From uunet.ca!ibmmail.IBMMAIL.COM!usech592@hyper.hyper.com Thu May 19 14:28:21 1994 Date: Thu, 19 May 1994 10:28:21 -0400 From: ibmmail.COM!usech592@hyper.hyper.com To: hyperchem@hyper.com Subject: (U) ----------------------- Mail item text follows --------------- To: INTERNET--IBMMAIL Internet Communica From: John C. Hubbs, Chemistry Research Division, B-150B Subject: (U) What is the least painless way to purchase a hyperchem upgrade (4.0 and Chemplus). Can orders now be placed direct to Hypercube or are you still using some sort of a network? John Hubbs ________________________________________________________________________ From slee@hyper.hyper.com Thu May 19 19:20:51 1994 From: slee@hyper.hyper.com (Thomas Slee) Subject: Re: purchasing HyperChem To: hyper!hyperchem@uunet.ca Date: Thu, 19 May 1994 15:20:51 -0400 John Hubbs writes... | What is the least painless way to purchase a hyperchem upgrade (4.0 and | Chemplus). Can orders now be placed direct to Hypercube or are you still | using some sort of a network? I hope you mean the most painless way! Anyway, we do still sell through a distribution network: most of the resellers who were selling HyperChem for Autodesk are continuing to do so for us. If you don't know who your reseller is, contact Hypercube at (519) 725-4040 or e-mail to info@hyper.com and we'll send a reseller in your direction. Tom Slee -- Tom Slee, Hypercube Inc., 419 Phillip St., Waterloo, Ont., Canada, N2L 3X2 E-Mail: slee@hyper.com, Tel. (519)725-4040, Fax. (519)725-5193. ________________________________________________________________________ From uunet.ca!triton.unm.edu!jborn@hyper.hyper.com Thu May 19 20:50:56 1994 From: triton.unm.edu!jborn@hyper.hyper.com Subject: Hydorgen bonding and Pentium based machines To: hyperchem@HYPER.COM Date: Thu, 19 May 1994 16:50:56 -0400 Hyperchem users Has anyone experience with hydrogen bonding and Hyperchem? I am interested in modeling a alpha hydroxy lactone the chemical reactivity of which may be related to hydorgen bondng between the alpha hydroxy and the carbonyl. All hints will be appreciated. Has anyone experience with the Pentium processor and Hyperchem? I believe the processor for which I obtained a quote was a 90. Thanks in advance. Jerry Born Professor of Pharmacy jborn@triton.unm.edu ________________________________________________________________________ From uunet.ca!ibmmail.IBMMAIL.COM!usech592@hyper.hyper.com Fri May 20 14:44:26 1994 Date: Fri, 20 May 1994 10:44:26 -0400 From: ibmmail.COM!usech592@hyper.hyper.com To: hyperchem@hyper.com Subject: (U) ----------------------- Mail item text follows --------------- To: INTERNET--IBMMAIL Internet Communica cc: U856601 --ECDVM1 HUBBS JOHN C From: John C. Hubbs, Chemistry Research Division, B-150B Subject: (U) Dr. Born, I was originally going to send you this note to you directly rather than to the 'user's group'. However, on reflection I changed my mind and hope it is ok with you. I would love to see an extensive discussion of this topic as it is also an interest of mine. There is a series of red books entitled 'Reviews in Computational Chemistry' edited by Lipkowitz (sp?). In volume 2 you will find a chapter devoted to hydrogen bonding. This chapter deals mostly with the ab initio level claiming that the semi-empirical level poorly treats hydrogen bonding. From the data presented you would be advised to proceed with extreme caution (i.e. the hydrogen bonding energies are quantitatively unreliable at the semiempirical level). However, you might be able to 'force' a hydrogen bond (especially an intramolecular one) and make some sense out of the molecular orbitals and Mulliken charge distribution. Good luck! John Hubbs ________________________________________________________________________ From uunet.ca!chemie.uni-paderborn.de!GF@hyper.hyper.com Wed May 25 10:54:31 1994 From: "Gregor Fels" To: hyperchem@HYPER.COM Date: Wed, 25 May 1994 06:54:31 -0400 Subject: HyperChem and Excel Dear all, can somebody give me a hint on how to run successfully the exercises on driving HyperChem from Excel (e.g. exercise 3 of the "Getting started" handbook page 207)? I am working with HyperChem 3 and Excel 4.0 (German) on a 486 DX2 with 16 MB RAM. Running e.g. exercise 3 yields the following error messages (translated from German): - name not specified then clicking on o.k. gives: - macro error: non valid argument in Plot.XLM!B9 Could the trouble come from using the German Excel version with HyperChem? Changing the window environment to US-parameters however does not effect the result (still the same error mesaages). Dr. Gregor Fels Tel.: +49-(0)5251-602181 Universitaet-GH-Paderborn Fax: +49-(0)5251-603245 FB 13: Chemie und Chemietechnik email: gf@chemie.uni-paderborn.de Organische Chemie Warburgerstr. 100 D-33098 Paderborn Germany ________________________________________________________________________ From uunet.ca!e154jos2.tuwien.ac.at!ujordis@hyper.hyper.com Wed May 25 09:14:56 1994 To: chemie.uni-paderborn.de!GF@hyper.hyper.com Subject: Re: HyperChem and Excel From: email.tuwien.ac.at!ujordis@hyper.hyper.com (Univ. Doz. Dr. Ulrich Jordis , Associate Professor) Reply-To: email.tuwien.ac.at!ujordis@hyper.hyper.com Cc: hyperchem@hyper.com Date: Wed, 25 May 1994 05:14:56 -0400 >>Return-Path: <@mail.uunet.ca:uunet.ca!chemie.uni-paderborn.de!GF@hyper.hyper.com> >>From: Gregor Fels >>To: hyperchem@HYPER.COM >>Date: Wed, 25 May 1994 06:54:31 -0400 >>Subject: HyperChem and Excel >> >>Dear all, >>can somebody give me a hint on how to run successfully the exercises >>on driving HyperChem from Excel (e.g. exercise 3 of the "Getting >>started" handbook page 207)? >>I am working with HyperChem 3 and Excel 4.0 (German) on a 486 DX2 >>with 16 MB RAM. >> >>Running e.g. exercise 3 yields the following error messages >>(translated from German): >>- name not specified >>then clicking on o.k. gives: >>- macro error: non valid argument in Plot.XLM!B9 >> >>Could the trouble come from using the German Excel version with >>HyperChem? Changing the window environment to US-parameters however >>does not effect the result (still the same error mesaages). >> >> >> >>Dr. Gregor Fels Tel.: +49-(0)5251-602181 >>Universitaet-GH-Paderborn Fax: +49-(0)5251-603245 >>FB 13: Chemie und Chemietechnik email: gf@chemie.uni-paderborn.de >>Organische Chemie >>Warburgerstr. 100 >>D-33098 Paderborn >>Germany >> Auf jeden Fall im Excel die Einstellungen auf International bzw. US vornehmen! Wir haben an sich alle uebungen nachvollziehen koennen! -- ----------------------------------------------------------- Univ.Doz. Dr. Ulrich JORDIS ujordis@email.tuwien.ac.at Assistant Professor Inst. Organic Chemistry, A-1060 Vienna, Getreidemarkt 9, AUSTRIA Tel: +43 1 58801-5013 Fax: +43 1 586 6931 ________________________________________________________________________ From slee@hyper.hyper.com Wed May 25 13:32:59 1994 From: slee@hyper.hyper.com (Thomas Slee) Subject: Re: HyperChem and Excel To: hyper!hyperchem@uunet.ca Date: Wed, 25 May 1994 09:32:59 -0400 Gregor Fels writes... | | Dear all, | can somebody give me a hint on how to run successfully the exercises | on driving HyperChem from Excel (e.g. exercise 3 of the "Getting | started" handbook page 207)? | I am working with HyperChem 3 and Excel 4.0 (German) on a 486 DX2 | with 16 MB RAM. | | Running e.g. exercise 3 yields the following error messages | (translated from German): | - name not specified | then clicking on o.k. gives: | - macro error: non valid argument in Plot.XLM!B9 | | Could the trouble come from using the German Excel version with | HyperChem? Changing the window environment to US-parameters however | does not effect the result (still the same error mesaages). We have seen a very similar problem from a user in Spain. The problem in that case turned out to be the Excel nomenclature for cells. In the macors supplied with HyperChem cells are referred to by their relative position, so that rc[1] means this row, one column over, and r[1]c means this column, one row down. The customer replaced these references with their Spanish equivalent of lc[1] etc., and all worked well. Tom -- Tom Slee, Hypercube Inc., 419 Phillip St., Waterloo, Ont., Canada, N2L 3X2 E-Mail: slee@hyper.com, Tel. (519)725-4040, Fax. (519)725-5193. ________________________________________________________________________ From uunet.ca!KENTVM.KENT.EDU!IMCVEY@hyper.hyper.com Thu May 26 14:46:13 1994 Date: Thu, 26 May 1994 10:46:13 -0400 From: Iain McVey Subject: Saving files in alternative file types within a script. To: hyperchem@hyper.com We are attmpting to save a large number of .HIN files in .ZMT and .ML2 format. I had hoped to do this using a script file (i.e. open the file then use write-file ????.ml2 etc...) BUT when I run this script the files produced have the correct extension but the contents are still formatted as .HIN files. Is there some way around this or am I going to have to spend a couple of days doing this by hand? All sugestions welcomed Iain Imcvey@Kentvm.kent.edu ________________________________________________________________________ From slee@hyper.hyper.com Thu May 26 15:36:32 1994 From: slee@hyper.hyper.com (Thomas Slee) Subject: constraining ring systems in HyperChem (morphine). To: hyper!hyperchem@uunet.ca Date: Thu, 26 May 1994 11:36:32 -0400 The following message was sent to the old list address... | | Hello All, | | Is there any way to constrain the chirality of atoms in a ring system?? I'm | using HyperChem release 3 to build morphine and other drugs containing | rings systems and as far as I can tell obtaining the correct chirality is a | trial and error process. I've been assigning chirality by shift-clicking on | the atom in question and then repeating model building, but Geometry | Optimisation often undoes this change. Is there anyway around this?? | | Rachel Vallance | | Rachel Vallance ^ ^ | School of Pharmacy ' ' | University of Otago ' | Dunedin, N.Z. \___/ | Email: rachel.vallance@stonebow.otago.ac.nz ________________________________________________________________________ From slee@hyper.hyper.com Thu May 26 15:34:03 1994 From: slee@hyper.hyper.com (Thomas Slee) Subject: Re: Saving files in alternative file types within a script. To: hyper!hyperchem@uunet.ca Date: Thu, 26 May 1994 11:34:03 -0400 Iain McVey writes... | | We are attmpting to save a large number of .HIN files in .ZMT and .ML2 | format. I had hoped to do this using a script file (i.e. open the file | then use write-file ????.ml2 etc...) BUT when I run this script the files | produced have the correct extension but the contents are still formatted | as .HIN files. | | Is there some way around this or am I going to have to spend a couple | of days doing this by hand? | Setting the extension by itself does not force a change of file format. For each file you need to do the following steps in your script: file-format hin open-file a.hin file-format zmt write-file a.zmt Tom -- Tom Slee, Hypercube Inc., 419 Phillip St., Waterloo, Ont., Canada, N2L 3X2 E-Mail: slee@hyper.com, Tel. (519)725-4040, Fax. (519)725-5193. ________________________________________________________________________ From slee@hyper.hyper.com Thu May 26 21:16:46 1994 From: slee@hyper.hyper.com (Thomas Slee) Subject: Memory Requirements. HyperChem Technote. To: hyper!hyperchem@uunet.ca Date: Thu, 26 May 1994 17:16:46 -0400 Dear HyperChemists, This is the first in a set of technical notes for HyperChem users that I'll be posting irregularly over the next few weeks, dealing with some of the most common HyperChem questions we get asked. This note deals with memory requirements for calculations using HyperChem. For those of you interested, this note is available in uuencoded RTF format or uuencoded Word for Windows 6.0 format, upon request to info@hyper.com. As usual, any feedback may help improve future technical notes and is welcomed (within reason). Tom _______________________________________________________________________ HyperChem(R) Technical Note Memory Requirements For Calculations Using HyperChem. Copyright (C) 1994 Hypercube, Inc. _______________________________________________________________________ The details of this application note refer to HyperChem Release 4 for Windows, but the calculations work the same way for earlier Windows releases, so you should be able to transfer the results to your system. Types of memory =============== The memory available to HyperChem is the sum of random access memory (RAM) and swap space, or virtual memory. The latter is a section of a hard disk set aside for use by programs during their execution. Virtual memory is much slower than RAM, as disk access is required. However, the size of calculation that can be done depends only on the total memory available, RAM + swap space. In Windows, the size of your swap space is set in the Control Panel application, that is part of the "Main" application group. Choose the "386-Enhanced" item, and click on the "Virtual Memory" button to set this size. Memory Requirements: an Outline =============================== The total memory that needs to be available in order to carry out a calculation using HyperChem is as follows: 1. Memory required by Windows, DOS and items specified in your config.sys and autoexec.bat files, such as Smartdrive. 2. Memory required by the HyperChem executable (CHEM.EXE) 3. Memory required by the computational "backend" executable (NDO.EXE, EHT.EXE, MMPLUS.EXE or NEWTON.EXE) 4. Memory required to carry out the particular calculation. Items 1, 2, and 3 are independent of the molecular system under study. Item 4 depends on the particular calculation you are carrying out. You should note that any other applications running will also consume memory: when doing large calculations it may be necessary to ensure that you are not using other Windows applications. Finding the Amount of Memory Available on your Computer ======================================================= If you click on the "About" item under the Help menu of Program Manager, you will see the amount of memory currently available to you. In general, this does NOT add up to the total of your RAM + swap space, but is substantially less. On a machine with 8 Mb RAM and 16 Mb of swap space, (which "should" have 24 Mb free) the value may be about 18 Mb. The difference is due to drivers and other items loaded in your config.sys and autoexec.bat files, as well as the basic DOS and Windows operating system requirements. Fixed Memory Requirements ========================= While running any calculation in HyperChem, memory is needed to load both the "front end" program (CHEM.EXE) and the computational "back end" program into memory. Fixed Memory Requirements for HyperChem Programs =================================================== Program Calculation Type Memory Required / KB --------------------------------------------------- HyperChem All 640 (CHEM.EXE) EHT.EXE Extended Huckel 670 NDO.EXE Other semi- 2,500 empirical MMPLUS.EXE MM+ 350 NEWTON.EXE Other molecular 200 mechanics =================================================== To find the memory available for a particular calculation, use the following procedure. 1. With no applications running in Windows, look at the About box in Program Manager to find the available memory. 2. Subtract 640 KB to account for loading HyperChem 3. Subtract the amount in the table above for loading the program appropriate for the method you are using. Calculation-Dependent Memory Requirements ========================================= NDO Calculations ---------------- The following figures are for AM1 or PM3 calculations. These methods are the most demanding of the semi- empirical methods: calculations on a similar size molecule using CNDO requires significantly less memory. SCF Calculation --------------- The major contribution to memory usage (not the only one) for a 'standard' RHF calculation is 104 * (Number of orbitals)2 bytes. If you are doing other kinds of calculation, additional memory is required: UHF: + 40 * (Number of orbitals)^2 bytes Convergence accelerator: + 160 * (Number of orbitals)^2 bytes Gradient Calculation -------------------- HyperChem computes the gradient for all kinds of calculation, so even for a single point calculation to complete, you will need space for a gradient evaluation. The gradient requirements are in addition to the SCF requirements. In the following expression, NHA = "non-hydrogen atoms", HA = "Hydrogen atoms". Memory required = 2400 * NHA * (NHA - 1) + 440 * NHA * HA + 24 * HA * (HA-1) bytes. For most systems, this is substantially less than the memory required for the SCF calculation. For systems with no hydrogens in, however (e.g., C60) the gradient requirements are comparable to that of the SCF. Examples --------- The "zero" in the following examples is the value given in the Program Manager Help with HyperChem running and NDO loaded. All calculations are AM1 RHF single points, with SCF convergence acceleration unchecked. NDO Memory Requirements ========================================== Molecular formula # of Extra memory orbitals used ------------------------------------------ CH4 (methane) 8 0 Mb C10H10 50 0.8 Mb (naphthalene) C16H10 (pyrene) 74 1.3 Mb C24H12 108 2.5 Mb (coronene) C30H18 138 4 Mb C40H22 182 8 Mb C48H24 216 9.5 Mb ========================================== Significant disk activity, and consequent slowing of the calculation, starts at around the amount of RAM in the computer. EHT Calculations ---------------- Extended Huckel calculations require significantly less memory than NDO calculations, because they do not include any three-electron integrals. The main data storage involves the orbital coefficients and various square matrices, such as the Hamiltonian and overlap matrices, each of which have N2 elements (N being the number of orbitals in the problem). The memory usage is proportional to the square of the number of orbitals involved in the calculation. Typical cases are shown in the figure. Extended Huckel Memory Requirements =============================== Number of Orbitals Memory / Mb ------------------------------- 0 0 90 0.4 180 1.5 270 3.4 360 6 =============================== MM+ Calculations ---------------- The memory requirements for the MMPlus program are proportional to the square of the number of atoms in the system. MMPlus keeps a list of all interactions in the system, and as each atom interacts with all others, this dictates a quadratic dependency. The graph below indicates requirements in addition to the static requirements described above. MM+ Memory Requirements ====================== Number of Memory atoms Used ---------------------- 10 0.58 60 0.58 258 0.8 652 2 904 3.2 1304 5.2 1956 9.7 ====================== Newton Calculations ------------------- The Newton program is more efficient than MMPlus in its memory requirements (as well as in speed) and maintains only information about each atom, not about each interaction. Consequently, the memory requirements for Newton are proportional to the number of atoms. The following graph indicates the requirements in addition to the static requirements outlined above. Newton Memory Requirements ====================== Number of Memory atoms Used ---------------------- 472 0.74 944 1.1 1888 1.8 3776 3 ====================== _______________________________________________________________________ HyperChem is a registered trademark of Hypercube, Inc. Hypercube, Inc. Tel. (519) 725-4040 419 Phillip Street Fax. (519) 725-5193 Waterloo, Ontario E-Mail. info@hyper.com Canada N2L 3X2 ________________________________________________________________________ From uunet.ca!stamail1.vut.edu.au!yurel@hyper.hyper.com Fri May 27 10:01:00 1994 From: "Yuriev, Elizabeth" To: hyperchem Subject: restraining planar geometry Date: Fri, 27 May 1994 06:01:00 -0400 Hello,netters, I'm trying to optimize geometry of cis-diammine platinum complexes using MM force field (I use Hyperchem, Release 3). NH3(1) ! ! Cl(2)----Pt(3)----NH3(4) ! ! Cl(5) Pt(II) usually produces square complexes, but in some cases in calculations structures collapse to tetrahedral ones with lower MM energy. I tried: 1)restraining (1)-(3)-(5) and (2)-(3)-(4) angles to 180 degrees - it put unnecessary limits on symmetry and produced N-Pt-N and Cl-Pt-Cl angles very close to 90 degrees (experimental values: 73 and 96 corresp.) 2)restraining (1)-(2)-(3)-(5) and (1)-(3)-(4)-(5) torsion angles to 180 degrees produced structure with Cl-Pt-Cl angle of 130 degrees (exper. 96) 3)restraining all five atoms to PLANE but this selection limited to 4 atoms The question is : how can I restrain the planar geometry during MM calculation, considering that the only limitation should be position of all five atoms in one plane without affecting bond lengthes and (especially!) bond angles. Authors of recent paper in Inorg. Chim. Acta ( 217(1994),159 ) suggested fixing atoms in xy plane, but tethering option in Hyperchem requires fixing of all three coordinates. Is there any way to fix only z-coordinate (e.g. z=0 for all atoms)? Thanks in advance to anybody who could help. I'm pretty desperate. Mrs Elizabeth Yuriev Victoria University of Technology Melbourne Australia Tel: 61 (3) 365 2217 Fax: 61 (3) 365 2465 E-mail:Elizabeth=Yurel@vut.edu.au ________________________________________________________________________ From slee@hyper.hyper.com Mon May 30 17:23:23 1994 From: slee@hyper.hyper.com (Thomas Slee) Subject: Building fused rings. To: hyper!hyperchem@uunet.ca Date: Mon, 30 May 1994 11:42:53 -0400 A recent posting addressed the question of building specific conformations of fused ring systems using HyperChem's model builder. While the stereochemistry tools provide help with this, there is not as far as I know any one panacea for the problem. The relevant section of the documentation is pp 257 to 263 of the Reference manual (Release 4) or pp 62 to 72 of the New Features book (Release 3). The following points are perhaps worth highlighting: o Building in an incremental fashion may be helpful: if portion of the molecule is selected, only those atoms are modified by the model builder. o Applying the model builder to an existing 3D structure keeps all existing stereochemistry. Therefore, if only one site has incorrect stereochemistry, using the Shift-Click mechanism to require that centre to change stereochemistry will leave all others unchanged. o Ring conformation is a somewhat different, though overlapping, problem compared to stereochemistry, and HyperChem does not have specific tools to impose ring conformations. o Side chain stereochemistry, and stereochemistry of non-fused rings, may be switched after building in a straightforward manner, so you don't have to worry about this in the setup of the initial building. The spcific molecule mentioned was morpphine, so here is an AM1 optimized structure of that system (there may be a couple of long lines that get wrapped in the mailer). Tom Slee ;COMPOUND: morphine ;STRUCTURE: AM1 optimized. forcefield mm+ sys 0 mol 1 atom 1 - C CA s -0.1224031 -0.06100124 -2.805998 -0.7519341 3 2 a 6 a 22 s atom 2 - C CA s -0.05076456 0.08064999 -1.417395 -0.9145519 3 1 a 3 a 7 s atom 3 - C CA s -0.1234546 -0.7610191 -0.622954 -0.1529213 3 2 a 4 a 10 s atom 4 - C CA s 0.05520916 -1.520777 -1.111963 0.9239396 3 3 a 5 a 11 s atom 5 - C CA s 0.05889273 -1.66 -2.492901 1.083589 3 4 a 6 a 17 s atom 6 - C CA s -0.1788683 -0.9408914 -3.324703 0.1993012 3 5 a 1 a 23 s atom 7 - C C4 s -0.1464343 1.167585 -0.7691268 -1.702831 4 2 s 8 s 24 s 25 s atom 8 - C C4 s 0.004302263 1.313697 0.7773888 -1.510266 4 7 s 9 s 18 s 26 s atom 9 - C C4 s -0.06565237 0.798133 1.16854 -0.1087079 4 8 s 10 s 13 s 27 s atom 10 - C C4 s -0.02168369 -0.7125361 0.8691396 -0.09604979 4 9 s 3 s 12 s 21 s atom 11 - O O2 s -0.1933584 -1.953124 -0.09682148 1.770105 2 4 s 12 s atom 12 - C C4 s -0.009635925 -1.424664 1.171443 1.249337 4 11 s 10 s 15 s 28 s atom 13 - C C3 s -0.1381788 1.020521 2.532937 0.4322784 3 9 s 14 d 29 s atom 14 - C C3 s -0.1723056 0.4082452 2.831522 1.589755 3 13 d 15 s 30 s atom 15 - C C4 s 0.05043936 -0.4551352 1.802895 2.264475 4 14 s 12 s 16 s 31 s atom 16 - O O2 s -0.3210549 -1.171064 2.446899 3.306682 2 15 s 32 s atom 17 - O O2 s -0.2333922 -2.454048 -2.970809 2.097987 2 5 s 33 s atom 18 - N N3 s -0.2591376 0.6711727 1.592564 -2.53765 3 8 s 19 s 20 s atom 19 - C C4 s -0.1148868 1.297315 1.519658 -3.834776 4 18 s 34 s 35 s 36 s atom 20 - C C4 s -0.06441832 -0.7689063 1.382468 -2.584862 4 21 s 18 s 37 s 38 s atom 21 - C C4 s -0.1350131 -1.437884 1.581682 -1.227198 4 20 s 10 s 39 s 40 s atom 22 - H H s 0.1357156 0.5420498 -3.494471 -1.360858 1 1 s atom 23 - H H s 0.1339177 -1.049041 -4.414715 0.2998289 1 6 s atom 24 - H H s 0.09701467 1.034871 -1.00266 -2.793035 1 7 s atom 25 - H H s 0.09370857 2.140442 -1.235357 -1.385697 1 7 s atom 26 - H H s 0.1008883 2.417956 1.012167 -1.552203 1 8 s atom 27 - H H s 0.1051623 1.314058 0.4611717 0.6110705 1 9 s atom 28 - H H s 0.1315443 -2.330108 1.82111 1.122423 1 12 s atom 29 - H H s 0.1468401 1.664106 3.22858 -0.1180371 1 13 s atom 30 - H H s 0.1525347 0.4919039 3.801131 2.097972 1 14 s atom 31 - H H s 0.09571958 0.1958311 0.9897468 2.70336 1 15 s atom 32 - H HO s 0.2131604 -1.704801 1.761922 3.730223 1 16 s atom 33 - H HO s 0.216315 -2.442206 -3.938102 2.047307 1 17 s atom 34 - H H s 0.0442239 1.197865 0.5172842 -4.335002 1 19 s atom 35 - H H s 0.0866099 0.8270284 2.292793 -4.49871 1 19 s atom 36 - H H s 0.08333975 2.388065 1.756072 -3.725519 1 19 s atom 37 - H H s 0.09113234 -1.202767 2.123391 -3.314341 1 20 s atom 38 - H H s 0.06010419 -1.021944 0.3454835 -2.95786 1 20 s atom 39 - H H s 0.09376234 -2.491416 1.203395 -1.293 1 21 s atom 40 - H H s 0.1001052 -1.475329 2.677058 -0.9860847 1 21 s endmol 1 ________________________________________________________________________ From slee@hyper.hyper.com Mon May 30 18:12:54 1994 From: slee@hyper.hyper.com (Thomas Slee) Subject: Re: restraining planar geometry To: hyper!hyperchem@uunet.ca Date: Mon, 30 May 1994 11:25:44 -0400 Yuriev, Elizabeth writes... | | I'm trying to optimize geometry of cis-diammine platinum complexes | using MM force field (I use Hyperchem, Release 3). | NH3(1) | ! | ! | Cl(2)----Pt(3)----NH3(4) | ! | ! | Cl(5) | | Pt(II) usually produces square complexes, but in some cases | in calculations structures collapse to tetrahedral ones with | lower MM energy. (material deleted) | | The question is : how can I restrain the planar geometry during MM | calculation, considering that the only limitation should be position | of all five atoms in one plane without affecting bond lengthes and | (especially!) bond angles. | There is a way of faking this: that may or may not meed your needs. rIif you add two "lone pairs" to the platinum atom and build it so they are opposite each other, the remaining groups will stay planar. | Authors of recent paper in Inorg. Chim. Acta ( 217(1994),159 ) | suggested fixing atoms in xy plane, but tethering option in Hyperchem | requires fixing of all three coordinates. Is there any way to fix only | z-coordinate (e.g. z=0 for all atoms)? There is not such a method at the moment. Yours Tom Slee -- Tom Slee, Hypercube Inc., 419 Phillip St., Waterloo, Ont., Canada, N2L 3X2 E-Mail: slee@hyper.com, Tel. (519)725-4040, Fax. (519)725-5193. ________________________________________________________________________ From uunet.ca!fox.cce.usp.br!szeinfel@hyper.hyper.com Tue May 31 10:27:29 1994 Return-Path: szeinfel@fox.cce.usp.br Date: Tue, 31 May 1994 09:24:24 -0400 From: Rafael N Szeinfeld Subject: Presentation To: hyperchem Hi All, I have just subscribed this list, I'm an undergraduated student at the Molecular Sciences Experimental Course, University of Sao Paulo, Brazil. I'm engaged in two research projects one deals with the inactivation of Trypsin at the active site by a carbon centered free radical and the other one deals with the simulation of protein structure using lattice models (with FORTRAN 77 in a sun workstation). I have Hyperchem 3.0 on a 486 dx50 MHz and I would like to use it for two porpouses: 1. try to simulate the structure of trypsin after the radical has reacted. 2. "play" with small peptides structure I'm as all you may be fascinated by the protein folding problem. Well, to finish this message I would like to know if there is any FAQ since I have basic questions that everybody have already asked once such as what for and how to use Molecular mechanics and/or Dynamics, where can I find references for the methods (something about the algorithms) used in hyperchem etc... Thanks for your attention. Rafael Najmanovich Szeinfeld