From owner-hyperchem@hyper.com Tue Dec 3 06:20:02 1996 From: Alan Schwartz Date: Tue, 3 Dec 1996 09:17:58 +0100 (MET) To: hyperchem@hyper.com Hi Hyperchemers, I have been modeling nucleic acid analogues using Amber. A particular interest of mine is introducing phosphonic acid (P-C) groups into these models. Since the Amber parameter files that are supplied (I am using Hyperchem Release 2) cannot handle these groups, I have been getting around the problem by restraining all of the modified bond lengths and angles. This is getting out of hand as my molecules get bigger. Can anyone tell me if there are newer parameter sets that would do the job and if so, how to obtain them and introduce them into the existing sets? Alan Schwartz University of Nijmegen The Netherlands _______________________________________________________________________________ From owner-hyperchem@hyper.com Tue Dec 3 16:18:43 1996 Date: Tue, 03 Dec 1996 19:33:26 +0100 From: Martina Havrankova To: hyperchem@hyper.com Subject: MOL, ZMT import/export I am using Hyperchem release 3. I wrote a script that reads a file in mol format and writes this file in *.zmt format. But when I run this script I receive message "file-format : Unknown file type mol Valid formats (HIN, PDB, SKC)". Also in Open dialog I am not able to open file in mol or zmt format, although in help is written that Hyperchem knows these formats. Whats the problem, please, help me? Thanks in advance Dan _______________________________________________________________________________ From owner-hyperchem@hyper.com Tue Dec 3 18:51:43 1996 Date: Tue, 3 Dec 96 16:44:57 -0500 From: polowin (Joel Polowin) To: Martina Havrankova , hyperchem@hyper.com Subject: Re: MOL, ZMT import/export > Date: Tue, 03 Dec 1996 19:33:26 +0100 > From: Martina Havrankova > > I am using Hyperchem release 3. I wrote a script that reads a file in > mol format and writes this file in *.zmt format. But when I run this > script I receive message "file-format : Unknown file type mol Valid > formats (HIN, PDB, SKC)". Also in Open dialog I am not able to open file > in mol or zmt format, although in help is written that Hyperchem knows > these formats. > > Whats the problem, please, help me? The problem appears to be that you do not have the correct information in your CHEM.INI file to describe the file filters. What is your serial number, please? 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 Dec 4 03:49:34 1996 From: somsak@atc.atccu.chula.ac.th (Somsak Tonmunphean) Subject: Hyperchem 3.0 on Windows 95 ? To: hyperchem@hyper.com Date: Wed, 4 Dec 1996 15:42:19 +0000 (WET) Dear All, I am using Hyperchem release 3 ( 16 bit program ) on Window 3.11 for Workgroup. Unfortunately I want to use it on Windows 95 which is 32 bit system so I had tried it on my PC ( Pentium 120 MHz, RAM 16 MB, Hard disk 2 GB). Everything was ok but when I tried to calculate some molecule with AM1 method, it hanged-up and the only way I can did was to reboot the machine. Is there anyone runing Hyperchem 3.0 on Windows 95 ? If yes, do you have this problem like me ? And how to solve it ( if you know )? Or I have to buy a new version for Windows95 ? Thank you very much in advance. Yours sincerely, Somsak Tonmunphean (Ph.D. Candidate) Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok, 10330 Thailand. _______________________________________________________________________________ From owner-hyperchem@hyper.com Wed Dec 4 18:32:35 1996 Date: Wed, 4 Dec 96 15:52:46 -0500 From: polowin (Joel Polowin) To: somsak@atc.atccu.chula.ac.th (Somsak Tonmunphean), hyperchem@hyper.com Subject: Re: Hyperchem 3.0 on Windows 95 ? > From: somsak@atc.atccu.chula.ac.th (Somsak Tonmunphean) > Date: Wed, 4 Dec 1996 15:42:19 +0000 (WET) > > I am using Hyperchem release 3 ( 16 bit program ) on Window 3.11 > for Workgroup. Unfortunately I want to use it on Windows 95 which is 32 > bit system so I had tried it on my PC ( Pentium 120 MHz, RAM 16 MB, Hard > disk 2 GB). Everything was ok but when I tried to calculate some molecule > with AM1 method, it hanged-up and the only way I can did was to reboot the > machine. Is there anyone runing Hyperchem 3.0 on Windows 95 ? If yes, do you > have this problem like me ? And how to solve it ( if you know )? Or I have to > buy a new version for Windows95 ? We have not done extensive testing of HyperChem 3 with Windows 95, since we no longer officially support releases 3 and earlier of HyperChem. But I just installed it on a Windows 95 machine and ran a couple of AM1 calculations, and everything seemed to be okay. Did you run the complete installation under Win'95? What kind of molecules are you working on? HyperChem 5 for Win'95 has been shipping for a couple of weeks, and the update for Windows NT has just been sent for manufacturing and should be shipping in ten days or so. 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 Fri Dec 6 13:48:02 1996 From: W R Tomlinson To: "'Hyperchem'" Subject: classical-quantum boundaries-Hyperchem5 Date: Fri, 06 Dec 96 14:36:00 PST Hi Joel and all HC users I have recently purchased Hyperchem 5.0 and I have loaded it on a new pentium pro workstation with Windows 95 and I am it running it alongside Hyperchem 4.0/Windows 3.1 on my 'old' PC With Hyperchem 5.0, when attempting to undertake calculations on specific aminoacid residues of a protein, after selecting the residue, extending to sp3, deducing the charge, etc, and then attempting a single point calculation, I receive error messages regarding the capping atoms. E.g. for the tutorial in the 'getting started' manual using testpti.hin, the message is: "error message received from node=0 Capping atom 28 with atomic number 6: the Slater exponent of s orbital is less than or equal to zero, please check your parameter file pm3_1.ab". I receive similar messages for other residues and for atomic number 7 capping atoms. When I try exactly the same excercises on Hyperchem 4.0/Windows 3.1, the calculations proceed normally. Note that no problems arise with Hyperchem 5.0 when undertaking calculations on whole small molecules. Any ideas? - please! Bill Tomlinson _______________________________________________________________________________ From owner-hyperchem@hyper.com Fri Dec 6 19:05:55 1996 Date: Fri, 6 Dec 96 15:47:14 -0500 From: polowin (Joel Polowin) To: W R Tomlinson , "'Hyperchem'" Subject: Re: classical-quantum boundaries-Hyperchem5 > From: W R Tomlinson > Date: Fri, 06 Dec 96 14:36:00 PST > > I have recently purchased Hyperchem 5.0 and I have loaded it on a new > pentium pro workstation with Windows 95 and I am it running it alongside > Hyperchem 4.0/Windows 3.1 on my 'old' PC > With Hyperchem 5.0, when attempting to undertake calculations on specific > aminoacid residues of a protein, after selecting the residue, extending to > sp3, deducing the charge, etc, and then attempting a single point > calculation, I receive error messages regarding the capping atoms. E.g. for > the tutorial in the 'getting started' manual using testpti.hin, the message > is: > "error message received from node=0 > Capping atom 28 with atomic number 6: the Slater exponent of s orbital is > less than or equal to zero, please check your parameter file pm3_1.ab". I > receive similar messages for other residues and for atomic number 7 capping > atoms. > When I try exactly the same excercises on Hyperchem 4.0/Windows 3.1, the > calculations proceed normally. It appears that the capping-atom parameters were omitted from the PM3 files that were shipped with HyperChem 5. The only capping-atom parameters in the PM3 set were for C; you can find them by looking for the line for atom number "-6" about halfway through the file. If you copy the values from your old file to the new one, it will solve that problem. I can send the numbers on request to anyone who wants them, and I will note this as a bug. The messages about atomic number 7 capping atoms should be seen from PM3 calculations under the same conditions in all releases of HyperChem, since we do not have capping parameters for N in any version of the PM3 parameter files. 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 Dec 7 05:47:28 1996 From: shivani@medinst.ernet.in Date: Sat, 7 Dec 96 14:04:56+050 Apparently-To: hyperchem@hyper.com dear Mr. polwin and hyperchem users, i have few problems how _______________________________________________________________________________ From owner-hyperchem@hyper.com Sat Dec 7 22:24:27 1996 X-Sender: lavelle@mbi.ucla.edu Date: Sat, 07 Dec 1996 17:11:39 -0800 To: "Adrian Parsegian" , grants@cancer.org, "A.E. Maris" , "AXUM 4.1 Technical Support" , "Carol Gross" , society@biophysics.faseb.org, "Bob Austin" , weiss@mbi.ucla.edu, "Brian Vicente" , "John Campbell" , "David Lavelle" , "Richard Dickerson" , "Duilio Cascio" , "Elliot Landaw" , "Evelyn Steckman" , howard%ww-jb@mhs.cstat.co.za, hyperchem@hyper.com, igor@mbi.ucla.edu, "Astrid Huizer" , "Evelyn Steckman" , polowin, Junko Hoshi , dickerson lab -- Gye-Won Han , Maria Grzeskowiak , Mark Filipowsky , Mary Kopka , "R. E. Dickerson" , Thang Chiu , "A.E. Maris" , "Laurence Lavelle" , "Luigi Nassimbeni" , marek@ewald.mbi.ucla.edu, Mary Kopka , sdavison@gm.olmsa.hq.nasa.gov, nature@nature.com, patenthelp@cnidr.org, listserv@pdb.pdb.bnl.gov, "Ramaswamy Sarma" , "Hoa Nguyen & Schutt" , "George Sheldrick" , "Tanya Paparella" , Thang Chiu , wbass@ucla.edu, wwalker@biomath.medsch.ucla.edu From: Laurence Lavelle Subject: NB:Info on email virus >>If anyone receives mail entitled: PENPAL GREETINGS! please delete it >>WITHOUT reading it. Below is a little explanation of the message, and >>what it would do to your PC if you were to read the message. >> >>This is a warning for all Internet users - there is >>a dangerous virus propagating across the Internet >>through an e-mail message entitled "PENPAL GREETINGS!". >>DO NOT DOWNLOAD ANY MESSAGE ENTITLED "PENPAL GREETINGS!" >> >>This message appears to be a friendly letter asking >>you if you are interested in a penpal, but by the time >>you read this letter, it is too late. The "trojan >>horse" virus will have already infected the boot >>sector of your hard drive, destroying all of the data >>present. It is a self-replicating virus, and once >>the message is read, it will AUTOMATICALLY forward >>itself to anyone who's e-mail address is present in >>YOUR mailbox! >> >>This virus will DESTROY your hard drive, and holds the >>potential to DESTROY the hard drive of anyone whose >>mail is in your inbox, and who's mail is in their >>inbox, and so on. If this virus remains unchecked, >>it has the potential to do a great deal of DAMAGE >>to computer networks worldwide!!!! >> >>Please, delete the message entitled "PENPAL GREETINGS!" >>as soon as you see it! And pass this message along to >>all of your friends and relatives, and the other readers >>of the newsgroups and mailing lists which you are on, >>so that they are not hurt by this dangerous virus!!!! """"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" 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 Sun Dec 8 02:13:55 1996 Date: Sun, 8 Dec 96 00:54:03 -0500 From: polowin (Joel Polowin) To: Laurence Lavelle , wwalker@biomath.medsch.ucla.edu, wbass@ucla.edu, Thang Chiu , "Tanya Paparella" , "George Sheldrick" , "Hoa Nguyen & Schutt" , "Ramaswamy Sarma" , listserv@pdb.pdb.bnl.gov, patenthelp@cnidr.org, nature@nature.com, sdavison@gm.olmsa.hq.nasa.gov, Mary Kopka , marek@ewald.mbi.ucla.edu, "Luigi Nassimbeni" , "Laurence Lavelle" , "A.E. Maris" , Thang Chiu , "R. E. Dickerson" , Mary Kopka , Mark Filipowsky , Maria Grzeskowiak , dickerson lab -- Gye-Won Han , Junko Hoshi , "Evelyn Steckman" , "Astrid Huizer" , igor@mbi.ucla.edu, hyperchem@hyper.com, howard%ww-jb@mhs.cstat.co.za, "Evelyn Steckman" , "Elliot Landaw" , "Duilio Cascio" , "Richard Dickerson" , "David Lavelle" , "John Campbell" , "Brian Vicente" , weiss@mbi.ucla.edu, "Bob Austin" , society@biophysics.faseb.org, "Carol Gross" , "AXUM 4.1 Technical Support" , "A.E. Maris" , grants@cancer.org, "Adrian Parsegian" Subject: Re: NB:Info on email virus HOAX No virus can propagate by E-mail unless your E-mail reader is specifically set up to automatically execute attached files. Most E-mail readers CAN'T execute program files; even those that can generally ask the user if an attached program should be executed before they do so, unless the user has deliberately disabled that warning. These virus warning messages -- the "Good Times" virus warning is probably the most popular -- are themselves "viruses" of a sort; they propagate by requesting well-meaning but insufficiently-informed people to pass warnings along to friends, mailing lists, etc. When you receive such a warning message, please explain things to whoever sent it to you, with the suggestion that that information should be relayed backwards. As people become better informed, such hoaxes may become less frequent. A good place to look for information on such messages is the DejaNews facility (http://www.dejanews.com), which allows you to look for old Usenet messages on a given subject. 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 Dec 9 13:58:48 1996 Date: Mon, 9 Dec 96 20:45:26+050 From: shivani@medinst.doe.ernet.in To: vikram!hyper.com!hyperchem hi hyperchem users and joel sir, i have few queries 1. where is the option in which we can calculate the rms deviation in angstrom fron the starting geometry which is a usual measure given in the article ? 2. is there any option in which we can reassign the values after specifsteps of mol. dynamics? 3. where is the option for rescaling of velocity ? please give me the answers as soon as possible. regards shivani all india medical institute New DElhi shivani@medinst.ernet.in _______________________________________________________________________________ From owner-hyperchem@hyper.com Mon Dec 9 18:01:17 1996 Date: Mon, 9 Dec 96 15:34:05 -0500 From: polowin (Joel Polowin) To: shivani@medinst.ernet.in Subject: HyperChem dynamics Cc: hyperchem@hyper.com > Date: Mon, 9 Dec 96 20:45:26+050 > From: shivani@medinst.doe.ernet.in > > 1. where is the option in which we can calculate the rms deviation in angstrom > fron the starting geometry which is a usual measure given in the article ? The ChemPlus enhancements package includes an "RMS Deviation" module that would allow you to compare the positions of the initial and final structures. You would need to have both structures in the workspace; the simplest way to do that is probably to use the File/Merge function of HyperChem. > 2. is there any option in which we can reassign the values after specifsteps of mol. dynamics? Which values? > 3. where is the option for rescaling of velocity ? If the system temperature changes, during a dynamics run, the velocities are rescaled automatically such that the velocity distribution is appropriate for that temperature. 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 Dec 10 14:11:54 1996 Date: Tue, 10 Dec 1996 17:09:20 +0100 (GMT+0100) From: Andrea Garelli To: hyperchem@hyper.com Cc: Gianfranco Cainelli Subject: help I received the HyperChem Release 5.0 (#500-10001228) and ChemPlus 1.5 (#CP10-7797-X-1814). While HyperChem alone works well in Windows 95, ChemPlus 1.5 does not. Apart from the fact that it is necessary to click the individual icons (the purple Erlenmeyer icon does not work) the conformational search does not work well. Also in the case of very small molecules after a small numbers of minimitations, the calculation is interrupted and a warning of low memory appears although the computer has 40Mb of RAM. If you try to restart the computation a message appears: Cannot iniziate DDE connection! Your system may be unstable. You may need to restart Windows. At this point trying to close the conformational search causes a fatal error. What can I do? Gianfranco Cainelli _______________________________________________________________________________ From owner-hyperchem@hyper.com Tue Dec 10 18:38:16 1996 Date: Tue, 10 Dec 96 14:49:56 -0500 From: polowin (Joel Polowin) To: Andrea Garelli Subject: Re: help Cc: hyperchem@hyper.com, Gianfranco Cainelli > Date: Tue, 10 Dec 1996 17:11:39 +0100 (GMT+0100) > From: Andrea Garelli > > I received the HyperChem Release 5.0 (#500-10001228) and ChemPlus > 1.5 (#CP10-7797-X-1814). While HyperChem alone works well in Windows > 95, ChemPlus 1.5 does not. Apart from the fact that it is necessary to click > the individual icons (the purple Erlenmeyer icon does not work) the > conformational search does not work well. Also in the case of very small > molecules after a small numbers of minimitations, the calculation is > interrupted and a warning of low memory appears although the computer has > 40Mb of RAM. If you try to restart the computation a message appears: > Cannot iniziate DDE connection! Your system may be unstable. You may need > to restart Windows. At this point trying to close the conformational > search causes a fatal error. What can I do? HyperChem 5.0 appears to exercise a subtle bug in Microsoft's DDE Management Library (DDEML.DLL). The low memory warnings are probably earlier manifestations of the same problem. This situation will be addressed by a maintenance upgrade (HyperChem 5.01) which is currently being manufactured and which will be sent automatically to all registered customers of release 5.0. The same upgrade will also make HyperChem 5 properly compatible with Windows NT. In the meantime, I am sorry, but there is not much that can be done to work around the problem. The problem seems to occur at variable times depending on the amount of DDE activity on your system. (DDE stands for "Dynamic Data Exchange", a common method for programs to interoperate under Microsoft Windows.) If you can reduce the number of other programs operating simultaneously with HyperChem, particularly those which use DDE such as MS Word, MS Excel, MS Hearts, Netscape, you may get better results. Once the DDE data has been corrupted, it is necessary to restart Windows to restore matters. 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 Dec 11 09:09:35 1996 From: Alan Schwartz Date: Wed, 11 Dec 1996 11:20:59 +0100 (MET) To: undisclosed-recipients:;@hyper.com As Joel suggested, I would like to be able to write Excel programs similar to those on the ftp site for selecting and restraining groups of atoms. However, I find that my experience with Excel is too limited to do so easily. I have had a look at one Excel handbook and found precious little help in writing this kind of program. Also, the information in the HyperChem Reference is rather condensed. Can anyone suggest a good book on Excel which might be a help? Alan Schwartz University of Nijmegen The Netherlands _______________________________________________________________________________ From owner-hyperchem@hyper.com Wed Dec 11 15:45:58 1996 Date: Wed, 11 Dec 96 22:32:18+050 From: shivani@medinst.doe.ernet.in To: vikram!hyper.com!hyperchem hi sir, and hyperchem users, i am sorry you couldn't undestand on eof the questions. i want to ask in one literature i saw it was written "20ps equlibration with reassignment of velocities after every 400 steps and then 30ps equilbration n with rescaling of the velocities(without reassignment) if the temperatureof the system fluctuates by more than 10k.so how to achive that? regards shivani aiims _______________________________________________________________________________ From owner-hyperchem@hyper.com Wed Dec 11 18:53:21 1996 Date: Wed, 11 Dec 1996 18:37:46 -0400 X-Sender: facien03@abello.dic.uchile.cl To: hyperchem@hyper.com From: facien03@abello.dic.uchile.cl (Juan S. Gomez-Jeria.) Subject: Compatibility of files. Who knows what is the compatibility of Hyperchem 5.0 files with Sculpt? Thanks. Juan S. Gomez-Jeria Associate Professor Universidad de Chile Facultad de Ciencias Casilla 653 Santiago CHILE. e-mail: facien03@abello.dic.uchile.cl Phone: (562)-672-7261. Fax: (562)-271-3888 _______________________________________________________________________________ From owner-hyperchem@hyper.com Wed Dec 11 19:04:20 1996 Date: Wed, 11 Dec 96 15:59:35 -0500 From: polowin (Joel Polowin) To: shivani@medinst.ernet.in Subject: HyperChem molecular dynamics Cc: hyperchem@hyper.com > Date: Wed, 11 Dec 96 22:32:18+050 > From: shivani@medinst.doe.ernet.in > > i want to ask in one literature i saw it was written "20ps equlibration > with reassignment of velocities after every 400 steps and then 30ps equilbration n > with rescaling of the velocities(without reassignment) if the temperatureof the > system fluctuates by more than 10k.so how to achive that? There is no simple way in HyperChem to reassign the velocities periodically through the dynamics run. You could do this by running several consecutive molecular dynamics sessions, with reassignment of velocities for each session ("Restart" turned off). You can run a series of sessions in this way by using a series of script commands or external software control, such as an Excel macro or Visual Basic. But there is no way to do this as a feature during a single dynamics run, and there is no way to get all of the short sessions combined into a single snapshot file. Velocities are automatically reassigned periodically through the dynamics run if you have the "Constant temperature" option turned on -- see the description in the _Reference_ manual. It does not operate only under the specific condition that the system temperature has fluctuated by some amount. 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 Dec 12 13:43:39 1996 Date: Thu, 12 Dec 96 10:20:50 -0500 From: polowin (Joel Polowin) To: facien03@abello.dic.uchile.cl (Juan S. Gomez-Jeria.), hyperchem@hyper.com Subject: Re: Compatibility of files. > Date: Wed, 11 Dec 1996 18:37:46 -0400 > From: facien03@abello.dic.uchile.cl (Juan S. Gomez-Jeria.) > > Who knows what is the compatibility of Hyperchem 5.0 files with Sculpt? Sculpt can read PDB files (which HyperChem can write) and its own data format; as far as I can tell from the demo and documentation that we obtained in July, and the information on their web page, it can write *only* its own data 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 Thu Dec 12 17:45:43 1996 Date: Thu, 12 Dec 1996 11:34:44 -0800 (PST) From: "Eric F. Johnson" X-Sender: johnson@kestrel To: Joel Polowin Cc: "Juan S. Gomez-Jeria." , hyperchem@hyper.com Subject: Re: Compatibility of files with Sculpt Sculpt will also export a pdb file. We are using ver 3.0 of hyperchem where heteroatoms are exported to pdb files without connectivity information. We have used babel to convert *.hin files for heteroatoms to pdb files. However, the pdb file does not conform correctly to the pdb file format, and sculpt requires strict conformance. This can be corrected in a text editor by removing an extra column of blank space from the file so that the fields are aligned properly with the pdb format. Eric F. Johnson, Ph.D. Member, Division of Biochemistry Department of Molecular and Experimental Medicine, NX-4 The Scripps Research Institute 10550 North Torrey Pines Road La Jolla, CA 92037 USA tel 619-784-7918 fax 619-784-7981 johnson@scripps.edu On Thu, 12 Dec 1996, Joel Polowin wrote: > > Date: Wed, 11 Dec 1996 18:37:46 -0400 > > From: facien03@abello.dic.uchile.cl (Juan S. Gomez-Jeria.) > > > > Who knows what is the compatibility of Hyperchem 5.0 files with Sculpt? > > Sculpt can read PDB files (which HyperChem can write) and its own data > format; as far as I can tell from the demo and documentation that we > obtained in July, and the information on their web page, it can write > *only* its own data 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 Thu Dec 12 19:27:48 1996 From: "Patrick Flash" To: http//.www.hyperchem@hyper.com Date: Thu, 12 Dec 1996 08:15:13 EST Subject: Stereo pairs in hyperchem New user with student version needs directions for producing a stereo pair of a mulecule. Thanks _______________________________________________________________________________ From owner-hyperchem@hyper.com Fri Dec 13 07:56:05 1996 Date: Fri, 13 Dec 1996 09:59:55 +0100 (MET) From: Jolanta Latosinska To: hyperchem@hyper.com Cc: http//.www.hyperchem@hyper.com, hyperchem@hyper.com Subject: EPR calculations Dear Netters, Could you point me some papers related to correlation between data from EPR spectra and quantum chemical calculations (especially spin densities) ? I will be gratefull for your help, Jolanta Latosinska _______________________________________________________________________________ From owner-hyperchem@hyper.com Fri Dec 13 14:52:32 1996 Date: Fri, 13 Dec 1996 10:27:27 -0800 From: Jolanta Latosinska Organization: Institute of Physics To: Joel Polowin Cc: hyperchem@hyper.com Subject: help Dear netters, Could you point me some papers related to EPR investigation and quantum chemical calculations, especially spin densities analysis? (I would like to analyze some spectra of free radicals.) I will be gratefull for any help, Jolanta Latosinska _______________________________________________________________________________ From owner-hyperchem@hyper.com Fri Dec 13 19:30:55 1996 Date: Fri, 13 Dec 96 10:53:37 -0500 From: polowin (Joel Polowin) To: "Eric F. Johnson" Subject: Re: Compatibility of files with Sculpt Cc: hyperchem@hyper.com, "Juan S. Gomez-Jeria." > Date: Thu, 12 Dec 1996 11:34:44 -0800 (PST) > From: "Eric F. Johnson" > > Sculpt will also export a pdb file. Thanks for the correction. > We are using ver 3.0 of hyperchem where heteroatoms are exported to pdb > files without connectivity information. I can't replicate this. When I save a file from HyperChem 3 in the PDB format -- with "Connectivity" turned on in the File/Save dialogue box -- the file includes connectivity information for all the bonds in the workspace. What kind of structure do you have? > We have used babel to convert > *.hin files for heteroatoms to pdb files. However, the pdb file does not > conform correctly to the pdb file format, and sculpt requires strict > conformance. This can be corrected in a text editor by removing an extra > column of blank space from the file so that the fields are aligned > properly with the pdb format. Just to clarify -- BABEL's PDB output is incorrectly formatted (and this causes problems for HyperChem as well). HyperChem's PDB output conforms to the PDB specifications. The most recent versions of BABEL that I have seen for PCs and for UNIX machines have *different* formatting errors in their PDB output; I have pointed the problem out to BABEL's owners. 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 Fri Dec 13 23:36:49 1996 Date: Fri, 13 Dec 1996 20:01:45 -0400 X-Sender: facien03@abello.dic.uchile.cl To: hyperchem@hyper.com From: facien03@abello.dic.uchile.cl (Juan S. Gomez-Jeria.) Subject: 3D?. 1. I cannot do a whole (i.e., around ALL the molecule) 3D surface of the molecular electrostatic potential. Someone knoews?. 2. It would be wiser to plot the molecules electrostatic potential in Kcal/mol!!!!!! (and not in the actual units!). Thanks. Juan S. Gomez-Jeria Associate Professor Universidad de Chile Facultad de Ciencias Casilla 653 Santiago CHILE. e-mail: facien03@abello.dic.uchile.cl Phone: (562)-672-7261. Fax: (562)-271-3888 _______________________________________________________________________________ From owner-hyperchem@hyper.com Sun Dec 15 10:14:07 1996 Date: Sun, 15 Dec 96 18:48:22+050 From: shivani@medinst.doe.ernet.in To: vikram!hyper.com!hyperchem hi sirand hyperchem cousers, is there any option in which we can plot ramachandran plo? -t? 2. can we plot the rmsd plot vs time during a molecular dynAmics calculation? _______________________________________________________________________________ From owner-hyperchem@hyper.com Sun Dec 15 10:47:54 1996 Date: Sun, 15 Dec 96 18:47:10+050 From: shivani@medinst.doe.ernet.in To: vikram!hyper.com!hyperchem hi sir and hyperchem cousers, where is the option in which we can plot the phi psi in the form of ramachandran plot? is there any option in which we can calculate the rms error during a md simulaton like how is it changing? regards shivani aiims _______________________________________________________________________________ From owner-hyperchem@hyper.com Mon Dec 16 11:07:05 1996 X-Sender: utinans@daina.ktf.rtu.lv Date: Mon, 16 Dec 1996 13:08:30 +0000 To: hyperchem@hyper.com From: Maris Utinans Subject: Output Hi! Who knows more detailed about output: "quantum print level" in chem.ini file (values and output information), and about other important options in this file? Thanks Maris _______________________________________________________________________________ From owner-hyperchem@hyper.com Mon Dec 16 12:10:01 1996 Date: Mon, 16 Dec 1996 08:52:08 -0500 X-Sender: U3NET224@VMESA12 To: hyperchem@hyper.com From: MARCEL.SARRAZIN@VMESA12.U-3MRS.FR (Marcel SARRAZIN) Subject: dipole moment I am a new user of Hyperchem. I intend to create a link with Excel (French version 5.0). I insert the order (Channel;"dipole-moment "). During a quantum calculation, hyperchem reply : Query Value : Unknown variable 'dipole-moment'. Where is the error ? _______________________________________________________________________________ From owner-hyperchem@hyper.com Mon Dec 16 14:02:29 1996 Date: Mon, 16 Dec 96 11:10:14 -0500 From: polowin (Joel Polowin) To: facien03@abello.dic.uchile.cl (Juan S. Gomez-Jeria.), hyperchem@hyper.com Subject: Re: 3D?. > Date: Fri, 13 Dec 1996 20:01:45 -0400 > From: facien03@abello.dic.uchile.cl (Juan S. Gomez-Jeria.) > > 1. I cannot do a whole (i.e., around ALL the molecule) 3D surface of the > molecular electrostatic potential. Someone knoews?. If the 3D surface appears to have had parts chopped off to fit into a rectangular box, the problem is that the 3D grid dimensions are too small. You need to change the Spatial Extents settings in the "Isosurface Grid" property sheet in the Plot Molecular Properties Options dialogue box. After you have plotted an isosurface, you can also change its properties with the Display/Isosurface menu item, or by pressing F4. If the surface seems to include only parts of the molecule, make sure that you selected the entire molecule for the calculation, or that no atoms were selected. If only some atoms were selected, only those atoms would be included in the calculation. If the surface is very "small", try a smaller Contour value for the isosurface display in the "Isosurface Rendering" property sheet in the Plot Molecular Properties Options dialogue box or the Display/Isosurface dialogue box. > 2. It would be wiser to plot the molecules electrostatic potential in > Kcal/mol!!!!!! (and not in the actual units!). The unit we use, e/a_0, is one of the standard units used for such calculations. Kcal/mol is not a unit for the electrostatic potential field, which has units of the form charge/distance. What we plot is the field strength, not an energy. 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 Dec 16 14:02:53 1996 Date: Mon, 16 Dec 96 11:21:00 -0500 From: polowin (Joel Polowin) To: shivani@medinst.ernet.in Subject: Ramachandran plots, RMSD Cc: hyperchem@hyper.com > Date: Sun, 15 Dec 96 18:48:22+050 > From: shivani@medinst.doe.ernet.in > > is there any option in which we can plot ramachandran plot? You can do this with the PHIPSI Excel macro which is part of the ChemPlus enhancements package. That macro is also available from our WWW site, http://www.hyper.com, in the Software Archive, and from our ftp site, ftp.hyper.com, in the /pub/macros directory as 'phipsi.xlm'. > 2. can we plot the rmsd plot vs time during a molecular dynAmics calculation? No; HyperChem does not have any built-in function for calculating RMSD. You would need to use an external program to do that calculation, and you cannot activate such a program to work with HyperChem at the same time that HyperChem is doing its MD calculations. What you could do would be to run the MD calculation and save the results in a snapshot file. Then you could use a macro, script, or other program to play back the snapshot file, selecting a specific frame of it for a specific time step. Then you could merge in the original structure and do the RMSD calculation -- for example, by running the RMS Fit module from ChemPlus -- and extract the RMSD value by retrieving the value of the 'status-message' variable from HyperChem. The macro could repeat this for each step of the snapshot file, storing the RMSD values, and then plot them after processing the entire file. 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 Dec 16 14:04:39 1996 Date: Mon, 16 Dec 96 11:24:58 -0500 From: polowin (Joel Polowin) To: Maris Utinans , hyperchem@hyper.com Subject: Re: Output > Date: Mon, 16 Dec 1996 13:08:30 +0000 > From: Maris Utinans > > Who knows more detailed about output: "quantum print level" in > chem.ini file (values and output information), and about other important > options in this file? See Appendix A of the _Reference_ manual, under "Log Files". 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 Dec 16 18:45:45 1996 Date: Mon, 16 Dec 1996 12:41:44 -0900 (AKST) From: KELLER JOHN W To: Marcel SARRAZIN Cc: hyperchem@hyper.com Subject: Re: dipole moment Hi, I think Joel has said in mail list that international users of HyperCHem should use the English version of Excel for DDE. Try that. John Keller.UAF On Mon, 16 Dec 1996, Marcel SARRAZIN wrote: > I am a new user of Hyperchem. > I intend to create a link with Excel (French version 5.0). I insert the > order (Channel;"dipole-moment "). > During a quantum calculation, hyperchem reply : Query Value : Unknown > variable 'dipole-moment'. > Where is the error ? > > _______________________________________________________________________________ From owner-hyperchem@hyper.com Mon Dec 16 19:19:39 1996 X-Sender: lavelle@mbi.ucla.edu Date: Mon, 16 Dec 1996 13:21:09 -0800 To: hyperchem@hyper.com From: Laurence Lavelle Subject: Undeliverable Mail to Joel Polowin Hi Joel, Since 12/12 I've tried to send this email to your private email address. >Date: Sun, 15 Dec 1996 13:39:50 -0800 >To: Joel Polowin >From: Laurence Lavelle >Subject: Undeliverable Mail > >Send again. > >>Date: Sun, 15 Dec 96 11:24:30 PST >>From: >>To: >>Subject: Undeliverable Mail >> >>MVS.OAC.UCLA.EDU unable to deliver following mail to recipient(s): >> >>MVS.OAC.UCLA.EDU unable to connect for 3 days to recipient host. >> >> ** Text of Mail follows ** >> with TCP; Thu, 12 Dec 96 10:32:27 PST (5.65/1.1.8.2/29Nov95-1114AM) >> id AA20405; Thu, 12 Dec 1996 10:37:22 -0800 >>X-Sender: lavelle@mbi.ucla.edu >>X-Mailer: Windows Eudora Pro Version 3.0 Demo (32) >>Date: Thu, 12 Dec 1996 10:34:36 -0800 >>To: polowin@hyper.hyper.com >>From: Laurence Lavelle >>Subject: >> >>Hi Joel, >> >>I am interested in doing an energy minimization on the organo-metallic >>complex bis(isothiocyanato)tetra(pyridine)nickel(II), >>i.e., [Ni(NCS)~2~(pyridine)~4~]. >>The nickel atom has an octahedral configuration and is Ni^2+^ >>i.e., [Ar] 3d6 4s2. >>This complex is of the type MX~2~L~4~ where, M = divalent transition metal >>cation, X = anionic ligand and L = electrically neutral substituted pyridine. >> >>I currently have HC 4 which does not include d orbitals. >>What version (if any) of HC has parameters to handle his calculation and at >>what level of sophistication are the parameters. >>If HC is suitable, let me know the upgrade price. >> >>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 >>""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" >> >> """"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" 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 Dec 17 03:49:31 1996 Date: Mon, 16 Dec 96 21:15:08 -0500 From: polowin (Joel Polowin) To: KELLER JOHN W , Marcel SARRAZIN Subject: Re: dipole moment Cc: hyperchem@hyper.com > Date: Mon, 16 Dec 1996 12:41:44 -0900 (AKST) > From: KELLER JOHN W > > I think Joel has said in mail list that international users of HyperCHem > should use the English version of Excel for DDE. Try that. John Keller.UAF No; any version of Excel -- or other software to send commands by DDE -- should be okay. There are a couple of other interesting quirks with Excel, depending on the language version, if one wishes a macro to be usable by people who are using different langauge versions. In the English version of Excel, the symbols used to designate spreadsheet rows and columns are "r" and "c", respectively, and the symbols used to delimit a cell label are "[" and "]". Other language versions of Excel use other symbols. In most cases, this does not matter, since the commands in an Excel macro are stored in an internal format, which is translated to the correct symbols when it is displayed to the user. But if the macro is constructing cell references from text strings, those text strings are *not* translated for language variations. In this case, if one wants to make the macro completely language-independent, one must determine inside the macro what the correct symbols are. When I revised the PHIPSI macro for ChemPlus 1.5, I included this feature. I also revised the PLOT macro to an "international" version. Both of these macros are available from our WWW site, in the Software Archive under "Macros", and from ftp.hyper.com in /pub/macros . The commands to determine the correct symbols are clearly marked in both. 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 Dec 17 13:37:32 1996 Date: Tue, 17 Dec 96 10:37:43 -0500 From: polowin (Joel Polowin) To: Marcel SARRAZIN , KELLER JOHN W Subject: Re: dipole moment Cc: hyperchem@hyper.com > Date: Mon, 16 Dec 96 21:15:08 -0500 > From: polowin (Joel Polowin) > > When I revised the PHIPSI macro for ChemPlus 1.5, I included this feature. > I also revised the PLOT macro to an "international" version. Both of these > macros are available from our WWW site, in the Software Archive under > "Macros", and from ftp.hyper.com in /pub/macros . The commands to determine > the correct symbols are clearly marked in both. Just to clarify a bit -- the "international" version of the PLOT macro is called PLOTA.XLM. The original reported problem, about an "unknown variable" in a script command, was most likely due to language settings in Windows/Win'95/Win'NT, not the language version of Excel. 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 Dec 17 16:45:37 1996 X-Sender: lavelle@mbi.ucla.edu Date: Tue, 17 Dec 1996 10:40:22 -0800 To: hyperchem@hyper.com, polowin From: Laurence Lavelle Subject: Undeliverable Mail to Joel Polowin Hi Joel, I'm still trying to send this email to you. I have no idea why there is a problem. >X-Sender: lavelle@mbi.ucla.edu >Date: Mon, 16 Dec 1996 13:21:09 -0800 >To: hyperchem@hyper.com >From: Laurence Lavelle >Subject: Undeliverable Mail to Joel Polowin > >Hi Joel, > >Since 12/12 I've tried to send this email to your private email address. > >>Date: Sun, 15 Dec 1996 13:39:50 -0800 >>To: Joel Polowin >>From: Laurence Lavelle >>Subject: Undeliverable Mail >> >>Send again. >> >>>Date: Sun, 15 Dec 96 11:24:30 PST >>>From: >>>To: >>>Subject: Undeliverable Mail >>> >>>MVS.OAC.UCLA.EDU unable to deliver following mail to recipient(s): >>> >>>MVS.OAC.UCLA.EDU unable to connect for 3 days to recipient host. >>> >>> ** Text of Mail follows ** >>> with TCP; Thu, 12 Dec 96 10:32:27 PST (5.65/1.1.8.2/29Nov95-1114AM) >>> id AA20405; Thu, 12 Dec 1996 10:37:22 -0800 >>>X-Sender: lavelle@mbi.ucla.edu >>>X-Mailer: Windows Eudora Pro Version 3.0 Demo (32) >>>Date: Thu, 12 Dec 1996 10:34:36 -0800 >>>To: polowin@hyper.hyper.com >>>From: Laurence Lavelle >>>Subject: >>> >>>Hi Joel, >>> >>>I am interested in doing an energy minimization on the organo-metallic >>>complex bis(isothiocyanato)tetra(pyridine)nickel(II), >>>i.e., [Ni(NCS)~2~(pyridine)~4~]. >>>The nickel atom has an octahedral configuration and is Ni^2+^ >>>i.e., [Ar] 3d6 4s2. >>>This complex is of the type MX~2~L~4~ where, M = divalent transition metal >>>cation, X = anionic ligand and L = electrically neutral substituted pyridine. >>> >>>I currently have HC 4 which does not include d orbitals. >>>What version (if any) of HC has parameters to handle his calculation and at >>>what level of sophistication are the parameters. >>>If HC is suitable, let me know the upgrade price. >>> >>>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 >>>""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" >>> >>> >""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" >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 >""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" """"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" 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 Dec 18 04:45:09 1996 From: somsak@atc.atccu.chula.ac.th (Somsak Tonmunphean) Subject: How to print the density matrix for calculating Bond Order ? To: polowin (Joel Polowin) Date: Wed, 18 Dec 1996 16:30:24 +0000 (WET) Cc: hyperchem@hyper.com Dear Hyperchem Users and Dr.Joel Polowin, Since I had a problem with calculating Bond order of compound, I asked Dr.Joel Polowin about this and he kindly answered my question as the following mail but I still have one problem on how to print the density matrices to the log file. Do I need to write a program to do that, if yes please tell me how to do so ? BTW, I am using HyperChem 3.0. Thank you very much in advance. Yours sincerely, Somsak Tonmunphean.(Ph.D. Candidate) Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330 Thailand. e-mail: somsak@atc.atccu.chula.ac.th > > > From: somsak@atc.atccu.chula.ac.th (Somsak Tonmunphean) > > Date: Thu, 12 Dec 1996 18:55:41 +0000 (WET) > > > > I am doing my thesis with the subject of QSAR of antimalarial > > drugs. My available chemical calculation softwares are Gaussian 92, > > Hyperchem release 3, ChemPlus, Alchemy, and Molgen. From some papers, > > they calculated bond orders and found that these had good correlations > > with activity so I would like to try it but unfortunately I really don't > > know how to calculate the bond order of molecules. Does anybody know how > > to do so (if possible with the programs I have) ? > > It is not possible to calculate bond orders automatically with HyperChem, > but they can be calculated manually from the density matrices, which can > be printed in a log file. The bond order between atoms A and B is the sum > of the squares of the elements in the density matrix with rows for atom A's > orbitals and columns for atom B's orbitals, or vice versa. If you are > doing UHF calculations, you must add the elements of the alpha and beta > matrices together before squaring. I tried this for C2H4 as model-built, > with an AM1 single-point calculation, and got a C--C bond order of 2.0004. > > 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 Wed Dec 18 13:07:00 1996 Date: Wed, 18 Dec 96 09:50:34 -0500 From: polowin (Joel Polowin) To: somsak@atc.atccu.chula.ac.th (Somsak Tonmunphean) Subject: Re: How to print the density matrix for calculating Bond Order ? Cc: hyperchem@hyper.com > From: somsak@atc.atccu.chula.ac.th (Somsak Tonmunphean) > Date: Wed, 18 Dec 1996 16:30:24 +0000 (WET) > > Since I had a problem with calculating Bond order of compound, I > asked Dr.Joel Polowin about this and he kindly answered my question as > the following mail but I still have one problem on how to print the > density matrices to the log file. Do I need to write a program to do > that, if yes please tell me how to do so ? BTW, I am using HyperChem 3.0. > > > It is not possible to calculate bond orders automatically with HyperChem, > > but they can be calculated manually from the density matrices, which can > > be printed in a log file. The bond order between atoms A and B is the sum > > of the squares of the elements in the density matrix with rows for atom A's > > orbitals and columns for atom B's orbitals, or vice versa. If you are > > doing UHF calculations, you must add the elements of the alpha and beta > > matrices together before squaring. I tried this for C2H4 as model-built, > > with an AM1 single-point calculation, and got a C--C bond order of 2.0004. To print the density matrix or matrices in the log file, you need to run a single-point calculation with a log file open and the Quantum Print Level set to 2 (or some higher levels). See Appendix B in the _New Features_ manual for HyperChem 3, or Appendix A of the _Reference_ manual for later releases. 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 Dec 18 14:02:31 1996 From: "Thomas Futterer" To: hyperchem@hyper.com Date: Wed, 18 Dec 1996 15:51:29 +100 Subject: crownether/cryptands, publications and HyperChem Dear HyperChem Users and Joel Polowin, Do you know some (recent) publications dealing with crownether/cryptands and molecular modelling, investigated with the HyperChem package ? One I know is: The Macrobicyclic Cryptate Effect in the Gas Phase V. Dearden et al.,JACS,1996, 118, 6335-6344 Bye, Thomas _________________________________________________ Dipl.-Chem Thomas Futterer Prof.Dr.A.Merz Institut fuer Organische Chemie der Universitaet Regensburg Universitaetsstrasse 31 D-93053 REGENSBURG,Germany Phone: (+) 49 941 943 4650 Fax: (+) 49 941 943 4505 Email: thomas.futterer@chemie.uni-regensburg.de _______________________________________________________________________________ From owner-hyperchem@hyper.com Wed Dec 18 15:43:02 1996 Date: Wed, 18 Dec 96 12:04:33 -0500 From: polowin (Joel Polowin) To: Laurence Lavelle , hyperchem@hyper.com Subject: Re: Undeliverable Mail to Joel Polowin > Date: Mon, 16 Dec 1996 13:21:09 -0800 > From: Laurence Lavelle > > Since 12/12 I've tried to send this email to your private email address. The machine "hyper.hyper.com" has had periodic failures such that it loses its E-mail connection to the outside world, until someone has noticed the problem and manually set things up again. Mail to addresses at "hyper.com" still would get through, which would delay anyone becoming aware of the problem. I have just done a bit of configuration work, and I *think* that I have set things up to automatically update that connection every few hours. > I am interested in doing an energy minimization on the organo-metallic > complex bis(isothiocyanato)tetra(pyridine)nickel(II), > i.e., [Ni(NCS)~2~(pyridine)~4~]. > The nickel atom has an octahedral configuration and is Ni^2+^ > i.e., [Ar] 3d6 4s2. > This complex is of the type MX~2~L~4~ where, M = divalent transition metal > cation, X = anionic ligand and L = electrically neutral substituted > pyridine. > > I currently have HC 4 which does not include d orbitals. > What version (if any) of HC has parameters to handle his calculation and at > what level of sophistication are the parameters. The ZINDO methods in HyperChem do include d orbitals, but they are not as reliable for optimizations of first-row transition metals as they are for second-row transition metals. I tried to optimize the above structure, and it got part of the way to an optimized configuration before the QM calculations became unstable and stopped converging. The _ab initio_ calculations available in HyperChem releases 4.5 and 5 would be able to optimize that structure, but to do _ab initio_ work on such a structure with a basis set large enough for accuracy would be quite a big calculation. We are working on implementing d-orbital versions of other semi-empirical methods, but that is a big development job, and I cannot predict when such an updated version of HyperChem might be available. It probably will not be soon, since we have just got HyperChem 5 out! 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 Dec 19 13:52:57 1996 Date: Thu, 19 Dec 1996 15:34:02 +0100 (MET) From: Jolanta Latosinska To: Joel Polowin Cc: hyperchem@hyper.com Subject: Re: How to print the density matrix for calculating Bond Order ? Dear Netters, I wish you a Merry Christmass and Happy New Year, Jolanta ----------------------------------------------------------------------- Jolanta Latosinska, Institute of Physics, Adam Mickiewicz University, Umultowska 85, 61-614 Poznan, Poland tel. +48-611-217011 ext.277 fax: +48-61-217991 URL: http://phys.amu.edu.pl/~jolanala E-mail: jolanala@phys.amu.edu.pl or jolanala@plpuam11.amu.edu.pl ------------------------------------------------------------------------- _______________________________________________________________________________ From polowin Thu Dec 19 18:49:46 1996 Date: Thu, 19 Dec 96 14:17:07 -0500 From: polowin (Joel Polowin) To: hyperchem@hyper.com Subject: Passing the baton... I would like to announce that I will be moving along from the position of Manager of Scientific Support. (Two years of customer support is about enough!) My position will be filled by my esteemed colleague, Victoria Barclay (barclay@hyper.com). I will still be subscribed to the mailing list, and you will probably still see occasional messages from me on it. So play nicely, everyone. In general, if you have a new support issue or a question to ask, you should address it to 'support@hyper.com' or 'info@hyper.com', rather than to a specific person. That way, if someone happens to be out of the office (or if the personnel change!), someone else can answer. You can, of course, continue to discuss some matter with a specific person. Enjoy your holidays! I certainly plan to! Regards, Joel ------------ Joel Polowin, Ph.D. Manager, Scientific Support (outgoing) Email to: polowin@hyper.com _______________________________________________________________________________ From owner-hyperchem@hyper.com Mon Dec 23 21:25:47 1996 Date: Mon, 23 Dec 96 18:26:23 -0500 From: barclay (Victoria Barclay) To: hyperchem@hyper.com Subject: Greetings Greetings, newsgroup and HyperChem aficionados: I'm pleased to announce that I've joined Hypercube, Inc. as the new technical and scientific support manager. I have been receiving intensive training from my new colleagues, and most particularly from Joel Polowin, who is well known to newsgroup members as well as to individuals who have contacted Hypercube through e-mail, phone, letter and fax over the years. Joel will be missed around here for more than his keen sense of humour and devilish chocolate cheesecake recipe. It is impossible to replace the wisdom/intuition/insight he has gained over the years in one fell swoop. I know there are some (metaphorically) big shoes to fill. There are a few different releases of HyperChem, as you know, running on several different platforms. I thus ask for your patience as I find my way among the myriad problems that arise, and while I determine which of the HyperChem implementation "gurus" at Hypercube that I must turn to in order to have more detailed questions answered. ------------ Victoria Barclay, Ph.D. Manager, Scientific Support Email to: barclay@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 Sun Dec 29 01:40:42 1996 Date: Sun, 29 Dec 96 09:20:04+050 From: mrraji@medinst.doe.ernet.in To: vikram!hyper.com!hyperchem Subject: help dear sir and other hyperchem users, i want to ask programme which can do this function? 2. how can we plot the graphs obtained by snapshots file reply soon please give your suggestion in this regards shivani aiims shivani@medinst.ernet.in