From Roman.Jerala@IJS.si Sat Nov 21 13:26:37 1992 Date: Sat, 21 Nov 1992 12:26:37 +0100 From: Roman.Jerala@IJS.si Message-Id: <"73623112112991/103673 MRX*"@MHS> To: CHEMISTRY@ccl.net Subject: How to get a program from QCPE? Hallo netters, could anybody tell me what is the QCPE (Quantum Chemistry Program Exchange) and how to obtain programs from this "organization(?)". I appologise it this is a FAQ as I haven't been following this group for long time. Specifically I would like to get a program MSEED, by Perrot et al. from Scharaga's lab (in the J.Comp.Chem. listed as QCPE 610). Thanks, Roman JERALA ## ## ### Department of Biochemistry ## ## ## # Jozef Stefan Institute ## ## ## Jamova 39, 61000 Ljubljana, SLOVENIA ## ## ## # ## E-mail: roman.jerala@ijs.si ## ## ### fax: +38 61 273 594 From zdenko@masc1.rice.edu Sat Nov 21 08:20:43 1992 Date: Sat, 21 Nov 92 14:20:43 CST From: zdenko@masc1.rice.edu (Zdenko Tomasic) Message-Id: <9211212020.AA06157@masc1.rice.edu> To: Louis.Grace@um.cc.umich.edu Subject: Gaussian 90/92 calculations have you remembered to use overlap ? AO's are noy in general mutually orthogonal. You may need something like a Mulliken population analysis to handle that right. From bak@isadora.albany.edu Sat Nov 21 10:44:04 1992 From: bak@isadora.albany.edu (Brian A. Kell) Message-Id: <9211212044.AA12283@isadora.albany.edu> Subject: Re: Quoting the list To: chemistry@ccl.net Date: Sat, 21 Nov 92 15:44:04 EST Regarding referencing material read on a mailing list or newsgroup: It seems to me that if a person actually had a personal communication with another, then the information could be referenced as "personal communication". This would be, perhaps, face-to-face, telephone, or e-mail exchange. In such cases, it's usually appropriate to obtain permission from the source before quoting the information in another work. In the case of a mailing list, the situation doesn't really represent a "personal communication". It's more like a seminar: the person speaking makes statements that many people hear (read) simultaneously. Would it be appropriate to quote someone else's work from a seminar without their knowledge (assuming there are no printed abstracts or proceedings)? At this point in the evolving history of computers, it's not yet generally accepted that archives of a mailing list are similar to printed books, and, I think, shouldn't be treated as such. So, I agree with the previous writer that a personal exchange with the poster is probably the best way to procede. ------------------------------------------------------------------ Brian A. Kell (bak@biosym.com) Disclaimer: The above comments are my own. From CHFW@cc.newcastle.edu.au Sun Nov 23 00:06:56 1992 Date: 22 Nov 1992 13:06:56 +1100 From: CHFW@cc.newcastle.edu.au Subject: MM summary To: chemistry@ccl.net Message-Id: <01GRGBTZITJ68X0XYM@cc.newcastle.edu.au> The summary for the MM Dear netters: Thanks very much for the useful comments and suggestions of answering my e mail questions: > A friend of mine is going to start her master degree soon. Part of > her work is to do some calculations on some crystal structure by MM2 or > MM3(Molecular Mechanics). She will be apreciated to listen to some comments > about MM2 and MM3 made by computational chemistist. Does anyone know well > about the MM's? > My friend and I are appreciated. It could be very helpful for her further reaserch. I myself is majoring some theoretical work on the rovibrational states of small molecules. I wish I could be able to get some suggestions and help from this group. I will quote them in my thesis. 1. Dr. Sauser wrote: Wolfgang Sauer Institut fuer Organische Chemie Henkestr. 42, D-8520 Erlangen, FRG As a 'subscriber' of the comp-chem mailing list you will surely have noticed the MM[23] related traffic of the past (esp. the questions of Joe Leonard); so one point to start for her might well be a look into the index files at the OSC mail/ftp server. The main point our group has been struggling with for years is the 'invention' of new parameters for unsupported functional groups in most of our systems (or the 'correction' of not quite realistic features, e.g. H-bonds in MM2). If she will run into this as well, two sources to look first would be the ($1000 !) 'MM2 Forcefield Parameter Databook' discussed on the net some time ago, and a compilation of references to published additional parameters (QCPE Bull., end of 1991 / begin of 1992, don't have it handy right now, sorry, but I can look it up, if needed). Another point of importance when systems get bigger is the availability of a easy-to-use graphics system that can display your structures (preferably straight from the MM[23] files). Depending on the platform to run on, there are a few programs around that combine a molecular modeling GUI with (adopted) MM2 calcs (e.g. Hyperchem and PCModel), but there are 'graphics-only' programs to visualise MM[23] files as well. Implementation of the programs on systems other than a VAX is a different problem alltogether... There are versions of MM[23] running on all possible hardware, but as far as I know, the code you get from Allinger is still very vaxish :-( so she may have to fiddle a bit. I've never done crystal structure calcs myself (the way I understand the term), but I guess if intermolecular forces are important, one would have to run a series with increasing numbers of unit cells included in the system. That should be it for the moment, but the probably best way to learn about these programs is to have a go and watch everthing with a cautious mind. 2. Dr. Joe Leonard said: Joe Leonard jle@world.std.com Judging from the recent MM3 literature, if the required parameters are present, it would be the preferred Allinger forcefield. They published 1-2 papers where they reproduce crystal structures. All in all, it looks like a nice improvement on MM2... 3. Dr. Jim Gano mentioned: From: Jim Gano/Chemistry Doing calculations with just the MM2 or MM3 program is difficult without a graphical front end. This would not be cutting edge technology because your student would not have the file creation flexibility needed to do good work. For a discussion of this from me see: Gano, J.E.; Park, B.-S.; Pinkerton, A.A.; Lenoir, D. "New Records for Sterically Congested Stilbenes: E- and Z-1-(2,2-Dimethyl-1-tetralinylidene)-2,2- dimethyltetralin" J. Org. Chem. 1990, 55, 2688-2693. I suggest you get a program like PCModel. If you have some cash and a faster computer than a PC, get Macromodel. 4. Dr. Yvonne Martin stated: Yvonne Martin, Senior Project Leader Computer Assisted Molecular Design Project D-47E, AP9A-LL Abbott Laboratories One Abbott Park Road IL 60064 Phone: 708 937-5362 FAX: 708 937-2625 We are big fans of MM2, haven't really evaluated MM3 yet. For a new project we routinely find several similar molecules in the Cambridge structural database, enough molecules to cover all the functional groups and substructures of interest, and put them through MM2. That way we can see how MM2 changes the structure & if it will be suitable. We do not search conformational space with MM2, rather we use distance geometry & minimize those structures with MM2. The dihedral driver has some documented problems "lag" because of the way it is implemented. You might find that you are missing several parameters. Then, its up to you. Allinger supplies his current list upon a reprint request for parameters. A comparison of MM2, MM3, and AM1 for some project of interest would be a neat project for a student & useful to the rest of us if it were published. 5. Dr. Thomas Strassner told me: Thomas Strassner email: strasner@organik.uni-erlangen.de I can only tell you about MM2, cause I didn't work with MM3 yet. There are special cards to calculate cristal structures (see manual). The very latest parameters are available, please send me a mail if you need them. I got them this summer of N.L. Allinger. I hope for your friend, that the structures contain only those bonds for which parameters are included in the program. If not, he will have a serious problem, where to get reliable parameters for his systems. If you can tell me about the type of molecule he wants to calculate, perhaps I can give him some hints where to find those. 6. Dr. Dora Schmur suggested: Dora Schnur head computationalchemistry/modeling Monsanto Agricultural Group 800 N. Lindbergh Blvd mailstop U3E St Louis, Mo 63167 phone 314-694-1563 fax 314-694-4039 dmschn@bb1t.monsanto.com Feng WANG hat kind of info does your friend need on mm2/3? If s/he needs to learn the basics of running the code, I suggest A Handbook of Computational Chemistry by Tim Clark and also the chapter in vol2 of Reviews in Computational Chemistry (editors: Boyd and Lipkowitz) by Allinger and Bowen. It might be worth pointing out that MM2 and MM3 are parameterized using electron diffraction and neutron diffraction in preference to x-ray where possible so the results describe gas phase isolated molecules rather than crystals. Allinger has however published papers on benzene crystal packing so there are appropriate uses for MM2 for crystals. I reccommend contacting Allinger himself. Since I am an extended member of Allingers group and have done parameter development for years(including some freeware available from the osc archives for parameter generation), your friend may contact me as well. (But, since I work in industry, I can't guarantee prompt responses.) ------------------------end of file--------------------------------------------- From CHFW@cc.newcastle.edu.au Sun Nov 23 00:10:05 1992 Date: 22 Nov 1992 13:10:05 +1100 From: CHFW@cc.newcastle.edu.au Subject: MM summary To: chemistry@ccl.net Message-Id: <01GRGBXTHMIA8X0XYM@cc.newcastle.edu.au> The summary for the MM Dear netters: Thanks very much for the useful comments and suggestions of answering my e mail questions: > A friend of mine is going to start her master degree soon. Part of > her work is to do some calculations on some crystal structure by MM2 or > MM3(Molecular Mechanics). She will be apreciated to listen to some comments > about MM2 and MM3 made by computational chemistist. Does anyone know well > about the MM's? > My friend and I are appreciated. It could be very helpful for her further reaserch. I myself is majoring some theoretical work on the rovibrational states of small molecules. I wish I could be able to get some suggestions and help from this group. I will quote them in my thesis. Thanks very much and best wishes. Feng -- | Feng WANG Department of Chemistry, The University of Newcastle | | Callaghan, N.S.W.2308, Australia | | Internet: chfw@cc.newcastle.edu.au Tel: +61 49 215 475 | |______________________________________________________________________________ 1. Dr. Sauser wrote: Wolfgang Sauer Institut fuer Organische Chemie Henkestr. 42, D-8520 Erlangen, FRG As a 'subscriber' of the comp-chem mailing list you will surely have noticed the MM[23] related traffic of the past (esp. the questions of Joe Leonard); so one point to start for her might well be a look into the index files at the OSC mail/ftp server. The main point our group has been struggling with for years is the 'invention' of new parameters for unsupported functional groups in most of our systems (or the 'correction' of not quite realistic features, e.g. H-bonds in MM2). If she will run into this as well, two sources to look first would be the ($1000 !) 'MM2 Forcefield Parameter Databook' discussed on the net some time ago, and a compilation of references to published additional parameters (QCPE Bull., end of 1991 / begin of 1992, don't have it handy right now, sorry, but I can look it up, if needed). Another point of importance when systems get bigger is the availability of a easy-to-use graphics system that can display your structures (preferably straight from the MM[23] files). Depending on the platform to run on, there are a few programs around that combine a molecular modeling GUI with (adopted) MM2 calcs (e.g. Hyperchem and PCModel), but there are 'graphics-only' programs to visualise MM[23] files as well. Implementation of the programs on systems other than a VAX is a different problem alltogether... There are versions of MM[23] running on all possible hardware, but as far as I know, the code you get from Allinger is still very vaxish :-( so she may have to fiddle a bit. I've never done crystal structure calcs myself (the way I understand the term), but I guess if intermolecular forces are important, one would have to run a series with increasing numbers of unit cells included in the system. That should be it for the moment, but the probably best way to learn about these programs is to have a go and watch everthing with a cautious mind. 2. Dr. Joe Leonard said: Joe Leonard jle@world.std.com Judging from the recent MM3 literature, if the required parameters are present, it would be the preferred Allinger forcefield. They published 1-2 papers where they reproduce crystal structures. All in all, it looks like a nice improvement on MM2... 3. Dr. Jim Gano mentioned: From: Jim Gano/Chemistry Doing calculations with just the MM2 or MM3 program is difficult without a graphical front end. This would not be cutting edge technology because your student would not have the file creation flexibility needed to do good work. For a discussion of this from me see: Gano, J.E.; Park, B.-S.; Pinkerton, A.A.; Lenoir, D. "New Records for Sterically Congested Stilbenes: E- and Z-1-(2,2-Dimethyl-1-tetralinylidene)-2,2- dimethyltetralin" J. Org. Chem. 1990, 55, 2688-2693. I suggest you get a program like PCModel. If you have some cash and a faster computer than a PC, get Macromodel. 4. Dr. Yvonne Martin stated: Yvonne Martin, Senior Project Leader Computer Assisted Molecular Design Project D-47E, AP9A-LL Abbott Laboratories One Abbott Park Road IL 60064 Phone: 708 937-5362 FAX: 708 937-2625 We are big fans of MM2, haven't really evaluated MM3 yet. For a new project we routinely find several similar molecules in the Cambridge structural database, enough molecules to cover all the functional groups and substructures of interest, and put them through MM2. That way we can see how MM2 changes the structure & if it will be suitable. We do not search conformational space with MM2, rather we use distance geometry & minimize those structures with MM2. The dihedral driver has some documented problems "lag" because of the way it is implemented. You might find that you are missing several parameters. Then, its up to you. Allinger supplies his current list upon a reprint request for parameters. A comparison of MM2, MM3, and AM1 for some project of interest would be a neat project for a student & useful to the rest of us if it were published. 5. Dr. Thomas Strassner told me: Thomas Strassner email: strasner@organik.uni-erlangen.de I can only tell you about MM2, cause I didn't work with MM3 yet. There are special cards to calculate cristal structures (see manual). The very latest parameters are available, please send me a mail if you need them. I got them this summer of N.L. Allinger. I hope for your friend, that the structures contain only those bonds for which parameters are included in the program. If not, he will have a serious problem, where to get reliable parameters for his systems. If you can tell me about the type of molecule he wants to calculate, perhaps I can give him some hints where to find those. 6. Dr. Dora Schmur suggested: Dora Schnur head computationalchemistry/modeling Monsanto Agricultural Group 800 N. Lindbergh Blvd mailstop U3E St Louis, Mo 63167 phone 314-694-1563 fax 314-694-4039 dmschn@bb1t.monsanto.com Feng WANG hat kind of info does your friend need on mm2/3? If s/he needs to learn the basics of running the code, I suggest A Handbook of Computational Chemistry by Tim Clark and also the chapter in vol2 of Reviews in Computational Chemistry (editors: Boyd and Lipkowitz) by Allinger and Bowen. It might be worth pointing out that MM2 and MM3 are parameterized using electron diffraction and neutron diffraction in preference to x-ray where possible so the results describe gas phase isolated molecules rather than crystals. Allinger has however published papers on benzene crystal packing so there are appropriate uses for MM2 for crystals. I reccommend contacting Allinger himself. Since I am an extended member of Allingers group and have done parameter development for years(including some freeware available from the osc archives for parameter generation), your friend may contact me as well. (But, since I work in industry, I can't guarantee prompt responses.) ------------------------end of file---------------------------------------------