From: Laurence Lavelle [lavelle@mbi.ucla.edu] Sent: Wednesday, July 01, 1998 7:06 AM To: hyperchem@hyper.com Subject: Using ChemPlus 1.6 to calculate hydration energy and log P of nucleic acids. Date: Tue, 30 Jun 1998 20:33:35 -0700 Sender: listadmin@hyper.com Precedence: bulk Reply-To: Laurence Lavelle Any comments on why one should or should not use ChemPlus 1.6 to calculate hydration energy and log P of nucleic acids. Laurence From: Ulrich Harttig [harttigu@ucs.orst.edu] Sent: Tuesday, June 30, 1998 10:07 PM To: Ed Bertaccini, MD Cc: hyperchem@hyper.com Subject: Re: Amber5 > .... I am disappointed that > Hyperchem has not been more responsive. Perhaps this discussion will spur > on some interest. I hope so, too, but I have my doubts about a quick fix. For me, the recent changes in HC point to an emphasis on ab-initio/semi-empirical calculations in the program development. FF development seems to be of lesser priority, but maybe HyperCube will be implementing AMBER94/96 on its own in a later version of HyperChem. A word from HyperCube about further development plans might be helpful here. > to be implemented in the current version of Hyperchem so as to lend further > credence to what many UNIX exclusivists consider "just a PC program." It is My understanding is that there is even a UNIX/SGI version of HC. > forth by SGI. Hyperchem is fantastic software and its interface in > particular brings readily complex capabilities to those of us who have > neither the time nor the patience to prepare a myriad of input files for > more command prompt-based software packages. I agree that HC is a very nice program which helped me a lot getting started with computational chemistry. But it's the results that count and if I have to use command line driven Unix programs to get the computational capabilities I want I will do so, even if I prefer programs with 'clicker-dee-click' interface and having all programs running under one OS. Regards ------------------------------------------------------------------ Ulrich Harttig, Ph.D. Department of Environmental and Molecular Toxicology Oregon State University, 100 Wiegand Hall, Corvallis, OR, 97331 Phone: 541-737-6514 Fax: 541-737-1877 -L-I-N-U-X--P-O-W-E-R--L-I-N-U-X--P-O-W-E-R--L-I-N-U-X--P-O-W-E-R- From: chapron [yves.chapron@wanadoo.fr] Sent: Thursday, July 02, 1998 1:17 AM To: hyperchem@hyper.com Cc: yves.chapron@wanadoo.fr Subject: new comer... As I am new comer, I have not found how to mesure distance between atoms of a pdb(ent) structure. I should like make solvatation of a protein in a cube of water of 50x50 A still with a pdb(ent) structure. At first reading it seems possible for HIN file how to do it with ENT? Thanks for any suggestions. Yves Yves CHAPRON, Modelisation group, Molecular & Cellular Biophysics. CEA/Grenoble, BMC, 17 rue des Martyrs, F38054 GRENOBLE cedex9 Ph:(+33)(-0)476884212, Fx:(+33)(-0)476885487, Em: ychapron@cea.fr, yves.chapron@wanadoo.fr NeXT-Mail: ypchapron@blavet.ceng.cea.fr From: Gerardo Burton [burton@qo.fcen.uba.ar] Sent: Friday, July 03, 1998 4:21 PM To: Hyperchem Subject: Incorrect chirality assignments Hello Hyperchemists I've come along another possible error in Hyperchem 5.02 (and probably in all HC versions). It seems that the chirality assignments do not follow strictly the Cahn-Ingold-Prelog rules but a somewhat "simplified" version that can lead to interesting errors. As an example the central carbon (the one with the CH3 substituent) in the following compound is given by HC 5.02 as not chiral although it is obviously chiral: i-Pr-C(OH)-C(CH3)-C(OCH3)-Et that is, HC 5.02 sees only 2 chiral centers here instead of 3. The reason appears to be that HC ignores the rule that says that when there is coincidence you should check differences in the chains with higher priority. Actually what HC does is just count substituents 1 atom away, 2 atoms away, etc independently of where they are located (so the CH3 over an oxygen on the right is "equivalent" to the CH3 over an ethyl (i.e. an isopropyl) on the left!) This simplification gives some other funny results as for example that C-4 of glucose is given as R although according to C-I-P rules it should be S. So beware and don't trust the HC chirality assignments these errors are more common than they appear. It should be noted however that HC is not the only program that makes these mistakes, The program NAME from ACDLabs (at least the version I've seen) makes exactly the same mistake, could it be that there is an erroneous algorithm around that is being used by these programs? For those who want to check this out here is the HIN file for the above compound: forcefield mm+ sys 0 view 40 0.22419 55 15 0.4921622 -0.3311406 0.8050604 -0.8482343 0.02541755 0.5290109 -0.1956396 -0.943239 -0.2683753 -0.54268 0.28223 -54.978 seed -1111 mol 1 atom 1 - C C4 - 0 -0.1781557 -0.5195197 0.05834718 4 2 s 3 s 4 s 5 s atom 2 - C C4 - 0 -0.9041078 -1.032847 -1.199066 4 1 s 6 s 7 s 8 s atom 3 - C C4 - 0 1.273772 -1.032847 0.05834718 4 1 s 9 s 10 s 11 s atom 4 - C C4 - 0 -0.1781557 1.02048 0.05834718 4 1 s 12 s 13 s 14 s atom 5 - H H - 0 -0.6919902 -0.8828571 0.9483248 1 1 s atom 6 - H H - 0 -1.931771 -0.6695181 -1.199066 1 2 s atom 7 - H H - 0 -0.3902761 -0.6694943 -2.089039 1 2 s atom 8 - H H - 0 -0.9040994 -2.122848 -1.199081 1 2 s atom 9 - C C4 - 0 1.273772 -2.572847 0.05834718 4 3 s 15 s 16 s 17 s atom 10 - H H - 0 1.787607 -0.6695102 -0.8316305 1 3 s atom 11 - O O2 - 0 1.94787 -0.556186 1.225945 2 3 s 18 s atom 12 - C C4 - 0 -1.630084 1.533808 0.05834718 4 4 s 19 s 20 s 21 s atom 13 - O O2 - 0 0.4959426 1.497142 1.225945 2 4 s 22 s atom 14 - H H - 0 0.3356788 1.383818 -0.8316305 1 4 s atom 15 - H H - 0 2.301435 -2.936177 0.05834718 1 9 s atom 16 - H H - 0 0.7599488 -2.936177 0.9483346 1 9 s atom 17 - C C4 - 0 0.5478045 -3.086186 -1.199052 4 9 s 23 s 24 s 25 s atom 18 - C C4 - 0 3.296089 -1.032847 1.225945 4 11 s 26 s 27 s 28 s atom 19 - C C4 - 0 -1.630084 3.073808 0.05834718 4 12 s 29 s 30 s 31 s atom 20 - C C4 - 0 -2.356036 1.02048 -1.199066 4 12 s 32 s 33 s 34 s atom 21 - H H - 0 -2.143918 1.17047 0.9483249 1 12 s atom 22 - H HO - 0 0.4959426 2.457142 1.225945 1 13 s atom 23 - H H - 0 0.5478087 -4.176187 -1.199045 1 17 s atom 24 - H H - 0 -0.4798602 -2.722861 -1.19904 1 17 s atom 25 - H H - 0 1.061625 -2.722853 -2.08904 1 17 s atom 26 - H H - 0 3.809913 -0.6695179 2.115932 1 18 s atom 27 - H H - 0 3.296089 -2.122847 1.225945 1 18 s atom 28 - H H - 0 3.809924 -0.66951 0.3359675 1 18 s atom 29 - H H - 0 -2.657747 3.437137 0.05834718 1 19 s atom 30 - H H - 0 -1.11626 3.437137 0.9483346 1 19 s atom 31 - H H - 0 -1.11625 3.437145 -0.8316305 1 19 s atom 32 - H H - 0 -3.383699 1.383809 -1.199066 1 20 s atom 33 - H H - 0 -1.842204 1.383833 -2.089039 1 20 s atom 34 - H H - 0 -2.356027 -0.06952006 -1.19908 1 20 s endmol 1 Cheers Gerardo Prof. Gerardo Burton Departamento de Quimica Organica Facultad de Ciencias Exactas y Naturales Universidad de Buenos Aires e-mail: burton@qo.fcen.uba.ar Tel/Fax: 54 1 788-6915 From: Morten_Langgård@hyper.com Sent: Monday, July 06, 1998 6:37 AM To: 'Hyperlist' Subject: Amber5 subject etc. Dear all, Last weeks posting about implementation of Amber5 parameters into HyperChem by Ed Bertaccini and Ulrich Harttig asked for some input on the development subject. I would also be very pleased if someone at HyperCube (just sometimes) would send out some signals on what kind of development the users can expect to see in the next release. This happens very rarely and almost only when somebody on this list have posted some provocative statements. I have usually made an annual (friendly) posting of complaints about a topic like the Amber5 case. My favorite topics have been about the MM+ implementation and the very slow ab initio performance (full discussions can be found in the archive if anybody should be interested, especially in June '97). The official response to these questions has been very limited-so I am not surprised that you haven't heard anything about the Amber5 problem. It appears to me that the development of HyperChem progresses very slowly-at least it is very hard to see if it is moving at all. That's really a petty because HyperChem is an outstanding product and is still the perfect choice for educational purposes. In my opinion HyperChem has only improved slightly since release 3 in spring '93. (I recognizes that there have been made some improvement in the graphics (version 5) and that we have had a worthless ab initio module since release 4.5.) The latest release 5.1 -- the "new line up" is really a joke! I bought it anyway :-) The Professional version is nothing but a re-wrapping of 5.0 bundle with the old visual basic program ChemPlus - not really what I had expected. By the way - The ChemPlus program as well as Marcio Cyrillo's HyperSpin program demonstrates beautifully some of the hidden power in the HyperChem design. The scripting language, DDE and the SDK package is a very unique feature for computational chemistry software. But what next HyperCube? When will HyperChem improve-significant? I recently received a letter from Wavefunction Inc. announcing the release of PC Spartan Pro this fall (they are usually right about release announcements). PC Spartan Pro should be a complete implementation of the current Spatan version 5.0 for UNIX. If that is true-I guess that your are facing a really hard competitor for small molecule modeling on the PC market. This release should include the DFT methods, MMFF(94) as well as the molecular spreadsheets known from version 5. I really which that HyperChem would be equally attractive. Anyway-HyperChem will still have the best builder. (I wonder if this statement is provocative enough). Kind regards Morten ======================== ======================== Morten Langgård, Dept. 814, Computational Chemistry. H. Lundbeck A/S, Ottiliavej 9 Dk-2500 Valby, Copenhagen. Denmark Phone: (+45) 36 44 24 25 tone 2936, Fax: (+45) 36 30 13 85 e-mail: mol@lundbeck.com ======================== ======================== From: jsalb@ix.netcom.com Sent: Tuesday, July 07, 1998 12:36 PM To: hyperchem@hyper.com Subject: Developments at Hypercube over the last year Almost exactly a year ago I posted a message to this list, commenting on the extremely slow pace of development and bug-fixing at Hypercube. My post read: >...I would point out that Hyperchem 5.0 and ChemPlus 1.6 > have been out for months and the bugs they contain > have still not been fixed. >Indeed, there seems to be no evidence that any > significant development is going on at Hypercube. >The GUI remains far behind those offered by other >computational chemistry packages. >OpenGL? Direct3D? Not likely. >Regards, >Jesse Neil Ostlund's response to the list is reposted below. I leave it to the readers of this list to judge to what extent Hypercube has fulfilled their commitment to their users, in terms of new features, technical support, and bug-fixes. >Recently, Jesse Salb (jsalb@ix.netcom.com) has made >comments about HyperChem that I find very misleading >and somewhat objectionable. I would like to comment on them. >HyperChem 5, LIKE EVERY MAJOR SOFTWARE PACKAGE, >contains a certain number of bugs. The bugs in our current >release seem to be quite minor, as far as we can tell, >and patches available on our www site have addressed the >principal ones. Like other major commercial software >developers, we don't issue informal and continuous bug fixing but >address known bugs in future software releases unless a bug >is really catastrophic. We are aware of no catastrophic bugs >in HyperChem 5. We generally are quite proud of HyperChem's >robustness compared to other molecular modeling software. >>Indeed, there seems to be no evidence that any significant >>development is going on at Hypercube. >We believe HyperChem 5, our relatively recent new release, >adds a host of new capability to HyperChem and we are very >proud of this product. Obviously, we don't describe the details >of our ongoing development and new products to the public > but you can be assured that much significant development is > going on at Hypercube - none of which I am sure Jesse >knows or should know about. >>The GUI remains far behind those offered by other >>computational chemistry packages. >I remain convinced that our GUI is far ahead of any other > manufacturer. A good GUI is primarily concerned with making >it easy to do chemistry and molecular modeling not just >with generating artwork. No one has features like HyperChem >for dealing with drawing 3D structures, selection, basis sets, >transition states, etc. A host of other major GUI features of >HyperChem seem to be beyond any competitor. >>OpenGL? Direct 3D? Not likely. >It is a mystery to me how Jesse knows anything about our >development plans much less details around whether we >are adopting specific libraries such as these. One of >HyperChem's great strengths in the past has been the >3D rendering capability that was available from in-house >code that required only 2D graphics cards and 2D primitives. >As 3D hardware primitives become available in commodity >PC graphics cards and 3D libraries like OpenGL and Direct3D >become mainstream, you can be sure Hypercube will be there. >Neil S. Ostlund President and CEO >Hypercube, Inc. 1115 NW 4th Street >Gainesville, Florida 32601 >Tel: (352) 371-744 Fax: (352) 371-3662 >E-Mail: ostlund@hyper.com WWW: http://www.hyper.com From: Todd Richmond [trichmon@jsd.claremont.edu] Sent: Tuesday, July 07, 1998 4:29 PM To: hyperchem@hyper.com Subject: Re: Developments at Hypercube over the last year My $0.02 >Almost exactly a year ago I posted a message to this list, commenting >on the extremely slow pace of development and bug-fixing at Hypercube. >My post read: > >>...I would point out that Hyperchem 5.0 and ChemPlus 1.6 >> have been out for months and the bugs they contain >> have still not been fixed. HC5 has been fairly robust on my machines...the only major problems I encountered were when I tried to run the program on a 6x86 machine. Intel and AMD machines have been fine though... >>Indeed, there seems to be no evidence that any >> significant development is going on at Hypercube. > >>The GUI remains far behind those offered by other >>computational chemistry packages. As far as I can tell, HC is the ONLY easy to use package that does large molecules. Are you comparing HC to other PC packages? To SGI packages? Do you think Macromodel has a more intuitive GUI/is easier to use? Not in my experience. WIth HC ALL of my undergrad students working in the lab now do a significant amount of protein modeling and virtual mutagenesis. This was not the case with SGI-based software, and was not possible with other PC software I am aware of. If there is other stuff out there, please let me know. >>OpenGL? Direct3D? Not likely. Don't know about what they are doing, but as long as I can easily do virtual mutagenesis, I don't care much about rendering and display...there are other programs that do that well. I need software that allows me to make the molecules and do calculations quickly and easily...and is user-friendly enough for undergrads. HC seems to do fairly well on these fronts. It ain't perfect, but it works for me. Have fun, Todd ------------------------------------ Todd Richmond, Ph.D. Assistant Professor of Chemistry The Claremont Colleges http://enzyme.claremont.edu From: Morten_Langg=E5rd?= [MOL@Lundbeck.com] Sent: Thursday, July 09, 1998 2:32 AM To: 'Hyperlist' Subject: Developments etc. Dear Todd, Jesse and anybody else interested. The last thing I wanted by my posting the other day was to start a "for or against" HyperChem war. I simply wanted to learn a little about what we can expect from HyperCube in the future. I am definitely a HyperChem fan - but it has become increasingly more difficult to recommend the program to colleagues and friends in the last couple of years. This is the situation I don't like - stagnation! I want to hear some constructive critics and suggestions from the list members (how many are we anyway). Nevertheless I can't help comment on some of Todd's comments - even though that I mostly agree with him. >HC5 has been fairly robust on my machines...the only major problems I >encountered were when I tried to run the program on a 6x86 machine. >Intel and AMD machines have been fine though... Yes - HyperChem is very robust but it is also very easy to stay on the road when your speed is only a few Mph. >As far as I can tell, HC is the ONLY easy to use package that does large >molecules. Are you comparing HC to other PC packages? To SGI packages? >Doyou think Macromodel has a more intuitive GUI/is easier to use? Not in >my experience. WIth HC ALL of my undergrad students working in the lab now >do a significant amount of protein modeling and virtual mutagenesis. This >was not the case with SGI-based software, and was not possible with other PC >software I am aware of. If there is other stuff out there, please let me know. I am truly impressed by your students - Todd. I personally find protein modeling very difficult with HyperChem but I realize that it can be done. What I really miss in HC is a depth cueing display and some = better options for selections and blanking off different parts of these large molecules.=20 Your are mentioning MacroModel which currently only is available for Unix workstations (an NT version will be available for the next version 7). MacroModel is just like HyperChem among my favorites. This is not because of the rather old GUI but because of the very fast and solid MM engine (BatchMin). All the force fields, the conformational search algorithms, solvations models and the MD stuff available in MacroModel are all "state of the art". It is really unfair to compare these implementations with the methods currently available in HyperChem.=20 HC is 5-10 years behind - but for what reason?=20 Most of these methods are fully described in the literature and more or less PD. HyperChem really needs an update in this field. It would be nice to see Amber 5, MMFF(94), MM3* and a fast conformational search module in HyperChem. However, it should be mentioned that MacroModel does not have any QM models implemented. It is a really nice thing that HyperChem can do = both MM and QM on the fly (keeping it all in the memory) - I do love this feature. But as I already have mentioned in some of my earlier postings the = value of the ab initio module is very limited (it is so slow and demanding that it only can be used for molecules with less than about 5 heavy atoms). The implementation is indeed user friendly but nevertheless worthless for anything else than teaching students about the Hydrogen molecule. Drop the ab initio module and use the resources saved to improve the other parts of the program. Regards Morten =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D = =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D = Morten Langg=E5rd,=20 Dept. 814, Computational Chemistry. H. Lundbeck A/S, Ottiliavej 9 Dk-2500 Valby, Copenhagen. Denmark Phone: (+45) 36 44 24 25 tone 2936, Fax: (+45) 36 30 13 85 e-mail: mol@lundbeck.com =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D = =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D = From: Stevie T [s.m.todd@chem.hull.ac.uk] Sent: Friday, July 10, 1998 2:58 AM To: hyperchem@hyper.com Subject: Re: Developments etc. Hello all.... As an original Cerius2 on the SGI user, I was introduced to Hyperchem at the start of this year. My experience of Cerius2 was based around basic MM of single molecules with torsional changes and some conformational analysis. I found all this very easy to do on Cerius2 but I couldn't do more complex things such as repetitious work without having to learn Tcl or some other scripting langauge. This is where I feel that Hyperchem excels itself. It is very easy to write reasonably complex scripts to output lots of data without having a massive knowledge of programming. The ability to control semi-empirical data is also very useful. However, I find the drawing interface quite annoying as it is very hard just to change a torsion angle (as compared with Cerius2 and Nemesis). I also find it annoying that you can minimise a structure, change one torsion angle and have to rebuild and re-minimise the whole lot again. Maybe this is just my limited experience. On the whole though, I find Hyperchem a very useful package for the power of it's scripting language, and, if the few other niggles were sorted out, it would be even better. Cheers for reading Steve -- "I used to think the brain was the most important organ in the body, 'til I realized yeah, look what's telling me that." -- Emo Phillips mail to : S.M.Todd@chem.hull.ac.uk web-site: http://www.hull.ac.uk/php/chpsmt/ From: Gianfranco Ercolani [ercolani@uniroma2.it] Sent: Thursday, July 09, 1998 11:33 PM To: 'Hyperlist' Subject: Hyperchem and G94W Dear All, Has anyone out there tried to interface Hyperchem with Gaussian 94W ? I know that G94W can be interfaced with Chem3D, so I think that exploiting the SDK it should be possible to interface G94W with HC. This would be a nice add-on remedying some of the deficiencies of the ab-initio module in HC and providing G94W with a powerful GUI. Any opinion about that ? Regards, Gianfranco 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: Kazuo Koyano [kkoyano@cbi.or.jp] Sent: Sunday, July 12, 1998 5:11 AM To: Gianfranco Ercolani Cc: hyperchem@hyper.com Subject: RE: Hyperchem and G94W Dear Prof. Gianfranco Ercolani; >Dear All, >Has anyone out there tried to interface Hyperchem with Gaussian 94W ? I >know that G94W can be interfaced with Chem3D, so I think that exploiting >the SDK it should be possible to interface G94W with HC. This would be a >nice add-on remedying some of the deficiencies of the ab-initio module >in HC and providing G94W with a powerful GUI. Any opinion about that ? > There were description on the interface Hyperchem with Gaussian 94W, in the 1st version of the book 'Exploring Chemistry with Electronic Structure Methods: A Guide to Using Gaussian' by Foresman and Frisch. The interfaces are two; one is the structure format conversion, and the other is displaying vibratinal analysis. As to the former, it is fairly covered by 'NewZMat File Conversion' utility in the utilities menu. For further conversion, it serves the 'Babel' a free software which has been introduced in this e-mail message corner, URL: http://mercury.aichem.arizona.edu/babel.html. As to the later, it is in a FAQ of Gaussian's home page, http://www.gaussian.com/. Sincerely Yours. Kazuo Koyano Koyano Research Laboratory Midorigoka 2-2-9, Meguroku Tokyo 152-0034, Japan Tel & Fax +81-3-3725-0319 E-mail kkoyano@cbi.or.jp From: Gerardo Burton [burton@qo.fcen.uba.ar] Sent: Monday, July 13, 1998 8:38 AM To: Hyperchem Subject: RE: Hyperchem and G94W Hi I agree that a good interface to Gaussian 94W (actually G98W is already available) would be great. Creating job files for G 94 from a .zmt file from Hyperchem is fairly straightforward with the Newzmat utility in G94 (of course writing directly a .gjf would be better), but getting the infomation out from a G 94 output file is another story. The conversion via PDB proposed by Gaussian is bad (coordinates are "rounded" to a fixed number of decimal places and the structure is no longer accurate) and MOPAC type files generated by the Newzmat utility are not always read correctly by Hyperchem (they may, however, be read with PCModel and then rewritten with this program in MOPAC format which is equivalent to .zmt files). Of course the really useful thing would be an utility that could read a G 94 output file and get info not only on coordinates, but on orbitals, vibrations, etc, etc so that all the great display features in Hyperchem could be used on the G 94 data (something like Gaussview or the GUI in AMPAC 6.0 can do). In this way we could run our ab initio or DFT calculations fast and efficiently with the highly optimized algorithms in G 94W and then have the friendly user interface in HC 5.x to view the results. Cheers Gerardo PS. By the way, there has been no answer yet from HC support on the chirality assignment errors in HC 5. Prof. Gerardo Burton Departamento de Quimica Organica Facultad de Ciencias Exactas y Naturales Universidad de Buenos Aires e-mail: burton@qo.fcen.uba.ar Tel/Fax: 54 1 788-6915 -----Original Message----- De: Gianfranco Ercolani Para: 'Hyperlist' Fecha: viernes 10 de julio de 1998 21:04 Asunto: Hyperchem and G94W >Dear All, >Has anyone out there tried to interface Hyperchem with Gaussian 94W ? I >know that G94W can be interfaced with Chem3D, so I think that exploiting >the SDK it should be possible to interface G94W with HC. This would be a >nice add-on remedying some of the deficiencies of the ab-initio module >in HC and providing G94W with a powerful GUI. Any opinion about that ? >Regards, >Gianfranco > > > >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: Pastorek, Christine [christine.pastorek@orst.edu] Sent: Monday, July 13, 1998 1:18 PM To: Hyperchem Subject: RE: Hyperchem and G94W I posted this same question to this list at least a year ago, and did not receive any answers-I'm hopeful that there is now a solution? Recently people in our department have been using Chem3D to read the checkpoint files from G94 and render spin densities, etc. The rendering quality in Chem3D is not nearly as nice as what HyperChem can do and I think that the only way to get the output is to do a printscreen. The Shareware program Babel is suppose to be able to convert many file types to .hin format, but that doesn't help if you want to render orbitals, or other molecular properties. I haven't had much luck using Babel anyway. Chris Pastorek Dr. Christine Pastorek Integrated Laboratory Program Director Department of Chemistry Gilbert Hall 153 Oregon State University Corvallis, OR 97331-4003 Voice: (541) 737-6732 FAX: (541) 737-2062 mailto:pastorekc@chem.orst.edu > -----Original Message----- > From: Gerardo Burton [SMTP:burton@qo.fcen.uba.ar] > Sent: Monday, July 13, 1998 8:38 AM > To: Hyperchem > Subject: RE: Hyperchem and G94W > > Hi > I agree that a good interface to Gaussian 94W (actually G98W is already > available) would be great. Creating job files for G 94 from a .zmt file > from > Hyperchem is fairly straightforward with the Newzmat utility in G94 (of > course writing directly a .gjf would be better), but getting the > infomation out from a G 94 output file is another story. The conversion via > PDB > proposed by Gaussian is bad (coordinates are "rounded" to a fixed number > of decimal places and the structure is no longer accurate) and MOPAC type > files generated by the Newzmat utility are not always read correctly by > Hyperchem (they may, however, be read with PCModel and then rewritten with > this > program in MOPAC format which is equivalent to .zmt files). > Of course the really useful thing would be an utility that could read a > G 94 output file and get info not only on coordinates, but on orbitals, > vibrations, etc, etc so that all the great display features in Hyperchem > could be used on the G 94 data (something like Gaussview or the GUI in > AMPAC 6.0 can do). In this way we could run our ab initio or DFT calculations > fast and efficiently with the highly optimized algorithms in G 94W and then > have the friendly user interface in HC 5.x to view the results. > Cheers > Gerardo > > PS. By the way, there has been no answer yet from HC support on the > chirality assignment errors in HC 5. > > Prof. Gerardo Burton > Departamento de Quimica Organica > Facultad de Ciencias Exactas y Naturales > Universidad de Buenos Aires > e-mail: burton@qo.fcen.uba.ar > Tel/Fax: 54 1 788-6915 > -----Original Message----- > De: Gianfranco Ercolani > Para: 'Hyperlist' > Fecha: viernes 10 de julio de 1998 21:04 > Asunto: Hyperchem and G94W > > > >Dear All, > >Has anyone out there tried to interface Hyperchem with Gaussian 94W ? I > >know that G94W can be interfaced with Chem3D, so I think that exploiting > >the SDK it should be possible to interface G94W with HC. This would be a > >nice add-on remedying some of the deficiencies of the ab-initio module > >in HC and providing G94W with a powerful GUI. Any opinion about that ? > >Regards, > >Gianfranco > > > > > > > >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: Marcio Cyrillo - pos [cyrillo@ifi.unicamp.br] Sent: Tuesday, July 14, 1998 12:05 PM To: hyperchem@hyper.com Subject: Re: HyperChem and G94W Dear Gianfranco and all HyperChemists, I was trying to develop an useful interface between HyperChem and Gaussian 94W as I told before to some people (Gerardo Burton for instance). Unfortunately I have only the evaluation copy of HyperChem, which has already expired. I have developed some applications to interact with HyperChem (see www.ifi.unicamp.br/~cyrillo/hyperspin/hspin.html) which was a very funny job for me and useful for some users (as they let me know). Krassimir Stravrev, formerly from HyperCube staff told me I deserved some award for my "precious job" but since then I haven't received anything (I expected at least a HyperChem copy for me to keep working). That is why I do not plan to continue developing tools specifically for HyperChem (which I found a very good package although it could be better in certain aspects). Next month or so, I am going to make available a new software that integrate commonly used freeware chemistry programs (like babel, rasmol, etc) in a useful way: a text editor specially designed to chemists. Best regards, Marcio. From: Stephan Benicke [benicke@vossnet.de] Sent: Friday, July 17, 1998 11:04 AM To: hyperchem@hyper.com Subject: Solvent Cage / IR spectra question Hello Hyperchem users , I've two , I hope little , problems . The first one is with the New Solvent Cage macro for Excel 7 from Dr. Jicsinszky . I could not get it to work properly ( sure I set the language to English/US ) . The expected solvent cage is produced but it does not open in HC 4.5 . Only a error message appears : bad atom record in file meoh_sb.hin . Has anyone experience with this macro , HC 4.5 , Excel 7 ( german ) and Win 95b ( german ) ? My second problem is that I want to correlate predicted and real IR spectra . For this reason I would find it easier if it were able to generate a spectra with gaussian or lorentzian band shapes of the HC data . Does anybody know a solution for this problem ? Thanks to all By Stephan Stephan Benicke Tel. : +49-4222-3559 Fahrenerweg 64 Fax : +49-4222-70686 27777 Ganderkesee benicke@vossnet.de Germany From: Laurence Lavelle [lavelle@mbi.ucla.edu] Sent: Tuesday, July 28, 1998 1:11 PM To: hyperchem@hyper.com Subject: Please try the following. If you have NT4 (SP3) and HyperChem 5.1 Professional I would appreciate your feedback on the following. Please email me directly. Thanks. Build a piece of DNA (single or double strand). Add sodium counter ions. Amber force field (distance dependent = 1) (1-4 scale factors 0.5) (no cutoff) Open log file. Run MD: Heat time 20 ps Starting temperature 0 K Run time 60 ps Simulation temp. 100K Cool time 20 ps Final temp. 0 K Step size 0.0001 ps Temperature step 0.0005 K In vacuum. Constant temperature and bath relaxation time of 0.2 ps. Data collection period and data step both = 1. Start and then stop after ~10mins. Open the log file and look at the temperature of each step. What do you see? Laurence From: Klaus-D. Warzecha [warzecha@cityweb.de] Sent: Thursday, July 30, 1998 2:40 AM To: hyperchem@hyper.com Subject: optimization (DDE vs. HAPI-Call) and Notification Dear HyperChemists, concerning the external control of force-field optimizations via visual basic (VB), I would like to ask a little question. Imagine a bunch of conformations to be optimized in a multi step process (coarse and fine optimization with different algorithms, etc.) using MM+. When an optimization is launched via a LinkExecute statement in VB, finalization of the process raises the LinkClose event of the referring control element in VB, e.g. a TextBox. This event thus might be used to trigger further actions in HyperChem, such as an evaluation, whether the run has converged. On the other hand, an optimization might be started using a HAPI call, such as lngRetVal=hbExecTxt("do_optimization"). Now, will a lngRetVal of 1 really indicate the finalization of the the calculation, or is it merely an acknowledgement of HyperChem, that the command was understood and the referring process was started. In case of the latter, what is the benefit using the HAPI call in this context. In general, it would be interesting to know, how a notification (without using the notification agent) can be established, i.e. how to setup the callback function in VB. Yours, K.-D. Warzecha From: Journal of Molecular Modeling [jmolmod@organik.uni-erlangen.de] Sent: Friday, July 31, 1998 7:35 AM To: hyperchem@hyper.com Subject: J.Mol.Model.: BioMedLink Award OFFICE MEMO Date: 31/07/1998 BioMedLink Award Dear colleague, The 'Journal of Molecular Modeling' Internet site at http://www.ccc.uni-erlangen.de/jmolmod has been included in the BioMedLink database. The editorial board of BioMedLink has rated the site particularly interesting. BioMedLink is an evaluated and annotated database of Internet resources for the bio/medical community jointly created by BioMedNet (http://biomednet.com) and the University of Indiana. New entries are added weekly, and existing entries are reviewed and rated by our editorial board. BioMedLink has been described as 'the Yahoo for biological and medical researchers'. You can view the entry of the 'Journal of Molecular Modeling' at: http://biomednet.com/db/biomedlink/BMLK.13130 We would like to invite you to have a look by yourself and to browse through the pages of the 'Journal of Molecular Modeling'. If you do have any question, the members of the editorial office will be pleased to help you. Sincerely Yours, Tim Clark Henryette Roth (editor-in-chief) (assistant editor) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ^ Journal of Molecular Modeling ^ Tel: [+49](0)9131 / 85-6567 ^ ^ Computer-Chemie-Centrum ^ ^ ^ Naegelsbachstrasse 25 ^ Fax: [+49](0)9131 / 85-6565 ^ ^ D-91052 Erlangen ^ ^ ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ^ email: jmolmod@organik.uni-erlangen.de ^ ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ^ http://www.ccc.uni-erlangen.de/jmolmod ^ http://link.springer.de ^ ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ JOURNAL OF MOLECULAR MODELING - YOU MAKE THIS JOURNAL A SUCCESS