From: "alaa abdel-aziz" To: hyperchem@hyper.com Subject: help Date: Fri, 26 Feb 1999 02:31:27 PST Dear hyperchem users: Hello all hyperchem users and I hope hypercube fix all bugs of hyperchem@and introduce a new function ro hyperchem.@Can any hyperchem user help me about 1- how I can make simulation for free@radical reaction ang give me any example with details steps? 2-Also If@any one can help me how I can make interaction between substrate and@receptors and what are the types of interaction ?Is it only by hydrogen bonding or hyperchem can make different interaction? Thank you for your help Abdel-Moenes Get Your Private, Free Email at http://www.hotmail.com From: cyclolab@cyclolab.hu To: "NEWSGROUP/HYPERCHEM" Subject: email address change Date: Fri, 26 Feb 1999 09:41:53 +0100 ************************************************************************ Kedves Barátok, Kollégák vagy Üzletfelek, Email címünk megváltozott, 1999. 03. 01.-től már csak a következő címen lehet minket elérni: cyclolab@cyclolab.hu A régi címünk (cyclolab@compuserve.com) 1999. március 1.-jén 0 óra 0 percig él. Kérlek a a címtárban a szükséges módosításokat megtenni. Üdvözlettel, Laci ************************************************************************ Dear Friends, Colleagues, or Partners, Please, note that our email address has been changed. Our new address is: cyclolab@cyclolab.hu The old address (cyclolab@compuserve.com) is valid till 01-03-1999, 00:00:00. Please, do all necessary modifications in your address book. Thank you. Regards, Laszlo ************************************************************************ Muy Estimados Amigos, Colegas, o Clientes, Por favor, nota que se ha cambiado nuestra dirección del email. Nuestra dirección nueva es: cyclolab@cyclolab.hu La dirección vieja (cyclolab@compuserve.com) está válido hasta 01-03-1999, 00: 00: 00. Por favor, hace todo modificaciones necesarias en tu libro de direcciones. Gracias. Saludos, Laszlo ************************************************************************ Stimati Amici, Collegi, o Partner, Per favore, nota che il nostro indirizzo del email č stato cambiato. Il nostro indirizzo nuovo č: cyclolab@cyclolab.hu L'indirizzo vecchio (cyclolab@compuserve.com) č valido fino a 01-03-1999, 00: 00: 00. Per favore, fa tutte modifiche necessarie nel tuo libro dell'indirizzo. Grazie. Ciao, Laszlo ************************************************************************ Geehrter Freund, Kollege, oder Partner, Bitte, Notiz daß unsere email-Adresse ist verändert worden. Unsere neue Adresse ist: cyclolab@cyclolab.hu Die alte Adresse (cyclolab@compuserve.com) ist gültig, bebaut 01-03-1999, 00: 00: 00. Bitte, tut alle notwendigen Modifikationen in deinem Adreßbuch. Danke. Grüße, Laszlo ************************************************************************ Dr. Laszlo JICSINSZKY Head of Synth. Dept. CYCLOLAB R&D Lab. Ltd. H-1525 Budapest, P.O. Box: 435 XI. Dombovari ut 5-7. email: cyclolab@cyclolab.hu Tel./Fax: (36-1)-206-51-36 or (36-1)-206-51-37 From: "Graham Wills-Johnson" Organization: RMIT Applied Physics To: dklapste@stfx.ca CC: hyperchem@hyper.com Subject: Re: Torsional angles beyond 4 atoms Date: Wed, 17 Feb 1999 11:52:51 EST-10ESUT > From: Dieter Klapstein > To: HyperChem > Subject: Torsional angles beyond 4 atoms > Date: Mon, 15 Feb 1999 13:27:39 -0400 > Reply-to: Dieter Klapstein > HyperChemists! I am looking for a way to define and contrain > "dihedral"angles beyond 4 atoms. Hello Dieter If you save this e-mail to disk and then edit it in a plain-ASCII text editor and run it, it might be what you were looking for. Chop off everything down to the line ;twist.scr. Also, if you already have all your settings the way you want them, maybe you should remove lines ;Standard opening etc etc to the line ending homo-minus - though I don't know how the script will run on your settings of course. Regards.... Graham Wills-Johnson Department of Applied Chemistry R M I T Melbourne, Australia. rcmwj@bunyip.ph.rmit.edu.au ;twist.scr ; ; Version 1.0 17FEB99 ; ; To address problem set by Dieter Klapstein on HyperChem user group ; on 15FEB99 ; ; ;Standard opening from in-house template.... ignore-script-errors yes errors-are-omsgs append-omsgs-to-file errors.pas factory-settings selection-target atoms file-needs-saved no menu-file-new render-method sticks show-multiple-bonds yes translate-whole-molecules yes allow-ions yes explicit-hydrogens no molecular-mechanics-method mm+ isosurface-mesh-quality medium isosurface-render-method Jorgensen-Salem graph-orbital-selection-type homo-minus ; ; Create monomer ; create-atom 6 create-atom 6 create-atom 6 create-atom 6 create-atom 6 create-atom 6 create-atom 6 create-atom 6 set-bond 1 1 1 2 a set-bond 2 1 1 2 a set-bond 3 1 1 2 a set-bond 4 1 1 2 a set-bond 5 1 1 2 a set-bond 1 1 6 1 a set-bond 1 1 1 2 s set-bond 7 1 1 2 t menu-build-model-build menu-display-scale-to-fit ; ; Position monomer ; select-atom 7 1 select-atom 8 1 translate-selection 0 0 0 un-select-atom 7 1 ; ; Name atoms to be removed on forming dimer ; select-atom 14 1 name-selection zap select-none ; ; Make dimer ; menu-select-select-all menu-edit-copy menu-edit-paste select-none selection-target molecules select-atom 1 2 rotate-molecules z 180 select-none selection-target atoms select-atom 7 2 select-atom 8 2 translate-selection 0 0 0 select-none select-name zap delete-selected-atoms set-bond 7 1 7 2 t menu-build-model-build menu-display-scale-to-fit ; ; Put temporary handles on ; create-atom 6 select-atom 1 2 translate-selection 0 1.5 0 select-none create-atom 6 select-atom 1 3 translate-selection 0 -1.5 0 select-none ;It seems to jump to a new set of co-ordinates here, ;so the dimer has to be realigned... select-atom 7 1 select-atom 19 1 align-molecule primary x translate-selection 0 0 0 select-none set-bond 7 1 1 2 s set-bond 19 1 1 2 s menu-display-scale-to-fit select-atom 2 1 select-atom 1 1 select-atom 7 1 select-atom 25 1 name-selection twist1 ;and now a bit of overkill, but we may as well be in total control... un-select-atom 2 1 un-select-atom 1 1 select-atom 19 1 select-atom 26 1 name-selection twist2 un-select-atom 7 1 un-select-atom 25 1 select-atom 13 1 select-atom 14 1 name-selection twist3 ;..and finally, for checking the desired improper torsion... un-select-atom 19 1 un-select-atom 26 1 select-atom 2 1 select-atom 1 1 name-selection imptor ;Looking at the final output it might have been better to ;choose imptor on different atoms, giving you a more direct ;estimate of the angle between the planes. However, we can ;see from the start and end of the .log files that optimization ;has hardly affected the angles at all. select-none write-file handlesa.hin ;Our in-house convention is model build = *a.hin, molecular ;mechanics = *b.hin, MNDO = *c.hin,.... PM3 = *f.hin ; ; Create ninety-degree twist at model-build level ; select-name twist1 set-bond-torsion 90 select-none select-atom 25 1 select-atom 26 1 delete-selected-atoms write-file ninetya.hin ; ; Create forty-five degree twist at model-build level ; open-file handlesa.hin select-name twist1 set-bond-torsion 45 select-none select-atom 25 1 select-atom 26 1 delete-selected-atoms write-file 45a.hin ; ; Optimize under PM3 to generate MOs and isosurfaces of 45 deg conformer ; write-file 45f.hin ;(in case someone comes along during optimization and too-helpfully ;saves back over 45a.hin) quantum-print-level 9 start-logging 45f.log no append-omsgs-to-file 45f.log message "Forty-five degree initial conformation. PM3 optimization. Joe Bloggs, RMIT Applied Chemistry, Hons 1999." message " " ;Joe Bloggs exists only on our template. Users personalise their own output. message "Improper torsion before optimization..." select-name imptor query-value status-message select-none stop-logging calculation-method semi-empirical semi-empirical-method pm3 quantum-total-charge 0 multiplicity 1 uhf no do-optimization write-file 45f.hin start-logging 45f.log yes do-single-point message "After PM3 optimization the improper torsion angle has become... " select-name imptor query-value status-message select-none message " " message "Output for Joe Bloggs ends here." stop-logging export-property-file 45f.ext append-omsgs-to-file errors.pas ; ; Now the same thing for the ninety degree conformation.... ; open-file ninetya.hin write-file ninetyf.hin quantum-print-level 9 start-logging ninetyf.log no append-omsgs-to-file ninetyf.log message "Ninety degree initial conformation. PM3 optimization. Joe Bloggs, RMIT Applied Chemistry, Hons 1999." message " " ;Joe Bloggs exists only on our template. Users personalise their own output. message "Improper torsion before optimization..." select-name imptor query-value status-message select-none stop-logging calculation-method semi-empirical semi-empirical-method pm3 quantum-total-charge 0 multiplicity 1 uhf no do-optimization write-file ninetyf.hin start-logging ninetyf.log yes do-single-point message "After PM3 optimization the improper torsion angle has become... " select-name imptor query-value status-message select-none message " " message "Output for Joe Bloggs ends here." stop-logging export-property-file ninetyf.ext append-omsgs-to-file errors.pas ; ; The .ext files can be used to generate isosurface representations ; rapidly at any subsequent date. We like our students to follow ; a routine of keeping all versions during project development in ; one file of ASCII, where the latest version is at the top, and ; active, with earlier versions from which it has been copied and ; modified further down. That is the reason for the remainder of ; this template. ; ; ;The next line must be in place to prevent execution of earlier versions. exit-script (C)1999 freeware. Linux-style conditions apply. rcmwj@bunyip.ph.rmit.edu.au Graham Wills-Johnson, Dept Applied Chemistry, RMIT, Melbourne, Australia. ########################################################################### From: "Westermayer, Manfred" To: "'Graham Wills-Johnson'" Cc: "'hyperchem@hyper.com'" Subject: RE: HC and Infrared Date: Tue, 16 Feb 1999 11:28:18 -0500 Dear Graham, some years ago you have sent me the program GRAHAM.EXE to extract the vibrational frequencies for a given atom of the molecule(and some more features). It worked nicely - many thanks. By change of computer ,..., I got problems, because your program was so huge. And now my problem is: it's not 32Bit application ! Would it be possible to get a new copy of your program ? And How ? Kind Regards Dr. Manfred Westermayer (IR-Lab) Goedecke / Parke-Davis Chemical Development Thermochemistry and Spectroscopy Tel.: 49 (761) 518-2925; FAX -3032 From: Gianfranco Ercolani To: Dieter Klapstein Subject: Re: Torsional angles beyond 4 atoms Date: Mon, 15 Feb 1999 20:45:40 +0100 Cc: HyperChem Dear Dieter: If I have understood your problem, you have a molecule, say, diphenylacetylene and you want to set the torsion angle between the planes of the two phenyl rings. If this is the problem you can define an improper torsion defining, for example, C1 as the ortho carbon of one phenyl, C2 as the ipso carbon of the same phenyl (i.e. that attached to the sp carbon), C3 as the ipso carbon of the other phenyl, and C4 as the ortho carbon of the other phenyl. Give a name to this improper torsion by "Name Selection" in the menu "Select", then choose "Restrains" in the menu "Setup", select the torsion, define the wanted torsion angle, and define the force constant. Finally run the calculation you feel more appropriate. I tried to optimize the geometry of diphenylacetylene with a torsion angle of 90° with AM1, and it worked fine. After the geometry optimization remove the restrain and do a single point calculation. Hope this can help you. Best regards, Gianfranco At 01:27 PM 2/15/99 -0400, you wrote: HyperChemists! I am looking for a way to define and contrain "dihedral"angles beyond 4 atoms. For example, imagine a carbon triple bond with planar groups attached at both ends. I wish to define and contrain the angle between the two planar groups, an angle that extends now over 6 atoms. Ideally I would like to attach two 'dummy atoms' onto each of the acetylenic carbons so that the dihedral between the dummy and the neighboring planar group is defined, and then the dihedral between the adjacent dummy atoms is also defined. Has anyone out there any tips on how to install dummy atoms or any thoughts of how to contrain this 'improper' dihedral in HyperChem? Thanks in advance! Dieter Klapstein, St. Francis Xavier University. Prof. Gianfranco Ercolani Dipartimento di Scienze e Tecnologie Chimiche Universita' di Roma Tor Vergata Via della Ricerca Scientifica 00133 Roma Italy E-mail: ercolani@uniroma2.it Phone: +39 6 72594379 Fax: +39 6 72594328 From: Dieter Klapstein To: HyperChem Subject: Torsional angles beyond 4 atoms Date: Mon, 15 Feb 1999 13:27:39 -0400 HyperChemists! I am looking for a way to define and contrain "dihedral"angles beyond 4 atoms. For example, imagine a carbon triple bond with planar groups attached at both ends. I wish to define and contrain the angle between the two planar groups, an angle that extends now over 6 atoms. Ideally I would like to attach two 'dummy atoms' onto each of the acetylenic carbons so that the dihedral between the dummy and the neighboring planar group is defined, and then the dihedral between the adjacent dummy atoms is also defined. Has anyone out there any tips on how to install dummy atoms or any thoughts of how to contrain this 'improper' dihedral in HyperChem? Thanks in advance! Dieter Klapstein, St. Francis Xavier University. From: "Graham Wills-Johnson" Organization: RMIT Applied Physics To: hyperchem@hyper.com Date: Wed, 10 Feb 1999 14:00:06 EST-10ESUT Subject: Where is everybody? CC: jinyg@alchemy.yonsei.ac.kr Hello... hello... is anyone there? About the only two postings I have received from the user group in 1999 are today's from yeungeeJIN , to which I hope to be able to give some sort of reply below, and one back in January sometime from alaa abdel-aziz which (apart from one lone reply) was met with deafening silence. The group seems never to have been the same since the spamming episode made it necessary to have it monitored.... having myself suffered the embarrassing experience during the few days when it was happening and everyone was wondering what the hell was going on, of having a very explicit message pop up in the middle of the screen while I was showing something to a student (I will get into trouble if I say she was a young lady of delicate sensibilites; so let's just say I could have wished it to have been almost any other of the students then studying here) we certainly don't want to go back to that - but either everyone is still away after Christmas (I thought that only happened in this hemisphere), or the job of filtering stuff manually onto the user group takes more resources than Hypercube has available. Either way,we seem to be just one step away from rigor mortis - a very bad thing. It's a long time since I've done what yeungeeJIN wants to do, so I've forgotten the precise details - but I do seem to remember that the vital and non-obvious line in the script I was using was do-single-point. In fact I seem to remember trying to get round this using the .ext because some molecules were large enough that waiting for single-point to execute was a nuisance which I felt didn't need to happen if you already had the .ext loaded. As can be seen from the script, which I have edited in below, it called a Delphi executable which I had created. The object of the whole exercise was to make isosurface pictures of the frontier orbitals, and the Delphi executable renamed the chem.bmp file so another could be created. So I have put the Pascal source code that I wrote before compiling it into Delphi at the bottom of this e-mail. Incidentally - the HyperChem restriction on having only ONE chem.bmp is very sensible and should be retained in all future versions, despite these days of multi-Gb hard drives... but the stuff I have added was actually a workaround to frustrate that. Graham Wills-Johnson Department of Applied Chemistry R M I T Melbourne, Australia. rcmwj@bunyip.ph.rmit.edu.au HYPERCHEM SCRIPT: isosurface-mesh-quality fine isosurface-map-function yes graph-orbital-selection-type homo-minus graph-data-type orbital graph-orbital-offset 0 do-qm-calculation yes do-qm-isosurface yes do-single-point image-destination-file yes image-destination-clipboard no menu-edit-copy-image path c:\cdktest execute-hyperchem-client getbmps.exe graph-orbital-offset 1 do-qm-isosurface yes do-single-point menu-edit-copy-image path c:\cdktest execute-hyperchem-client getbmps.exe graph-orbital-offset 2 do-qm-isosurface yes do-single-point menu-edit-copy-image etc etc for as many as you wish Pascal source code for Delphi .exe unit Unit1; interface uses SysUtils, WinTypes, WinProcs, Messages, Classes, Graphics, Controls, Forms, Dialogs; type TForm1 = class(TForm) procedure FormCreate(Sender: TObject); private { Private declarations } public { Public declarations } end; var Form1: TForm1; implementation {$R *.DFM} procedure TForm1.FormCreate(Sender: TObject); var ans: char; f, g: Textfile; n: integer; ExceptionRaised: boolean; begin {$S+} n:= 0; ExceptionRaised:= false; while ((n < 21) and not ExceptionRaised) do begin n:= n+1; AssignFile(g,'c:\pic'+IntToStr(n)+'.bmp'); Try reset(g) Except on Exception do begin ExceptionRaised:= true; rewrite(g); AssignFile(f,'c:\chem.bmp'); reset(f); while not(eof(f)) do begin read(f,ans); write(g,ans) end {while not(eof(f))}; CloseFile(g) end {Except on Exception}; end {(n < 21) and not ExceptionRaised)}; end {????}; If n > 20 then begin MessageDlg('Convert all c:\picn.bmp files to .gif using Lview.', mtInformation,[mbOK],0); MessageDlg('Then remove .bmps, which are taking up 10M of scarce disk space.', mtInformation,[mbOK],0) end; Close end; end. Message-ID: <007e01be5580$ccc6fb80$3a1f84a5@yonsei.ac.kr> From: "yeungee JIN" To: Subject: e-mail me about Ques. :about isomapping " Date: Thu, 11 Feb 1999 14:38:48 +0900 In my questions (about isosurface-mapping) below, I forgot to write my e-mail address, it's jinyg@alchemy.yonsei.ac.kr. Again, any suggestions will be welcomed. Regards, Yeungee Jin From: "yeungee JIN" To: Subject: e-mail me about Ques. :about isomapping " Date: Thu, 11 Feb 1999 20:53:59 +0900 In my questions (about isosurface-mapping) below, I forgot to write my e-mail address, it's jinyg@alchemy.yonsei.ac.kr. Again, any suggestions will be welcomed. Regards, Yeungee Jin From: "Graham Wills-Johnson" Organization: RMIT Applied Physics To: hyperchem@hyper.com Date: Wed, 10 Feb 1999 14:00:06 EST-10ESUT Subject: Where is everybody? CC: jinyg@alchemy.yonsei.ac.kr Hello... hello... is anyone there? About the only two postings I have received from the user group in 1999 are today's from yeungeeJIN , to which I hope to be able to give some sort of reply below, and one back in January sometime from alaa abdel-aziz which (apart from one lone reply) was met with deafening silence. The group seems never to have been the same since the spamming episode made it necessary to have it monitored.... having myself suffered the embarrassing experience during the few days when it was happening and everyone was wondering what the hell was going on, of having a very explicit message pop up in the middle of the screen while I was showing something to a student (I will get into trouble if I say she was a young lady of delicate sensibilites; so let's just say I could have wished it to have been almost any other of the students then studying here) we certainly don't want to go back to that - but either everyone is still away after Christmas (I thought that only happened in this hemisphere), or the job of filtering stuff manually onto the user group takes more resources than Hypercube has available. Either way,we seem to be just one step away from rigor mortis - a very bad thing. It's a long time since I've done what yeungeeJIN wants to do, so I've forgotten the precise details - but I do seem to remember that the vital and non-obvious line in the script I was using was do-single-point. In fact I seem to remember trying to get round this using the .ext because some molecules were large enough that waiting for single-point to execute was a nuisance which I felt didn't need to happen if you already had the .ext loaded. As can be seen from the script, which I have edited in below, it called a Delphi executable which I had created. The object of the whole exercise was to make isosurface pictures of the frontier orbitals, and the Delphi executable renamed the chem.bmp file so another could be created. So I have put the Pascal source code that I wrote before compiling it into Delphi at the bottom of this e-mail. Incidentally - the HyperChem restriction on having only ONE chem.bmp is very sensible and should be retained in all future versions, despite these days of multi-Gb hard drives... but the stuff I have added was actually a workaround to frustrate that. Graham Wills-Johnson Department of Applied Chemistry R M I T Melbourne, Australia. rcmwj@bunyip.ph.rmit.edu.au HYPERCHEM SCRIPT: isosurface-mesh-quality fine isosurface-map-function yes graph-orbital-selection-type homo-minus graph-data-type orbital graph-orbital-offset 0 do-qm-calculation yes do-qm-isosurface yes do-single-point image-destination-file yes image-destination-clipboard no menu-edit-copy-image path c:\cdktest execute-hyperchem-client getbmps.exe graph-orbital-offset 1 do-qm-isosurface yes do-single-point menu-edit-copy-image path c:\cdktest execute-hyperchem-client getbmps.exe graph-orbital-offset 2 do-qm-isosurface yes do-single-point menu-edit-copy-image etc etc for as many as you wish Pascal source code for Delphi .exe unit Unit1; interface uses SysUtils, WinTypes, WinProcs, Messages, Classes, Graphics, Controls, Forms, Dialogs; type TForm1 = class(TForm) procedure FormCreate(Sender: TObject); private { Private declarations } public { Public declarations } end; var Form1: TForm1; implementation {$R *.DFM} procedure TForm1.FormCreate(Sender: TObject); var ans: char; f, g: Textfile; n: integer; ExceptionRaised: boolean; begin {$S+} n:= 0; ExceptionRaised:= false; while ((n < 21) and not ExceptionRaised) do begin n:= n+1; AssignFile(g,'c:\pic'+IntToStr(n)+'.bmp'); Try reset(g) Except on Exception do begin ExceptionRaised:= true; rewrite(g); AssignFile(f,'c:\chem.bmp'); reset(f); while not(eof(f)) do begin read(f,ans); write(g,ans) end {while not(eof(f))}; CloseFile(g) end {Except on Exception}; end {(n < 21) and not ExceptionRaised)}; end {????}; If n > 20 then begin MessageDlg('Convert all c:\picn.bmp files to .gif using Lview.', mtInformation,[mbOK],0); MessageDlg('Then remove .bmps, which are taking up 10M of scarce disk space.', mtInformation,[mbOK],0) end; Close end; end. From: "yeungee JIN" To: Subject: Ques. :about isomapping by scripting - Date: Tue, 9 Feb 1999 22:01:11 +0900 Hello, users! Is there anyone who has tried to make isosurface-mapping by scripting? To obtain min/max electrostatic potential values as a result of isosurface-plotting, I found some deviations(!!) in values ( through plot-molecular -properties with all fixed constaints) on sevaral CONTINUOUS TRIAL. -------( I wonder if anyone has exprienced those variations, if so, let me know , I 'd like to report this with more confidence.) However, as hyperchem's recommendation, I've made scripts using commands like "do-qm-isosurface" "graph-data-type electrostatc" etc. But I can't even make it start ( as we can see if we do it manually by status-line "getting grid data..." ) . if I use "import-property-file" instead "do-single-point" in scripts. And , even I used "do-single-point" and "do-qm-isosurface", I couldn't set the constrains like " isosurface-threshold 0.001" "isosurface-x-node 128" etc. ( I checked the plot-molecular-properties windows after it had done by script). Any suggestion will be welcomed. Thank you. Yeungee Jin