical methods'. What I am interested in is whether there is any further reference regarding the value of semiempiric methods (AM1, PM3, also ZINDO-1) especially for the description of intermolecular pi-pi interaction of aromatic molecules. I would appreciate any hint on reported results or experience with that, will summarize if it seems appropriate. Greetings Michael Neuber @ Berlin _______________________________________________________________________________ From owner-hyperchem@hyper.com Mon Nov 11 14:06:16 1996 Date: Mon, 11 Nov 1996 10:11:59 -0500 X-Sender: txd6@email.psu.edu To: hyperchem@hyper.com From: txd6@psu.edu (Tim Dunbar) Subject: *.hin format to z-matrix Hi, I am using Hyperchem to check and display the output from Gaussian 94 ab intio calculations. I would like to know two things: 1) Is it possible to have Hyperchem output in a z-matirx format suitable for use in Gaussian 94? 2) Is it possible to import Gaussian 94 x,y,z output into Hyperchem? (the format is atom number, Z number of atom, x position, y position, z position) Thanks, Tim Dunbar Tim Dunbar Chemistry Department, 230 Innovation Blvd., Materials Research Institute, Room 110 phone: (814) 865-0149 home phone: 234-9625 fax: (814) 863-0618 e-mail: txd6@psu.edu _______________________________________________________________________________ From owner-hyperchem@hyper.com Mon Nov 11 21:27:38 1996 From: "Udo Haberl" To: hyperchem@hyper.com Date: Tue, 11 Nov 1996 18:04:58 GMT+1 Subject: script errors in hyperchem 4.5 ? Reply-To: haberl@uni-bonn.de Hello, I have a problem with some scripts. They were written for hyperchem 3.0, but when I want to run them under hyperchem 4.5, some of the script commands, for example "select-none", cause error messages like "unknown script command". What is wrong? Udo Haberl ---------------------------------------------------------------------- Dipl.-Chem. Udo Haberl Institut fuer Organische Chemie und Biochemie der Universitaet Bonn Gerhard-Domagk-Str. 1 D-53121 Bonn Germany e-mail: haberl@uni-bonn.de ---------------------------------------------------------------------- _______________________________________________________________________________ From owner-hyperchem@hyper.com Mon Nov 11 22:21:34 1996 Date: Tue, 12 Nov 1996 10:10:54 +1000 From: Tony Hughes Subject: SoftWindows and HyperChem To: HyperChem user group Subject: Time: 9:51 AM OFFICE MEMO SoftWindows and HyperChem Date: 12/11/96 Dear HyperChem Users, We are planning to purchase copies of HyperChem Lite for use in an undergraduate course on drug design. Before we go out and purchase a bunch of PCs, we'd be interested to know if anyone has ever tried running HyperChem Lite on a Mac under SoftWindows? Cheers, Tony Hughes Department of Pharmacology University of Melbourne _______________________________________________________________________________ From owner-hyperchem@hyper.com Tue Nov 12 16:06:48 1996 Date: Tue, 12 Nov 96 11:32:25 -0500 From: polowin (Joel Polowin) To: txd6@psu.edu (Tim Dunbar), hyperchem@hyper.com Subject: Re: *.hin format to z-matrix > Date: Mon, 11 Nov 1996 10:11:59 -0500 > From: txd6@psu.edu (Tim Dunbar) > > I am using Hyperchem to check and display the output from Gaussian 94 ab > intio calculations. I would like to know two things: > 1) Is it possible to have Hyperchem output in a z-matirx format suitable > for use in Gaussian 94? I do not know which formats Gaussian can read, but you can check them against the list of formats that HyperChem can write. HyperChem's output is in the MOPAC Z-matrix format, which is not the same as the Gaussian Z-Matrix format. You may be able to convert using other software, such as BABEL (finger babel@mercury.aichem.arizona.edu, or send E-mail to that address); BABEL's output of HIN and PDB files is not formatted quite correctly, but it might do better with Gaussian Z-matrix. > 2) Is it possible to import Gaussian 94 x,y,z output into Hyperchem? (the > format is atom number, Z number of atom, x position, y position, z position) If you can change this into lines with the element symbol and the coordinates, you can use the "XRAY2HIN" utility on our WWW page and ftp site to convert the data into a (simple) HIN file. The utility is in our Software Archive under "Other software"; by ftp, go to ftp.hyper.com, /pub/other/xray2hin.exe . Again, something like BABEL may be able to convert the format. Joel ------------ Joel Polowin, Ph.D. Manager, Scientific Support Email to: polowin@hyper.com WWW: http://www.hyper.com/ Hypercube Inc, 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" (or "unsubscribe hyperchem") to hyperchem-request@hyper.com; please do not send such administrative messages to the group itself. _______________________________________________________________________________ From owner-hyperchem@hyper.com Tue Nov 12 16:29:26 1996 Date: Tue, 12 Nov 96 11:48:23 -0500 From: polowin (Joel Polowin) To: hyperchem@hyper.com, haberl@uni-bonn.de Subject: Re: script errors in hyperchem 4.5 ? > From: "Udo Haberl" > Date: Tue, 11 Nov 1996 18:04:58 GMT+1 > > I have a problem with some scripts. They were written for hyperchem > 3.0, but when I want to run them under hyperchem 4.5, some of the > script commands, for example "select-none", cause error messages like > "unknown script command". What is wrong? A few of the script commands were renamed between versions, but that is not one of them. In general, all of the script commands from older versions should still be valid in the new versions. The best way to check, of course, is to look in the list of scripts in the _Reference_ manual (chapter 10). The most likely cause of trouble in this case is because of a change to Windows 95 or Windows NT 4. With Windows 95, it is necessary to have the "Regional Settings" set to "English (United States)"; with Windows NT 4, it is necessary to set the "Default Locale" to "US". It doesn't make sense; it's a Microsoft thing. With the wrong settings, our software is not able to properly understand a text string that it reads from a file (or receives through the DDE interface to other software). The problem does not seem to occur with HyperChem release 5. Joel ------------ Joel Polowin, Ph.D. Manager, Scientific Support Email to: polowin@hyper.com WWW: http://www.hyper.com/ Hypercube Inc, 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" (or "unsubscribe hyperchem") to hyperchem-request@hyper.com; please do not send such administrative messages to the group itself. _______________________________________________________________________________ From owner-hyperchem@hyper.com Tue Nov 12 19:18:07 1996 Date: Tue, 12 Nov 1996 13:37:46 -0800 X-Sender: lavelle@ewald.mbi.ucla.edu To: hyperchem@hyper.com From: lavelle@ewald.mbi.ucla.edu (Laurence Lavelle) Subject: Deleted atoms reappear. I am using HC 4 and Windows 95. Using the nucleic acid database I make a 10-mer and delete the terminal phosphate groups. I then add a H atom to each terminal oxygen so that the sugars of this DNA duplex have terminal OH groups. This file is saved and closed. When this file is opened the terminal phosphates are present!!! I have closed HC and started over with the same result. I have also done a power down reboot and I get the same result. Anybody know whats going on? Your help would be appreciated. Thanks Laurence Lavelle """"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" Laurence Lavelle, Ph.D. University of California Los Angeles Molecular Biology Institute Los Angeles, CA90095-1570, USA Email:LAVELLE@MBI.UCLA.EDU Phone:(310)206-8270 Fax:(310)825-0982 http://www.mbi.ucla.edu/people/lavelle/lavelle.html """"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" _______________________________________________________________________________ From owner-hyperchem@hyper.com Wed Nov 13 01:02:00 1996 Date: Tue, 12 Nov 96 21:37:56 -0500 From: polowin (Joel Polowin) To: lavelle@ewald.mbi.ucla.edu (Laurence Lavelle), hyperchem@hyper.com Subject: Re: Deleted atoms reappear. > Date: Tue, 12 Nov 1996 13:37:46 -0800 > From: lavelle@ewald.mbi.ucla.edu (Laurence Lavelle) > > I am using HC 4 and Windows 95. Using the nucleic acid database I make a > 10-mer and delete the terminal phosphate groups. I then add a H atom to each > terminal oxygen so that the sugars of this DNA duplex have terminal OH groups. > > This file is saved and closed. > > When this file is opened the terminal phosphates are present!!! The problem is that the file as saved -- in a HIN or PDB format, I assume -- contains information about the nucleotide residues. When the file is read in again, HyperChem matches each residue against the matching residue in the template database. (This allows it to connect atoms correctly, add missing H atoms, etc., if these data are omitted from the file.) And, knowing that the terminal phosphates *should* be present in the standard residues, it adds them, according to the templates. We should make this residue checking optional, rather than compulsory, for file reading; I've added that to the development wishlist. For now, there are a couple of possible work-arounds. One would be to omit all residue information, if you do not need it, by saving the file in one of the other file formats (MOL, for example) and reading it back in. Another would be to edit the HIN file to remove the "res" and "endres" lines for the terminal groups (making them no longer residues and no longer requiring checking against the templates), and to renumber the remaining residues. A third would be to add new residues to your templates which lack the phosphate groups, and change the terminal residues to the new residue types. Joel ------------ Joel Polowin, Ph.D. Manager, Scientific Support Email to: polowin@hyper.com WWW: http://www.hyper.com/ Hypercube Inc, 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" (or "unsubscribe hyperchem") to hyperchem-request@hyper.com; please do not send such administrative messages to the group itself. _______________________________________________________________________________ From owner-hyperchem@hyper.com Wed Nov 13 12:05:43 1996 Date: Wed, 13 Nov 1996 11:19:05 +0000 To: hyperchem@hyper.com From: Peter Jackson Reply-To: Peter Jackson Subject: Network installation of Hyperchem Help!! Out network administrator has installed hyperchem on our LAN (to save disk space on PCs etc) onto a write protected drive. When trying to carry out single point geometry optimisations I receive error messages stating that the parameter files cannot be accessed. I have checked that these parameter files are on the correct network path, which they are. Could the problem be that hyperchem needs write access to this parameter files?? Thanks -- Peter Jackson _______________________________________________________________________________ From owner-hyperchem@hyper.com Wed Nov 13 12:12:45 1996 From: Stormbom Lars LES To: "hyperchem@hyper.com" Subject: RE:hin-format to z-matrix Date: Wed, 13 Nov 1996 08:39:00 +0200 I do this all the time: 1.Build/initial optimization in Hyperchem. 2.Save the file in pdb-format in hyperchem 3.read the pdb-file into gaussian by the newZmat utility. 4.be sure to specify a checkpoint file in the gaussian job (%CHK='your file name') 5.Run your job. 6.Convert the optimized structure from the checkpoint file to pdb-format, again using the newZmat-utility. 7.Rejoice! you can now read the geometry data into Hyperchem for visualization! This generally works quite well except when you have a lot of atoms crowded together. In that case newZmat may create extra 'bonds' ,but the atoms are all there at the right places. Best Regards Lars Stormbom _______________________________________________________________________________ From owner-hyperchem@hyper.com Wed Nov 13 12:40:55 1996 Sender: neuber@exp.bessy.de Date: Wed, 13 Nov 1996 10:47:19 MET From: Michael Neuber To: hyperchem@hyper.com Subject: script errors in HC4.5 and 4.0 Hello folks ! Udo Haberl wrote on tue ,11 Nov 1996 > I have a problem with some scripts. They were written for hyperchem > 3.0, but when I want to run them under hyperchem 4.5, some of the > script commands, for example "select-none", cause error messages like > "unknown script command". What is wrong? Joel Polowin answered: >A few of the script commands were renamed between versions, but that is >not one of them. In general, all of the script commands from older >versions should still be valid in the new versions. The best way to >check, >of course, is to look in the list of scripts in the _Reference_ manual >(chapter 10). > >The most likely cause of trouble in this case is because of a change to >Windows 95 or Windows NT 4. With Windows 95, it is necessary to have >the >"Regional Settings" set to "English (United States)"; with Windows NT 4, >it is necessary to set the "Default Locale" to "US". It doesn't make >sense; it's a Microsoft thing. With the wrong settings, our software is >not able to properly understand a text string that it reads from a file >(or receives through the DDE interface to other software). The problem >does not seem to occur with HyperChem release 5. And perhaps its worth to note my experience with another script command: When concatenating some scripts in sequence by adding the read-script (drive):\(path)\(nextscriptname).scr comand at the end of a script in order to start the next one, this will work for HC 3.0, but failed here with HC 4.5 ! And, as both versions have been running under Win95 with the same configuration on the same computer, this is definitely not only a problem of Microsoft, I would say ! I found a workaround for the Problem with HC4.5 and the details of this might indicate the way to solve the problem: When I observed the error message I got for the read-script command, I noted that the returned path and file name have been truncated always after about 12 characters. (One can check this by varying the subfolder name length...). Thus I got the idea to place all scripts which have to run in sequence in the root directory, say C:\scrpt1.scr C:\scrpt2.scr C:\scrpt3.scr ... and each script script(n).scr again directing the programm control to its successor script(n+1).scr with a corresponding command line at its end. This way the path+filename length may still be truncated but this truncation will not have any effect as the location info is kept within a 12 char string, thus the successor script was successfully found. Note that within the scripts, there are references to *.log and *.hin files with long path and file names and it worked this way. I guess there is some string mismanagement accidently implemented in HC 4.5, maybe even in HC 4.0. I would appreciate any comment on that, also if any other users have been able to reproduce such faults.... (Lets collect these messages somewhere, maybe with infos on special OS settings in order to give help to debug this ! I will look up such infos in my case as soon as other time consuming struggles will allow it..) By the way, Udo Haberl, I noted the 'select-none' command to fail in HC4.5, too, only by changing from HC 3.0 to HC4.5, without any further changes of operating system and computer. Therefore, Joel, I think its not sufficient only to refer to Microsoft. ;-) Greetings from Berlin Michael Neuber --------------------------------------------------------------------------- Dr. Michael Neuber Universitaet Heidelberg c/o BESSY Lentzeallee 100 D-14195 Berlin Phone (++49/0) 30 82004-237/-176 FAX ..-149 e-mail neuber@exp.bessy.de --------------------------------------------------------------------------- _______________________________________________________________________________ From owner-hyperchem@hyper.com Wed Nov 13 14:59:01 1996 X-Sender: graham@mail.sentex.net Date: Wed, 13 Nov 1996 11:56:13 -0500 To: hyperchem@hyper.com From: Graham Hurst Subject: Re: Deleted atoms reappear. At 01:37 PM 11/12/96 -0800, Laurence Lavelle wrote: >I am using HC 4 and Windows 95. Using the nucleic acid database I make a >10-mer and delete the terminal phosphate groups. I then add a H atom to each >terminal oxygen so that the sugars of this DNA duplex have terminal OH groups. > >This file is saved and closed. > >When this file is opened the terminal phosphates are present!!! > >Anybody know whats going on? Hi Laurence - remember me? It sounds like you're saving it as a PDB file. For atoms that are in the templates but not in the PDB, HyperChem 4 adds them when it reads the PDB. (Don't know if the newer versions do it differently.) This doesn't happen if you save as HIN format. Cheers, Graham ------- Graham Hurst, PhD or Cambridge, Ontario, Canada _______________________________________________________________________________ From owner-hyperchem@hyper.com Wed Nov 13 14:59:43 1996 Date: Wed, 13 Nov 96 11:38:18 -0500 From: polowin (Joel Polowin) To: hyperchem@hyper.com, Michael Neuber Subject: Re: AW: script errors in hyperchem 4.5 ? > Date: Wed, 13 Nov 1996 10:14:54 MET > From: Michael Neuber > And perhaps its worth to note my experience with the following script command: > When concatenating some scripts in sequence by adding the > read-script (drive):\(path)\(nextscriptname).scr > comand at the end of a script in order to start the next one, > this will work for HC 3.5, but failed here with HC 4.5 ! And, as both > versions have been running under Win95 with the same configuration. on the > same computer, this si definitely not only a problem of Microsoft, I would > say ! This was an error added in HyperChem 4.5; it has been fixed in HyperChem 5. > By the way, Udo Haberl, I noted the 'select-none' command to fail in HC4.5, > too, only by changing from HC 3.0 to HC4.5, without any further changes of > operating system and computer. Therefore, Joel, I think its not enough > only to refer to Microsoft. ;-) The effect seems to be due to an effect of the compiler; we have not deliberately eliminated the problem from HyperChem 5, it simply has not appeared, apparently because of the 32-bit compilation of the front end for HyperChem 5. The compilers used for release 3 were not the same as for later releases. But it comes down to this: the script commands in HyperChem 4 and 4.5 work perfectly well under Windows 3.1x or Windows NT 3.51, or under Windows 95 or Windows NT 4 if the settings are correct. With the other settings in Win'95 or NT 4, a piece of software (which does not change with the settings) reads a text file (which also does not change) and interprets it incorrectly. It certainly *looks* like an effect of the operating system. Joel ------------ Joel Polowin, Ph.D. Manager, Scientific Support Email to: polowin@hyper.com WWW: http://www.hyper.com/ Hypercube Inc, 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" (or "unsubscribe hyperchem") to hyperchem-request@hyper.com; please do not send such administrative messages to the group itself. _______________________________________________________________________________ From owner-hyperchem@hyper.com Wed Nov 13 15:12:55 1996 Date: Wed, 13 Nov 96 12:19:03 -0500 From: polowin (Joel Polowin) To: hyperchem@hyper.com, Peter Jackson Subject: Re: Network installation of Hyperchem > Date: Wed, 13 Nov 1996 11:19:05 +0000 > From: Peter Jackson > > Out network administrator has installed hyperchem on our LAN (to save > disk space on PCs etc) onto a write protected drive. When trying to > carry out single point geometry optimisations I receive error messages > stating that the parameter files cannot be accessed. I have checked > that these parameter files are on the correct network path, which they > are. Could the problem be that hyperchem needs write access to this > parameter files?? It should not. It *does* require write access for the directory that CHEM.INI and CHEMBIN.INI are written to; this directory is described in the "[HyperChem]" section of WIN.INI in the ChemIniPath setting. The directory for the parameters is shown in the same place as the ChemParmPath setting; please make sure that that setting is correct. If the installation was not done on your local PC, it is likely that the settings in WIN.INI have not been done correctly. See the section "Win.ini Settings" in the first chapter of the _Getting Started_ manual, and the preceding section about sharing files on a network. Joel ------------ Joel Polowin, Ph.D. Manager, Scientific Support Email to: polowin@hyper.com WWW: http://www.hyper.com/ Hypercube Inc, 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" (or "unsubscribe hyperchem") to hyperchem-request@hyper.com; please do not send such administrative messages to the group itself. _______________________________________________________________________________ From owner-hyperchem@hyper.com Wed Nov 13 18:13:46 1996 Date: Wed, 13 Nov 1996 12:31:48 -0800 X-Sender: lavelle@ewald.mbi.ucla.edu To: hyperchem@hyper.com From: lavelle@ewald.mbi.ucla.edu (Laurence Lavelle) Subject: Re: Deleted atoms reappear. Hi Joel, Since your reply I did the same process but changed the file save format (i.e., HIN or PDB). I get the reappearing atom problem for the PDB format. I do not have a problem when saving in HIN format. Thought you would like to know. Thanks Laurence Lavelle >> Date: Tue, 12 Nov 1996 13:37:46 -0800 >> From: lavelle@ewald.mbi.ucla.edu (Laurence Lavelle) >> >> I am using HC 4 and Windows 95. Using the nucleic acid database I make a >> 10-mer and delete the terminal phosphate groups. I then add a H atom to each >> terminal oxygen so that the sugars of this DNA duplex have terminal OH groups. >> >> This file is saved and closed. >> >> When this file is opened the terminal phosphates are present!!! > >The problem is that the file as saved -- in a HIN or PDB format, I assume -- >contains information about the nucleotide residues. When the file is read >in again, HyperChem matches each residue against the matching residue in >the template database. (This allows it to connect atoms correctly, add >missing H atoms, etc., if these data are omitted from the file.) And, >knowing that the terminal phosphates *should* be present in the standard >residues, it adds them, according to the templates. > >We should make this residue checking optional, rather than compulsory, for >file reading; I've added that to the development wishlist. For now, >there are a couple of possible work-arounds. One would be to omit all >residue information, if you do not need it, by saving the file in one >of the other file formats (MOL, for example) and reading it back in. >Another would be to edit the HIN file to remove the "res" and "endres" >lines for the terminal groups (making them no longer residues and no >longer requiring checking against the templates), and to renumber the >remaining residues. A third would be to add new residues to your >templates which lack the phosphate groups, and change the terminal >residues to the new residue types. > >Joel > >------------ >Joel Polowin, Ph.D. Manager, Scientific Support >Email to: polowin@hyper.com WWW: http://www.hyper.com/ """"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" Laurence Lavelle, Ph.D. University of California Los Angeles Molecular Biology Institute Los Angeles, CA90095-1570, USA Email:LAVELLE@MBI.UCLA.EDU Phone:(310)206-8270 Fax:(310)825-0982 http://www.mbi.ucla.edu/people/lavelle/lavelle.html """"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" _______________________________________________________________________________ From owner-hyperchem@hyper.com Thu Nov 14 14:25:09 1996 Date: Thu, 14 Nov 96 09:50:12 -0500 From: polowin (Joel Polowin) To: lavelle@ewald.mbi.ucla.edu (Laurence Lavelle), hyperchem@hyper.com Subject: Re: Deleted atoms reappear. > Date: Wed, 13 Nov 1996 12:31:48 -0800 > From: lavelle@ewald.mbi.ucla.edu (Laurence Lavelle) > > Since your reply I did the same process but changed the file save format > (i.e., HIN or PDB). > > I get the reappearing atom problem for the PDB format. > I do not have a problem when saving in HIN format. Yes; as Graham Hurst pointed out, I was mistaken in thinking that the automatic reconstruction of the residues would happen with the HIN files. In general, with HyperChem it's best to use the HIN format except for the specific purpose of communicating with other software or data sources. The HIN format was specifically designed to match the data structures in HyperChem, and contains more of the information which is relevant to HyperChem than the other formats can. Joel ------------ Joel Polowin, Ph.D. Manager, Scientific Support Email to: polowin@hyper.com WWW: http://www.hyper.com/ Hypercube Inc, 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" (or "unsubscribe hyperchem") to hyperchem-request@hyper.com; please do not send such administrative messages to the group itself. _______________________________________________________________________________ From owner-hyperchem@hyper.com Thu Nov 14 16:29:42 1996 Date: Thu, 14 Nov 1996 14:52:54 +0000 (GMT) From: Michael Hodgson To: hyperchem@hyper.com Subject: Coverting .HIN files Hi I am wondering if anyone knows of a way of converting a hyperchem .HIN file to a Karplus (CHARMM) .CRD file ? I have tried going via .pdb files and this places atoms correctly, but some of the types are unrecognised by CHARMM. Thanks, -Michael Hodgson If it's green and wiggles, it's biology. If it stinks, it's chemistry. If it doesn't work, it's Physics. _______________________________________________________________________________ From owner-hyperchem@hyper.com Fri Nov 15 03:40:11 1996 Date: Thu, 14 Nov 1996 13:44:39 -0500 (EST) From: Steven Clarke To: hyperchem@hyper.com Subject: DDE commands and HOMO-LUMO energies Hi all I working on a DDE program in Visual Basic to load up several large molecules, do Zindo-S calculations on them, and then get out some info into Excel. I'm having some trouble getting to the HOMO and LUMO energies though, and was wondering if someone has a suggestion or if I missing something. scf-orbital-energy(int) will get the energy of the orbital (int). However, it seems that this command indexes exclusively by orbital count, not by homo-minus or lumo-plus. First question: can scf-orbital energy be set to index relative to homo-minus? Second question: If not, is there an easy way to get to the absolute index count of the homo so I can then get the energies through scf-orbital. Currently, my program counts electrons and then divides by two, but that is really a pain, and computationally wastefull since Hyperchem already knows! We are running HC 4.0 on Win 3.11, Excel 5, Visual Basic 4.0pro Thanks for your help Steve Clarke ************************************************************* * STEVEN CLARKE * ************************************************************* * Graduate Student * E-mail : CLARKES@Chem.Lsa.Umich.Edu * * Dept. of Chemistry * Post : 930 North University Ave * * Univ. of Michigan * : Ann Arbor MI 48109-1055 * ************************************************************* _______________________________________________________________________________ From owner-hyperchem@hyper.com Fri Nov 15 16:49:22 1996 Date: Fri, 15 Nov 96 13:16:00 -0500 From: polowin (Joel Polowin) To: Steven Clarke , hyperchem@hyper.com Subject: Re: DDE commands and HOMO-LUMO energies > Date: Thu, 14 Nov 1996 13:44:39 -0500 (EST) > From: Steven Clarke > > scf-orbital-energy(int) will get the energy of the orbital (int). > However, it seems that this command indexes exclusively by orbital count, > not by homo-minus or lumo-plus. > > First question: > can scf-orbital energy be set to index relative to homo-minus? No. > Second question: > If not, is there an easy way to get to the absolute index count of the > homo so I can then get the energies through scf-orbital. Currently, my > program counts electrons and then divides by two, but that is really a > pain, and computationally wastefull since Hyperchem already knows! I do not know of an *easy* way to do this. I have found only a rather round-about method, with a command series such as graph-orbital-selection-type homo-minus graph-orbital-offset 0 do-qm-graph yes do-qm-calculation no do-single-point query-value status-message Here, the first line specifies that orbitals are to be numbered relative to the HOMO; the second specifies #0, i.e., the HOMO itself. The third says that the specified orbital should be plotted after the next single- point calculation; the fourth that the actual calculation should not be performed. The fifth line does that "calculation", which with the current settings merely shows a plot of the current orbital. This also puts a message about that orbital number, and its energy, into the status line. The sixth line returns the current contents of the status line as a text string. You would then have the problem of parsing that string to extract the orbital index (or other data). (This is, incidentally, how the Molecule Presentations module of ChemPlus figures out the current orbital index.) This is awkward, I know. If one is doing this stuff manually, it is trivial -- setting the orbital selection type and the orbital offset in the dialogue box will display the orbital energy; switching to the orbital-index orbital selection type then calculates the orbital index of the LUMO or HOMO. But running these operations from a script command bypasses the error-checking and recalculation steps. A while ago, I added an entry to the development wish list that there should be some way of determining the orbital indices of the HOMO and LUMO from script commands without this sort of running around. Joel ------------ Joel Polowin, Ph.D. Manager, Scientific Support Email to: polowin@hyper.com WWW: http://www.hyper.com/ Hypercube Inc, 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" (or "unsubscribe hyperchem") to hyperchem-request@hyper.com; please do not send such administrative messages to the group itself. _______________________________________________________________________________ From owner-hyperchem@hyper.com Mon Nov 18 10:32:48 1996 Date: Mon, 18 Nov 1996 13:27:55 +0100 From: e08bp@cx1.cyf.gov.pl (Beata Paluchowska) To: hyperchem@hyper.com Dear HyperChem-Co-User, I am extremely willing to calculate something which unfortunately contain calcium. Can you provide me with some information where to find some parameters for Ca? Preferably for PM3 calculation, but any other will be welcome! Really grateful. Beata Paluchowska. _______________________________________________________________________________ From owner-hyperchem@hyper.com Mon Nov 18 19:19:05 1996 Date: Mon, 18 Nov 96 16:31:24 -0500 From: polowin (Joel Polowin) To: e08bp@cx1.cyf.gov.pl (Beata Paluchowska), hyperchem@hyper.com Subject: Ca semi-empirical parameters > Date: Mon, 18 Nov 1996 13:27:55 +0100 > From: e08bp@cx1.cyf.gov.pl (Beata Paluchowska) > > I am extremely willing to calculate something which unfortunately contain > calcium. Can you provide me with some information where to find some > parameters for Ca? Preferably for PM3 calculation, but any other will be > welcome! HyperChem does have Ca parameters for ZINDO/1, though you will receive a warning about negative coefficients. This is because, unlike the parameters for all other elements and methods, in this case Ca really does have negative parameters; in all other cases, negative parameters would indicate an error in the parameter file. Just ignore the warning in this case and let the calculation run. Joel ------------ Joel Polowin, Ph.D. Manager, Scientific Support Email to: polowin@hyper.com WWW: http://www.hyper.com/ Hypercube Inc, 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" (or "unsubscribe hyperchem") to hyperchem-request@hyper.com; please do not send such administrative messages to the group itself. _______________________________________________________________________________ From owner-hyperchem@hyper.com Tue Nov 19 05:12:47 1996 Date: Tue, 19 Nov 1996 16:03:37 -0800 From: tomita Organization: TGK To: hyperchem Subject: iodine index in use of ZINDO/S Dir computer chemists or staff of Hyperchem I am now trying to speculate the UV spectrum of the compound containing iodine. However, there no exists the index of iodine atom. Please inform me of the data. -- Kyoichi Tomita,Ph.D. Senior Researcher, 3rd Group Email to: tomita@mxm.meshnet.or.jp Photosensitive Materials Research Laboratory, Toyo Gosei Kogyo Co.,LTD. 3805 Hagiwara Inbamura Inbagun Chiba 270-16 ,Japan Tel 0476-98-3368,3361 Fax 0476-98-3368 _______________________________________________________________________________ From owner-hyperchem@hyper.com Tue Nov 19 07:05:21 1996 Sender: From: "Galeazzi Roberta" To: hyperchem@hyper.com Date: Tue, 19 Nov 1996 10:46:54 +0000 Subject: problems with script commands Dear Hyperchemists, I have problems with some script commands. I am using Hyperchem 4.5 installed under Windows 95 on a PC-Pentium 133 MHz. We changed the PC last month and till this moment using the same version of Hyperchem under Windows 3.11 I never had any problem. Now I've tried to use some Excell Macros or Scripts I've done before, I 'm not able to use them becouse Hyperchem can't recognize some commands. Some of this are: select-none select-name(torsion) atom-labels symbol name-selection torsion and so on. I've also tried to reinstall the program but nothing changed. Is there anyone who has the same problem? Any suggestions? Thanks in advance Roberta ********************************************************* Dr. Roberta Galeazzi Dipartimento di Scienze dei Materiali e della Terra Universita di Ancona via Brecce Bianche 60131 Ancona - Italy e-mail: roberta@popcsi.unian.it fax: 0039-71-2204714 tel.: 0039-71-2204707 ******************************************************* _______________________________________________________________________________ From owner-hyperchem@hyper.com Tue Nov 19 07:14:00 1996 Date: Tue, 19 Nov 1996 10:15:08 +0000 (GMT) From: Peter Gedeck To: Beata Paluchowska Cc: hyperchem@hyper.com Subject: Re: your mail On Mon, 18 Nov 1996, Beata Paluchowska wrote: > Dear HyperChem-Co-User, > I am extremely willing to calculate something which unfortunately > contain calcium. Can you provide me with some information where to find > some parameters for Ca? Preferably for PM3 calculation, but any other > will be welcome! > Really grateful. > Beata Paluchowska. Hi Beata, Wavefunctions Inc. has developed PM3 parameter for Ca and included them in their program Spartan (http://www.wavefun.com/spartan/spartan.html). The parameters were not published yet, but are available on their FTP site. ftp://ftp.wavefun.com/pub/PARAMS/params.PM3 I am not sure if there is a problem using these parameters in e.g. HyperChem. But, W. Hehre from Wavefunction sent a email to the CCL mailing list about their PM3 Boron parameters and said that they could be found at their FTP site and that they should be cited as: Yu, J.; Hehre, W. J. To be published, Wavefunction, Inc., Irvine, California (1995). So I assume that the parameters are somehow public. Unfortunately, I tried to implement their PM3 parameters for Ca in Vamp and Mopac but was not very successful. The results differed considerably from Spartan calculations. I also tested the Boron parameters with much more success, i.e. identical results. Therefore, I assume that Spartan uses additional terms for the PM3 calculation and/or different integrals? But you never know, maybe I did something wrong. So, if you are more successful including the parameters in HyperChem please let me know. regards, Peter Dr. Peter Gedeck Centrum f. Computer Chemie - Institut f. Organische Chemie I Naegelsbachstrasse 25 - D-91052 Erlangen Deutschland / Germany Tel: ++9131 - 85 6581 Fax: ++9131 - 85 6565 E-Mail: gedeck@organik.uni-erlangen.de WWW: http://organik.uni-erlangen.de/clark/gedeck _______________________________________________________________________________ From owner-hyperchem@hyper.com Tue Nov 19 16:59:50 1996 Sender: From: "Galeazzi Roberta" To: hyperchem@hyper.com Date: Tue, 19 Nov 1996 18:05:48 +0000 Subject: solved problem about scripts commands Priority: normal Hi all, I solved the problem: I tried to change the Inernational setting to English(USA) and it works. I don't know if it can be useful to anyone. Thanks Roberta ********************************************************* Dr. Roberta Galeazzi Dipartimento di Scienze dei Materiali e della Terra Universita di Ancona via Brecce Bianche 60131 Ancona - Italy e-mail: roberta@popcsi.unian.it fax: 0039-71-2204714 tel.: 0039-71-2204707 ******************************************************* _______________________________________________________________________________ From owner-hyperchem@hyper.com Thu Nov 21 17:08:32 1996 Date: Thu, 21 Nov 1996 11:05:52 -0800 X-Sender: lavelle@ewald.mbi.ucla.edu To: hyperchem@hyper.com From: lavelle@ewald.mbi.ucla.edu (Laurence Lavelle) Subject: Warning to all using HC for nucleic acid structures obtained from PDB. If you are downloading nucleic acid structures from the PDB and then using HyperChem 4.0 to view these structures you should be aware that: HyperChem will mess with the termini by: adding a phosphate group at one end and deleting the hydrogen of the hydroxyl group at the other, for both strands. ******There is no warning or any indication that this is occuring.************* There appears to be no way around this because one has to open a PDB file in HC in the PDB format. If you create a structure within HC and save it in HIN format this problem does not occur. Laurence Lavelle """"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" Laurence Lavelle, Ph.D. University of California Los Angeles UCLA-DOE Laboratory of Structural Biology & Molecular Medicine Molecular Biology Institute Los Angeles, CA90095-1570, USA Email:LAVELLE@MBI.UCLA.EDU Phone:(310)206-8270 Fax:(310)825-0982 http://www.mbi.ucla.edu/people/lavelle/lavelle.html """"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" _______________________________________________________________________________ From owner-hyperchem@hyper.com Thu Nov 21 19:27:02 1996 Date: Thu, 21 Nov 96 17:22:42 -0500 From: polowin (Joel Polowin) To: lavelle@ewald.mbi.ucla.edu (Laurence Lavelle), hyperchem@hyper.com Subject: Re: Warning to all using HC for nucleic acid structures obtained from PDB. > Date: Thu, 21 Nov 1996 11:05:52 -0800 > From: lavelle@ewald.mbi.ucla.edu (Laurence Lavelle) > > HyperChem will mess with the termini by: adding a phosphate group at one end > and deleting the hydrogen of the hydroxyl group at the other, for both strands. Can you give me the names of a specific PDB file or two that this happens for? I know that HyperChem will add atoms to a structure if its template shows that a residue should have them; I've never seen it delete atoms that were actually described in the file. If a PDB file does not include hydrogen atoms, then if the template does not show them at the terminus, HyperChem would not add them. As for the addition of the phosphate, there was some discussion of this on this list about two years ago. The 5' oxygen at the beginning of the chain should not have a phosphate group added. (Happens for pdb1bna.ent which we distribute.) The spec says these should be called OXT, but changing the name to OXT adds two extra atoms (not less as it should)! Graham Hurst commented: The PDB spec does indicate that the repeating units are nucleoTides (sugar, base and phosphate), but also states (p 25 of the March 89 version): The extra oxygen atom at the free 5' phosphate terminus is designated OXT. This atom will be placed first in the coordinate set. Apparently the pdb1bna.ent depositors (and presumably others) didn't follow the spec! (A common problem with PDB entries unfortunately.) When I change the O5* to OXT HyperChem does act differently - it adds a 5CAP residue, which it probably shouldn't. I'll put this in the bug list, but in the meantime you should fix the end yourself the first time you read a file and then work with HIN files (to avoid automatic adding of atoms). Joel ------------ Joel Polowin, Ph.D. Manager, Scientific Support Email to: polowin@hyper.com WWW: http://www.hyper.com/ Hypercube Inc, 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" (or "unsubscribe hyperchem") to hyperchem-request@hyper.com; please do not send such administrative messages to the group itself. _______________________________________________________________________________ From owner-hyperchem@hyper.com Sat Nov 23 16:02:29 1996 Date: Sat, 23 Nov 1996 18:49:39 +0100 (MET) From: Sandy Yates To: hyperchem@hyper.com Subject: A tip for reading PDB files. HyperChemers, If you have difficulty reading PDB files with HyperChem, which I always do. ( I collect the PDB files from the hugh resource BC.CA) I used to edit the files so that HyperChem liked them (there are column format problems). Now I use WebLab to read them then resave them as another file type which HyperChem will read. This work well Sandy ------------------------------------------------------------------------ Sandy Yates / Area de Mecanica de Fluidos / Centro Politecnico Superior Maria de Luna, 3 / 50015 ZARAGOZA. SPAIN Phone: Spain (76) 761000 ext 5045. Fax: Spain (76) 761882 Email: sandy@ideafix.cps.unizar.es _______________________________________________________________________________ From owner-hyperchem@hyper.com Sat Nov 23 16:43:44 1996 Date: Sat, 23 Nov 1996 14:01:31 -0500 X-Sender: b1byzd58@pop1.sympatico.ca To: hyperchem@hyper.com From: "Rob O'Brien" Subject: spd basis for chlorine Part 2 of 2 Joel Polowin pointed out that I did not clarify a few items in part one of this message. Since, it is likely others will have the same confusions I have included my clafification below (note: > indicates Joel's response); ========================================== >The actual reaction may be controlled kinetically, rather than thermo- >dynamically, in which case the critical factor is the energies of the >transition states of the various reactions rather than the energies of >the fragments, etc. The possibility of kinetic control was considered. I step wise lengthened each C-Cl bond by a small increment and then with this fixed reoptimized the geometry and calculated the heat of formation which was plotted to map the reaction coordinate (UHF was used for this). No significant deviations that would suggest the exclusive loss of chlorine were indicated and since this is a rather labor extensive process it was not examined further. >One colleague noted that you've got to make sure that you're working >with the correct spin multiplicity. He says that the ground state for >some dissociated fragments would be a triplet rather than a singlet. Yes both the triplet and singlet states were calculated and in some cases there is a switch between which is the ground state. However, neither case permitted the determination of the site of prefered dechlorinations. Geometry relaxation in the anion might be significant; this would be hard >to predict. You might find literature on the subject, or you could try >optimizing the anion. Also, are these results in the gas phase or in >solution? -- solvent effects may be significant. The literature values I refer to were the gas phase values as calculated from the solution phase reduction potentials. The solvent effects were taken into account. The authors demonstrated the accuracy of their calculation by comparison to the few available literature values. By the way I used the electron affinity as a check on the ability to calculate reliable radical anion energies. My "bible literature reference" (Lias et al, J. Phys. Chem. Ref. Data, Vol 17(1), (1988)) defines the electron affinity as the difference in heat of formation between the neutral and anion with the same geometry. I don't quite understand why if I can change the basis sets by ; >........... you just need to edit them with >a text editor; the file names and formats are given in Appendix C of the >_Reference_ manual. then why this won't work with ... >This won't work with the semi-empirical methods currently available in >HyperChem. The published basis sets that I indicated were for a MNDO type calculation. As a novice I am not quite sure where the limitation could be. If I edit the basis sets won't that then permit the calculation ? thanks, R.O'B ============================================ >From the shared desktop of ; Melanie Reed & Rob O'Brien Ottawa, Ontario, Canada m-r.obrien@sympatico.ca _______________________________________________________________________________ From owner-hyperchem@hyper.com Sat Nov 23 16:47:44 1996 Date: Sat, 23 Nov 1996 13:53:28 -0500 X-Sender: b1byzd58@pop1.sympatico.ca To: hyperchem@hyper.com From: "Rob O'Brien" Subject: spd basis for chlorine Part 1 of 2 This message was originaly sent to the wrong address. Fortunately, I cc'ed a copy to Joel Polowin and have already recieved a reply. Since my questions have not been completely resolved and I would greatly appreciate feedback I am now reposting my question here. ============================================= I am very interesting in modeling the ionic forms of chlorinated aromatics, specifically PCB's, Naphthalenes, dioxins, etc. In fact, I have already performed a series of AM1 level calculations on a significant set of PCB molecules. I have been looking for methods that will enable me to determine which of chlorine(s) would be most likely lost after ionization. This is not a completely academic question as I have determined that very specific dechlorinations do occur by monitoring these reactions using isotopic labeled chlorine. Thus far I have monitored the appropriate heat of formations, bond orders, and heat of formation of the fragement molecules produced by extracting specific chlorine. Using this approach I would not have been able the magnitude of chlorine bias I observe. For example, I observe the exclusive loss of specific chlorine from some molecules. When I was examining the anions I calculated the electron affinity by determining the heat of formation of the "optimized" neutral and then with the same geometry calculated the corresponding anion heat of formation (anion Hf calculaed using both the uhf and rhf methods). This electron affinity did not correspond with "absolute electron affinities" determined from reduction potentials (ref 1). The calculated values were not wrong because of a simple offset so that their relative vlaues could be used but rather scattered in an apparent random manner around the literature values. This indicated to me that either I performed the calculation incorrrectly or the calculation was wrong. Thiel & Voityuk (ref 2 and 3), have published parameters that extend the sp basis set used in the AM1, PM3 etc. programs in Hyperchem to include the d orbitals. I suspect that my calculation problems is related to the sp rather than spd nature of the chlorine basis set. Therefore, my questions are ; 1) is there any has anyone else with experience in this area that could help me 2) has anyone upgraded the chlorine basis set to include the spd parameters 3) how would I change the basis set used 4) was my approach to the problem appropraite (my background is in the crossover between analytical and experimental physical chemistry) references 1. Wiley, Chen et al, J. Electroanal. Chem., 307, 169-182 (1991) 2. Thiel & Voityuk, Int. J. Quantum Chem., 44, 807-829 (1992) 3. Thiel & Voityuk, J. Phys. Chem., 100, 616-626 (1996) ============================================ >From the shared desktop of ; Melanie Reed & Rob O'Brien Ottawa, Ontario, Canada m-r.obrien@sympatico.ca _______________________________________________________________________________ From owner-hyperchem@hyper.com Sun Nov 24 10:24:43 1996 From: ps@ocisgi7.unizh.ch (Serge Pachkovsky) Subject: Re: spd basis for chlorine Part 1 of 2 To: m-r.obrien@sympatico.ca (Rob O'Brien) Date: Sun, 24 Nov 1996 11:19:46 +0100 (MET) Cc: hyperchem@hyper.com Rob O'Brien wrote: > Thiel & Voityuk (ref 2 and 3), have published parameters that extend > the sp basis set used in the AM1, PM3 etc. programs in Hyperchem to include > the d orbitals. I suspect that my calculation problems is related to the > sp rather than spd nature of the chlorine basis set. Ok, there probably is a misunderstanding here. MNDO, AM1 and PM3 are semiempirical *methods* defined by: MNDO: {M.J.S. Dewar and W. Thiel, {\sl J. Am. Chem. Soc.}, {\bf 99}, 4899, 4907 (1977) AM1: {M.J.S. Dewar, E.G. Zoebisch, E.F. Healy, and J.J.P. Stewart, {\sl J. Am. Chem. Soc.}, {\bf 107}, 3902 (1985)} and PM3: {J.J.P. Stewart, {\sl J. Comp. Chem.}, {\bf 10}, 209, 221 (1989)}, respectively. Some of the relevant issues (such as parameters for the elements not parametrized in the original work and a few technical details) are discussed elsewhere, but these three pretty much describe the *methods* themselves. Hyperchem (or Mopac, or Ampac, or VAMP, or MNDO94, or Gaussian, or Spartan, or whatever) are all *programs* implementing the *methods*. All and every of them should be equivalent (modulo the implementation bugs) *if* *they* *implement* *the* *method* you are interested in. Now, MNDO/d, despite a seemingly insignificant difference in the name from MNDO, is a different method, and in some aspects quite a different method from (although sharing a lot of ideas and even some parameters with) the original MNDO. To get an impression of the difference, take a look at the publication describing the two-electron repulsion integrals in MNDO/d: {W. Thiel and A.A. Voityuk, {\sl Theor. Chim. Acta}, {\bf 81}, 391 (1992); {\bf 93}, 315 (1996)} and compare it with the MNDO reference above. Implementing all the necessary integrals is fairly non-trivial, and several pitfalls are there for the unwary (I was there, so I know ;-). The situation is complicated by the fact what most of the semiempirical codes out there attempt to use simplifications arising from the sp nature of the basis set in the MNDO,AM1 and PM3 aggressively, and chasing all the cases where the original author of the code (which may be not available for the comment by now, or may not remember himself, even if he is) cut the corner, knowing that he'll newer ever use anything but s and p functions, might easily become a nightmare. To my knowledge (which is admittedly incomplete), only two codes out there (Thiel's MNDO94 and on, and Wavefunction's Spartan) actually implement the MNDO/d. (Slight differences between these two implementations were rumored, which are probably due to Spartan implementing the original TCA 92 publication to the letter, despite a few typografic errors, which were corrected in TCA 96, but I do not *know* for sure.) The bottom line is clear: until the esteemed Hyperchem team *implements* the MNDO/d method in their program, you won't be able to use MNDO/d parameters with Hyperchem. If you don't want to wait for this to happen (Joel should know better whether and when it will or not, but he probably can't tell anyway), you'd have to try your look with other programs. Regards, /Serge.P _______________________________________________________________________________ From owner-hyperchem@hyper.com Sun Nov 24 19:18:45 1996 Date: Sun, 24 Nov 1996 17:17:58 +0100 (MET) From: Sandy Yates To: "Dr. S. Shapiro" Cc: hyperchem@hyper.com Subject: Re: A tip for reading PDB files. Hi, I discovered WebLab at http://www.biosym.com/weblab/index.html You will find many details therein. THE ORIGINAL INFORMATION CAN BE FOUND AT http://www.msi.com/weblab/index.html Supported Operating Systems WindowsNT* 3.51 or higher Windows95* Windows 3.1 Power Macintosh Macintosh ------------------------------------------------------------------------ Sandy Yates / Area de Mecanica de Fluidos / Centro Politecnico Superior Maria de Luna, 3 / 50015 ZARAGOZA. SPAIN Phone: Spain (76) 761000 ext 5045. Fax: Spain (76) 761882 Email: sandy@ideafix.cps.unizar.es _______________________________________________________________________________ From owner-hyperchem@hyper.com Mon Nov 25 17:42:26 1996 Date: Mon, 25 Nov 96 15:04:03 -0500 From: polowin (Joel Polowin) To: ps@ocisgi7.unizh.ch (Serge Pachkovsky), m-r.obrien@sympatico.ca (Rob O'Brien) Subject: Re: spd basis for chlorine Part 1 of 2 Cc: hyperchem@hyper.com > From: ps@ocisgi7.unizh.ch (Serge Pachkovsky) > Date: Sun, 24 Nov 1996 11:19:46 +0100 (MET) > > The bottom line is clear: until the esteemed Hyperchem team *implements* the > MNDO/d method in their program, you won't be able to use MNDO/d parameters > with Hyperchem. If you don't want to wait for this to happen (Joel should > know better whether and when it will or not, but he probably can't tell anyway), > you'd have to try your look with other programs. Thanks for the summary. You are correct: we are working on this, but I can't -- in any sense of "cannot" -- predict when d orbitals might be included in the HyperChem semi-empirical methods other than E.H. and the two ZINDO calculations. Joel ------------ Joel Polowin, Ph.D. Manager, Scientific Support Email to: polowin@hyper.com WWW: http://www.hyper.com/ Hypercube Inc, 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" (or "unsubscribe hyperchem") to hyperchem-request@hyper.com; please do not send such administrative messages to the group itself. _______________________________________________________________________________ From owner-hyperchem@hyper.com Mon Nov 25 18:35:58 1996 Date: Mon, 25 Nov 1996 12:31:45 -0800 X-Sender: lavelle@ewald.mbi.ucla.edu To: hyperchem@hyper.com From: lavelle@ewald.mbi.ucla.edu (Laurence Lavelle) Subject: Problem with snapshot file. Hi, It has been a while since I did a molecular dynamics simulation. When I open the x.hin file I get a message "Dynamics snapshot file x.snp incompatible with system" but the x.hin files opens anyway, but I am unable to playback stored snapshots. My problem may be related to the following questions: HyperChem ver 4: 1) What is the max number of parameters that can be monitored (average only) and stored in the x.csv file? 2) The max number that can be Averaged & Graphed is 4. 3) Is there a problem with the following file names ?: drew2.hin (initial hin file) drew2.log (log file) drew2s.hin (snapshot file) drew2s.snp (snapshot file) drew2s.csv (average and average & graph values). Thanks Laurence """"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" Laurence Lavelle, Ph.D. University of California Los Angeles UCLA-DOE Laboratory of Structural Biology & Molecular Medicine Molecular Biology Institute Los Angeles, CA90095-1570, USA Email:LAVELLE@MBI.UCLA.EDU Phone:(310)206-8270 Fax:(310)825-0982 http://www.mbi.ucla.edu/people/lavelle/lavelle.html """"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" _______________________________________________________________________________ From owner-hyperchem@hyper.com Tue Nov 26 19:51:51 1996 Date: Tue, 26 Nov 1996 14:22:05 -0800 X-Sender: lavelle@ewald.mbi.ucla.edu To: hyperchem@hyper.com, polowin From: lavelle@ewald.mbi.ucla.edu (Laurence Lavelle) Subject: Re: Problem with snapshot file. Hi Joel and HC users, Joel and I had communicated about this, but since my email to Joel letting him know that the problem went away, the same problem has returned. So I'm duplicating previous email (below) and asking people to contact me or Joel if they also have problems with snapshot files and if they solved them. Thanks Laurence Lavelle >To: polowin@hyper.hyper.com (Joel Polowin) >From: lavelle@ewald.mbi.ucla.edu (Laurence Lavelle) >Subject: Re: Problem with snapshot file. > >Hi Joel, > >Thanks for your response. > >***The Error message does not appear anymore.*** >***All fine*** > >My computer had not been rebooted for about 5 days. This morning I powered up and currently there is no problem with the snapshot file(?). > >Laurence > >>> Date: Mon, 25 Nov 1996 12:31:45 -0800 >>> From: lavelle@ewald.mbi.ucla.edu (Laurence Lavelle) >>> >>> It has been a while since I did a molecular dynamics simulation. >>> >>> When I open the x.hin file I get a message "Dynamics snapshot file x.snp >>> incompatible with system" but the x.hin files opens anyway, but I am unable >>> to playback stored snapshots. >> >>Were the snapshots generated with the same version of HyperChem that you >>are trying to play them back with? Old snapshot files should be readable >>by newer versions of HyperChem, but the opposite may not be true. > >Ans. Same version. Dynamics run was done over the weekend. > >> >>> HyperChem ver 4: >>> 1) What is the max number of parameters that can be monitored (average only) >>> and stored in the x.csv file? >> >>I am not sure that there is a maximum. I just tried a moderately extreme >>case, in which I modified a structure to have 23 named selections, and >>ran dynamics on it. I saved all the selections, plus EKIN, EPOT, ETOT, >>and TEMP, plus the "D x" values for all of these, in a .csv file, and I >>ended up with the expected 54 values (plus TIME) in each line in the file. > >Ans. Seems OK. > >>Joel >> >>------------ >>Joel Polowin, Ph.D. Manager, Scientific Support >>Email to: polowin@hyper.com WWW: http://www.hyper.com/ >> >>Hypercube Inc, 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" (or "unsubscribe hyperchem") to >>hyperchem-request@hyper.com; please do not send such administrative >>messages to the group itself. >> >> >> >> > """"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" Laurence Lavelle, Ph.D. University of California Los Angeles UCLA-DOE Laboratory of Structural Biology & Molecular Medicine Molecular Biology Institute Los Angeles, CA90095-1570, USA Email:LAVELLE@MBI.UCLA.EDU Phone:(310)206-8270 Fax:(310)825-0982 http://www.mbi.ucla.edu/people/lavelle/lavelle.html """"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" _______________________________________________________________________________ From owner-hyperchem@hyper.com Wed Nov 27 21:26:31 1996 Date: Wed, 27 Nov 1996 16:51:22 -0800 X-Sender: lavelle@ewald.mbi.ucla.edu To: polowin, hyperchem@hyper.com From: lavelle@ewald.mbi.ucla.edu (Laurence Lavelle) Subject: From fractional atomic coordinates to bond lengths and angles. Hi Joel and HC users, Any advise on how to get bond lengths and angles from fractional atomic coordinates. I have the fractional atomic coordinates of half of an organometalic compound (asymmetric unit) and I want to: 1) determine the bond lengths and angles 2) generate the other half of the molecule 3) look at the molecular packing in the unit cell. HyperChem should be able to do (1) but I'm not sure which way to start. Create a *.hin file (?), use MM+ (?) with print level=9 (?) and do single point calculation (?). Will this give bond lengths and angles? Any software suggestions to do (2) and (3). Thanks Laurence Lavelle """"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" Laurence Lavelle, Ph.D. University of California Los Angeles UCLA-DOE Laboratory of Structural Biology & Molecular Medicine Molecular Biology Institute Los Angeles, CA90095-1570, USA Email:LAVELLE@MBI.UCLA.EDU Phone:(310)206-8270 Fax:(310)825-0982 http://www.mbi.ucla.edu/people/lavelle/lavelle.html """"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" _______________________________________________________________________________ From owner-hyperchem@hyper.com Thu Nov 28 04:26:31 1996 Date: Thu, 28 Nov 1996 01:52:04 -0500 (EST) From: "William T. Winter" To: Laurence Lavelle Cc: polowin, hyperchem@hyper.com Subject: Re: From fractional atomic coordinates to bond lengths and angles. On Wed, 27 Nov 1996, Laurence Lavelle wrote: > > Any advise on how to get bond lengths and angles from fractional atomic > coordinates. > > I have the fractional atomic coordinates of half of an organometalic > compound (asymmetric unit) and I want to: > > 1) determine the bond lengths and angles > 2) generate the other half of the molecule > 3) look at the molecular packing in the unit cell. > > HyperChem should be able to do (1) but I'm not sure which way to start. > Create a *.hin file (?), use MM+ (?) with print level=9 (?) and do single > point calculation (?). Will this give bond lengths and angles? > > Any software suggestions to do (2) and (3). a group at the University of Arizona developed a program called "Babel" which is intended to take transform molecular structure information between input formats to various programs. they accept crystallographic fractional coordinates and they also handle Hypoerchem *.hin files. You reach them by e-mail at "babel@mercury.aichem.arizona.edu" They also have a WWW site, the software is free. =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= Dr. William T. Winter Phone: (315)470-6876 315 Baker Lab FAX: (315)470-6856 SUNY-ESF Internet: wtwinter@mailbox.syr.edu Syracuse, NY 13210-2786 URL http://www-chem.esf.edu _______________________________________________________________________________ From owner-hyperchem@hyper.com Thu Nov 28 12:58:39 1996 Date: Thu, 28 Nov 96 10:33:36 -0500 From: polowin (Joel Polowin) To: "William T. Winter" , Laurence Lavelle Subject: Re: From fractional atomic coordinates to bond lengths and angles. Cc: hyperchem@hyper.com Oh yes, forgot to mention -- the XRAY2HIN utility is on our WWW site in the Software Archive, under "Other Software". It is also on our ftp site, ftp.hyper.com , as /pub/other/xray2hin.exe . It is a tool to be used in DOS or in a DOS window. For syntax, run the program as xray2hin /? Joel ------------ Joel Polowin, Ph.D. Manager, Scientific Support Email to: polowin@hyper.com WWW: http://www.hyper.com/ Hypercube Inc, 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" (or "unsubscribe hyperchem") to hyperchem-request@hyper.com; please do not send such administrative messages to the group itself. _______________________________________________________________________________ From owner-hyperchem@hyper.com Thu Nov 28 13:53:21 1996 Date: Thu, 28 Nov 96 10:30:53 -0500 From: polowin (Joel Polowin) To: "William T. Winter" , Laurence Lavelle Subject: Re: From fractional atomic coordinates to bond lengths and angles. Cc: hyperchem@hyper.com > Date: Thu, 28 Nov 1996 01:52:04 -0500 (EST) > From: "William T. Winter" > > On Wed, 27 Nov 1996, Laurence Lavelle wrote: > > > > I have the fractional atomic coordinates of half of an organometalic > > compound (asymmetric unit) and I want to: > > > > 1) determine the bond lengths and angles > > 2) generate the other half of the molecule > > 3) look at the molecular packing in the unit cell. > > > > HyperChem should be able to do (1) but I'm not sure which way to start. > > Create a *.hin file (?), use MM+ (?) with print level=9 (?) and do single > > point calculation (?). Will this give bond lengths and angles? The "XRAY2HIN" utility which I wrote can convert a structure file of fractional atomic coordinates into a simple HIN file of separate atoms. Then you can read that file, and save and read it in the MOPAC Z-matrix format, to add bonds -- approximately; the algorithm that adds bonds when a Z-matrix file is read is good but not perfect. An MM+ single-point calculation with the print level at 1 will give you a log file with all of the bond lengths, bond angles, non-bonded distances, etc. With the Crystal Builder module of ChemPlus, you can build a 3D lattice from a single structure. It works by replicating the structure according to the unit cell angles and lengths, but it cannot generate atoms by symmetry. I do not know of any free software that generates symmetry atoms. > a group at the University of Arizona developed a program called "Babel" > which is intended to take transform molecular structure information > between input formats to various programs. they accept crystallographic > fractional coordinates and they also handle Hypoerchem *.hin files. > > You reach them by e-mail at "babel@mercury.aichem.arizona.edu" > They also have a WWW site, the software is free. BABEL is good -- to a certain point. However, it also does not generate symmetry atoms, as far as I know; it definitely ignores the symmetry information in Cambridge Structural Database files. Also, its output formatting is not too good. If a structure file contains multiple unconnected structures, its HIN output will have all of them labelled as "mol 1" (molecule #1). And its PDB output is incorrectly formatted, to the point that HyperChem generally cannot read it. Joel ------------ Joel Polowin, Ph.D. Manager, Scientific Support Email to: polowin@hyper.com WWW: http://www.hyper.com/ Hypercube Inc, 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" (or "unsubscribe hyperchem") to hyperchem-request@hyper.com; please do not send such administrative messages to the group itself. _______________________________________________________________________________ From owner-hyperchem@hyper.com Thu Nov 28 14:44:41 1996 Date: Thu, 28 Nov 96 22:02:25+050 From: shivani@medinst.doe.ernet.in To: vikram!hyper.com!hyperchem Subject: help hi hyperchem cousers, i am shivani. i am working on computer simulation of a peptide 15 aminoacid long. i have few queries: q1) what are the steps which are followed in molecular dynamics calculation? q2) how many optimal picosecond simulation are essential to get the minimized structure? q3) in the end of the simulation how do you check that the end product is the minimized structure? what are the parameters you see in the end to find whether you have resolved to the allowed conformation or not? q4) what are the steps involved in homology modelling? Q5 ) what are the options you give during molecular dynaics? i will be thankful to you if you can clear my queries. regards shivani chhabra all india institute of medical sciences New Delhi _______________________________________________________________________________ From owner-hyperchem@hyper.com Fri Nov 29 07:08:35 1996 From: W R Tomlinson To: "'Hyperchem'" Subject: 2 electron integral storage Date: Fri, 29 Nov 96 09:32:00 PST Hello Joel and all HC users The readme files arriving with Hyperchem 5.0 (Windows 95 version) state that the drive for storage of the 2-electron integrals can be specified (via File/preferences/paths). However, when the drive for 'ab initio integrals' is specified as d:\ (which is simply a 2 GB drive partitioned from a 9 GB hard drive, and NOT the CD) the calculation aborts (e.g. "Error message from node=0. Hypergauss cannot open the 2 electron integral file d:\\s3vgup3h"). I have re-booted the computer after changing the path, but with the same result. How might I use d:\ as the storage drive? Bill Tomlinson Department of Chemical and Life Sciences University of Northumbria at Newcastle Newcastle upon Tyne, NE1 8ST UK xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx EMail: w.r.tomlinson@unn.ac.uk _______________________________________________________________________________ From burton@qo.fcen.uba.ar Fri Nov 29 10:34:42 1996 From: Gerardo Burton To: "'Hyperchem'" Subject: RE: 2 electron integral storage Date: Fri, 29 Nov 1996 12:24:07 -0300 Hello I think that you should specify the path as D: the program is adding = the "\", so if you write d:\ it tries to use d:\\ which will not work. By the way I just installed version 5.0 and I must say that the 3D = graphics capabilities are excellent. Gerardo Gerardo Burton e-mail: burton@qo.fcen.uba.ar Departamento de Quimica Organica Facultad de Ciencias Exactas y Naturales Universidad de Buenos Aires Tel/FAX 54 1 788-6915 ---------- From: W R Tomlinson[SMTP:w.r.tomlinson@unn.ac.uk] Sent: Viernes 29 de Noviembre de 1996 14:32 To: 'Hyperchem' Subject: 2 electron integral storage Hello Joel and all HC users The readme files arriving with Hyperchem 5.0 (Windows 95 version) state = that=20 the drive for storage of the 2-electron integrals can be specified (via=20 File/preferences/paths). However, when the drive for 'ab initio = integrals'=20 is specified as d:\ (which is simply a 2 GB drive partitioned from a 9 = GB=20 hard drive, and NOT the CD) the calculation aborts (e.g. "Error message = from node=3D0. Hypergauss cannot open the 2 electron integral file=20 d:\\s3vgup3h"). I have re-booted the computer after changing the path, = but=20 with the same result. How might I use d:\ as the storage drive? Bill Tomlinson Department of Chemical and Life Sciences University of Northumbria at Newcastle Newcastle upon Tyne, NE1 8ST UK xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx EMail: w.r.tomlinson@unn.ac.uk _______________________________________________________________________________ From owner-hyperchem@hyper.com Fri Nov 29 14:14:12 1996 Date: Fri, 29 Nov 96 11:04:29 -0500 From: polowin (Joel Polowin) To: W R Tomlinson , "'Hyperchem'" Subject: Re: 2 electron integral storage > From: W R Tomlinson > Date: Fri, 29 Nov 96 09:32:00 PST > > The readme files arriving with Hyperchem 5.0 (Windows 95 version) state that > the drive for storage of the 2-electron integrals can be specified (via > File/preferences/paths). However, when the drive for 'ab initio integrals' > is specified as d:\ (which is simply a 2 GB drive partitioned from a 9 GB > hard drive, and NOT the CD) the calculation aborts (e.g. "Error message > from node=0. Hypergauss cannot open the 2 electron integral file > d:\\s3vgup3h"). I have re-booted the computer after changing the path, but > with the same result. How might I use d:\ as the storage drive? > > From: Gerardo Burton > Date: Fri, 29 Nov 1996 12:24:07 -0300 > > I think that you should specify the path as D: the program is adding = > the "\", so if you write d:\ it tries to use d:\\ which will not work. I think that it is not that simple -- I am running HyperChem 5 on one computer and have my integral storage path set to f:\ , which is a network- linked drive on another machine. It is working properly. Changing the "f" to "F", and omitting the "\", do not seem to make a difference. But if I have a blank space after the drive specification, so that it reads "f: ", I get an error message that "HyperGauss cannot open the 2 electron integral file f: \\s3o..." Could that be the problem, Bill? > By the way I just installed version 5.0 and I must say that the > graphics capabilities are excellent. Thanks for the kind words! Joel ------------ Joel Polowin, Ph.D. Manager, Scientific Support Email to: polowin@hyper.com WWW: http://www.hyper.com/ Hypercube Inc, 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" (or "unsubscribe hyperchem") to hyperchem-request@hyper.com; please do not send such administrative messages to the group itself.