From: "alaa abdel-aziz" To: hyperchem@hyper.com Subject: I need help Date: Wed, 21 Oct 1998 03:12:48 PDT Hi I am Alaa Abdel-Aziz I have hyperchemsuite 5.1 for window95 I did not know how I can make docking between substrate and receptors so If any one intersted in this can help me in full details Thank you alaa Abdel-Aziz Fac.of Pharm.Sci. Kumamoto University Kumamoto862 japan Get Your Private, Free Email at http://www.hotmail.com From: "Gary Grant" To: Subject: Date: Mon, 19 Oct 1998 23:18:27 +0200 Has anyone got information or suggestion before I start attemting to start docking studies on Hyperchem specifically to methodologies and problems that anyone has experienced regards Gary Grant From: "Gary Grant" To: Subject: Date: Mon, 19 Oct 1998 22:54:11 +0200 Hi, i was just wandering if anyonne could help me with a few questions or more like concerns that I have ! I'm busy creating a solvent box of DMSO.... I've filled the box with these molecules and have run MD run on it for 1 Ps ... the molecules always leave the box partially and re-enter on the other side ...partially ... so I get these llong lines ...all across the screen ... How do i prevent this from happening ....and does this affect the property of the solvent at all ??? Any help will be appreciated Gary From: Yangqing Xu To: hyperchem@hyper.com Subject: Question about energy minimization in case of restraints Date: Sat, 17 Oct 1998 15:10:50 -0400 (EDT) Hello, Dear Hyperchemists, I'm pretty new to hyperchem molecular mechanics calculation. Recently, I was puzzled by what happened in the process of energy minimization when I apply "Tether to Other". I'm studying a single alpha-helix. Then I tether both its N-terminal and C-terminal to a new position. Because I choose rather large force constant, say, 10000, as I expected, the total energy increases a lot after I apply restraints. Then I start energy minimization. I found after several steps, the total energy increases (though very slowly), instead of minimizing. I calculated the energy of alpha-helix itself by removing the restraints and noticed that the alpha-helix energy is still being decreased while the total energy is increasing. So, I'm wondering whether HyperChem is doing energy minimization ONLY With the Energy of Alpha-Helix Itself, in stead of the total energy, which is the sum of helix energy and restraints energy. Besides, the total energy seems to keep decreasing if I choose SMALL force constant. I guess this is due to the small contribute of restraint energy. Is that correct? If anyone ever met this kind of problem, I am eager to hear from your suggestion. Thanks a lot for your help. Sincerely, Yangqing Xu From: "Pate, Millard" To: Hyperchem List Server Cc: "'mdavis@utep.edu'" Date: Tue, 13 Oct 1998 15:10:39 -0400 Hi Michael, Thank you for your inquiry regarding PalmChemTM . We expect HyperChem for the Palmtop PC, to be released in the fourth quarter of this year. We have not yet announced a price for this software. We are quite likely to bundle the software along with either the HP 620 or 660 palmtop PC models. Current projections for pricing are in the $999 range for the hardware and software Please watch our web page http://www.hyper.com/news/press/press_palm.html for more details on the latest developments for this exciting new platform! Thanks, Millard Pate Thank you for your interest in Hypercube Scientific Software. Millard E. Pate Director of Sales & Dealer Relations pate@hyper.com Hypercube, Inc. Florida Science and Technology Park 1115 NW 4th Street Gainesville, Florida 32601 U.S.A. Voice: 352-371-7744 Fax: 352-371-3662 Web Site: http://www.hyper.com -----Original Message----- From: Michael I. Davis [mailto:mdavis@utep.edu] Sent: Tuesday, October 13, 1998 8:47 AM To: hyperchem@hyper.com Subject: Palmtop - hyperchem I saw the ad on the back page of C & E News for the HP palmtop version of Hyperchem. I have a few questions. 1) When is this likely to hit the market? 2) What is the software price? 3) Is there any plan to bundle the software with either the HP 620 or 660? This looks like a fascinating combination. Michael I. Davis From: "Michael I. Davis" To: hyperchem@hyper.com Subject: Palmtop - hyperchem Date: Tue, 13 Oct 1998 09:47:01 -0600 I saw the ad on the back page of C & E News for the HP palmtop version of Hyperchem. I have a few questions. 1) When is this likely to hit the market? 2) What is the software price? 3) Is there any plan to bundle the software with either the HP 620 or 660? This looks like a fascinating combination. Michael I. Davis From: "Michael I. Davis" To: hyperchem@hyper.com Subject: Palmtop - hyperchem Date: Tue, 13 Oct 1998 09:47:01 -0600 I saw the ad on the back page of C & E News for the HP palmtop version of Hyperchem. I have a few questions. 1) When is this likely to hit the market? 2) What is the software price? 3) Is there any plan to bundle the software with either the HP 620 or 660? This looks like a fascinating combination. Michael I. Davis From: "Klaus-D. Warzecha" To: hyperchem@hyper.com Cc: Subject: Re:script problems Date: Thu, 08 Oct 1998 23:22:11 +0200 Gianluca Ottolina wrote >The following commands failed to achieve the desired setting : >mechanics-dielectric distancedependent >mechanics-dielectric-scale-factor 1 >mechanics-electrostatic-scale-factor 0.5 >mechanics-van-der-waals-scale-factor 0.5 >Any hint on that topic is highly appreciated. Gianluca, please note that all these script commands seemingly need 4 values (for MM+, AMBER, BIO+ and OPLS). Means that it's not possible to set the = values for AMBER and ignore the rest.You thus might consider to modify your = script as follows : mechanics-dielectric DistanceDependent DistanceDependent = DistanceDependent Constant mechanics-dielectric-scale-factor 1.0 1.0 1.0 1.0 mechanics-electrostatic-scale-factor 0.5 0.5 0.5 0.5 mechanics-van-der-waals-scale-factor 0.5 0.5 0.5 0.5 I've no idea whether these values are meaningful (my fault, not yours), = but at least HC doesn't complain about this script :-) Hope it helps. Yours,=20 Klaus -- Klaus-D. Warzecha Max-Planck-Institut f=FCr Strahlenchemie P. O. Box 101365 D-45413 M=FClheim an der Ruhr Germany fax: x49/x208-306-3951 email: warzecha@cityweb.de From: Support To: "'Gianluca Ottolina'" , Hyperchem List Server Subject: RE: script problems Date: Thu, 8 Oct 1998 15:49:47 -0400 Gianluca Ottolina wrote... > Dear Hyperchem, > I've been performing MD calculations under HC 5.02 on PC >using the > script commands. > I was not able to set appropriately the following >parameters for > MM/amber with distance dependent dielectric permittivity >with a scale > factor of 1 and 1-4 scale factors 0.5 for both >electrostatic and van der > Waals. > The following commands failed to achieve the desired >setting : > mechanics-dielectric distancedependent > mechanics-dielectric-scale-factor 1 > mechanics-electrostatic-scale-factor 0.5 > mechanics-van-der-waals-scale-factor 0.5 > Any hint on that topic is highly appreciated. > Greetings, > > Dr Gianluca Ottolina > Istituto di Biocatalisi e Riconoscimento Molecolare, CNR The most probable reason for the commands not having the desired effect is due to an insufficient number of arguments. Pages 361 and 362 of the Reference manual describe the type and arguments to the "mechanics-..." variables. Page 367 of the same book describes the note b, which states that the arguments enum1/float1, enum2/float2... to each of these mechanics-... variables apply to MM+, AMBER, BIO+ and OPLS parametrizations. Hence the need for a set of 4 values. Thus, use the following set of commands instead: mechanics-dielectric = distancedependent, distancedependent, distancedependent,constant mechanics-dielectric-scale-factor = 1,1,1,1 etc. Regards, Rajiv --- Rajiv Bendale, Ph.D., Director of Scientific Support Hypercube, Inc. Florida Science and Technology Park 1115 N.W. 4th Street Gainesville, Florida 32601 Voice:(352) 371-7744/(800) 960-1871 Fax:(352) 371-3662 From: "Klaus-D. Warzecha" To: hyperchem@hyper.com Subject: .SNP files - different versions Date: Thu, 08 Oct 1998 20:52:22 +0200 Dear HyperChemists, I'm looking for some information on the structure of snapshot files. So far, I got the infos for the versions 3.0, 5.0x and some 4.x (don't know which exactly) as provided in the manuals but there's some points I'm not to sure about : 1. Has there been anaother change in .SNP between HC version 5.0x and version 5.1x ? 2. Are version 4.0 and version 4.5 snapshot files identical ? If not, where's the difference ? I know that the variable sized headers of 5.0x and a version 4.?? differ by 4*N bytes (N=number of atoms), it's the data where the atomic masses are stored, but I'm not sure whether this counts for both 4.0, 4.5 and any version in between. 3. Has anyone ever tried to decode the information kept in the reserved data of a .SNP ? Is there something useful hidden ? Maybe, one of the officials can give us a hint :-) The one I miss the most is the (internally stored) information whether a .SNP was created in a MM or QM run. Yours, Klaus -- Klaus-D. Warzecha Max-Planck-Institut für Strahlenchemie P. O. Box 101365 D-45413 Mülheim an der Ruhr Germany fax: x49/x208-306-3951 email: warzecha@cityweb.de From: Ron Starkey To: hyperchem@hyper.com Cc: Joel Polowin , starkeyr@gbms01.uwgb.edu Subject: Error on changing calculation types revisited/ Date: Thu, 08 Oct 1998 11:56:00 -0700 (PDT) HyperChem support, This is a follow up to my e-mail of 6 Oct 98. This is related to the problem mentioned on 6 Oct 98 by Joel Polowin. I also get an error when I change from one optimization method to another when HyperChem is driven by Excel via DDE. It happens only with HyperChem 5.1. It does not matter if I am using Excel 5.0 or 97; and Windows 95 or 3.1 does not matter. I do not get the error in HyperChem 4.5. The HyperChem error message is: Cannot initialize DDE connection! Your system may be unstable. You may have to restart Windows. Followed by the HyperChem message: Computation aborted. Unable to initialize conservation with backend. If I OK these two messages the computations proceed fine. It appears that HyperChem is trying to open a new backend communication with a method (e.g. am1) before it closes communication with the method (e.g. mm+) previously used. I have never had a problem with changing methods if I do it in HyperChem from the Setup menu. The old communication is always closed before the new one opened when done from the Setup menu selection. Is there a command I can send, via DDE from Excel, to close the old method before I start the optimization or single point calculation (either of which should open communication with the new method). I think this will solve the problem. Even if this bug is fixed in the next release of HyperChem there will still be software out there with the problem. Since this fix is needed for an Excel macro that will soon be published by J.Chem.Educ. I need to have a fix that will work with the HyperChem 5.x versions that are now in the field. There is no apparent problem like this with HyperChem 4.5 I am open to any other suggestions on how to work around this HyperChem 5.1 bug. Ronald Starkey Chemistry Univ Wisconsin - Green Bay From: Gianluca Ottolina To: HyperChem Subject: script problems Date: Thu, 08 Oct 1998 15:46:03 +0200 Dear Hyperchem, I've been performing MD calculations under HC 5.02 on PC using the script commands. I was not able to set appropriately the following parameters for MM/amber with distance dependent dielectric permittivity with a scale factor of 1 and 1-4 scale factors 0.5 for both electrostatic and van der Waals. The following commands failed to achieve the desired setting : mechanics-dielectric distancedependent mechanics-dielectric-scale-factor 1 mechanics-electrostatic-scale-factor 0.5 mechanics-van-der-waals-scale-factor 0.5 Any hint on that topic is highly appreciated. Greetings, Dr Gianluca Ottolina Istituto di Biocatalisi e Riconoscimento Molecolare, CNR From: Todd Richmond To: hyperchem@hyper.com Subject: concantenated xyz Date: Wed, 7 Oct 1998 13:52:14 -0800 Greetings, Can Hyperchem "do" concantenated xyz files? Actually, I would welcome any input (via direct email) on how to go about creating these animation files. Thanks, Todd Todd A. Richmond, Ph.D. Assistant Professor of Chemistry The Claremont Colleges http://enzyme.claremont.edu From: Felipe Chibante To: "'hyperchem@hyper.com'" Subject: MD question Date: Tue, 6 Oct 1998 13:10:36 -0500 Dear Hyperchem, I've been performing MD calculations under HC 4.5 on SGI, and saving snapshot files. However, when I port both the hin and snp files to HC 5.02 on PC I find that the snapshot file cannot be read due to "Number of atoms are incompatible" This is quite frustrating as I need to easily share results between the two platforms. Any suggestions? Regards, Felipe From: Ron Starkey To: hyperchem@hyper.com Cc: Joel Polowin , starkeyr@gbms01.uwgb.edu Subject: Re: Error in changing calculation type Date: Tue, 06 Oct 1998 11:58:06 -0700 (PDT) On Mon, 5 Oct 1998, Joel Polowin wrote: > When my HAPI-based application tells HyperChem to start a semi-empirical > calculation after it had been doing an MM calculation, or vice versa, it > usually has a DDE error. It appears that HyperChem is attempting to > communicate with the new calculation module before the old module has > been terminated and the new module loaded. > I reported this as a problem in HyperChem 5.01, and it was (if I recall > correctly) fixed for Hyperchem 5.02. But it appears that the bug came > back for release 5.1 . To: HyperChem, I have experienced the same problem that was described by Joel (e-mail of 6 Oct 98) when driving HyperChem 5.1 from Excel. Can you provide me with an Excel based (4.0 macro format) command to perform a manual termination of the old calculation module? This will make my life much easier when running my Excel programs driving HyperChem. Thanks for your assistance. Ronald Starkey Chemistry Univ Wisconsin - Green Bay From: Barry Lever To: "hyperchem@hyper.com" Subject: glitch Date: Tue, 06 Oct 1998 09:42:37 -0400 You recall that there is a conflict between hyperchem 5.1 and Wordperfect 6 etc Eventually I stopped using wordperfect and switched to Word 97- no problems then with hyperchem. Recently I installed REalPlayer G2 as a plugin for my browser- the same conflict problems as with WP re-arose ! I uninstalled Realplayer G2 and the problems seem to have disappeared- so it looks like there is also a conflict here. do you yet have a patch to fix these conflicts ?? -- A. B. P. Lever Distinguished Research Professor Dept. of Chemistry, CCB124, York University 4700 Keele St., Toronto, Ont. Canada M3J 1P3 Tel: 416-736-2100 x22309 Fax: 416-736-5936 url:http://www.science.yorku.ca/chem/profs/blever/blever.htm From: Joel Polowin To: hyperchem@hyper.com Subject: Error in changing calculation type Date: Mon, 5 Oct 1998 15:44:29 -0400 When my HAPI-based application tells HyperChem to start a semi-empirical calculation after it had been doing an MM calculation, or vice versa, it usually has a DDE error. It appears that HyperChem is attempting to communicate with the new calculation module before the old module has been terminated and the new module loaded. I reported this as a problem in HyperChem 5.01, and it was (if I recall correctly) fixed for Hyperchem 5.02. But it appears that the bug came back for release 5.1 . I have been using a work-around: manual termination of the old calculation module. This little Visual Basic routine activates a module specified by name, sends it an ALT-F4, and then waits a little while until the module dies. Public Sub KillApp(ByVal AppName$) Rem Kills an application by name Dim I% On Error GoTo AppDoesntExist AppActivate (AppName$) SendKeys "%{F4}", True For I% = 1 To 20000 DoEvents AppActivate (AppName$) Next I% Exit Sub AppDoesntExist: End Sub So, before I do an MM+ calculation (for example), I do: Call KillApp("HyperNDO") Call KillApp("HyperGauss") Call KillApp("HyperNewton") ... which isn't a perfect solution but seems to work most of the time. Joel Polowin jpolowin@idsdetection.com From: Simon Hogg To: hyperchem@hyper.com Subject: NH3 and constrain angles ... Date: Fri, 02 Oct 1998 18:38:36 +0000 Building NH3 (add N, then 'Add H / Model build') gives a structure where H-N-H angles are 109.471 deg. Choosing to constrain them to 106.67 deg. I select each angle, constrain them, then do 'model build'. However, this only seems to constrain one of the bond angles. Suppose the N is numbered 1 and the H's are 2, 3 and 4. only 2-1-3 is constrained, irrespective of the order the atoms are picked. The other bonds SAY they are constrained (when you pick the angle, the bottom left corner says 'Angle of atoms a-b-c is 109.471 (build to 106.67)' but when you 'build' it doesn't change. How can I constrain this model? · Simon Hogg, Imperial College, London, UK Tel. +44 171 589 5111 ext. 56721 Fax. +44 171 584 3194 Email: s.hogg@ic.ac.uk Glass-List: glass-list@ic.ac.uk PGP: Key ID 0x4C048B49 Send "get public key" as subject for key FingerPrint B9C7 4E40 C73D 0E15 15E0 D6C6 79C4 AB59 4C04 8B49 Subject: Blood pressure ... Date: Thu, 01 Oct 1998 16:43:57 -0700 From: support Organization: Hypercube, Inc. To: bendale@bellsouth.net see http://207.211.141.25/Heart_and_Stroke_A_Z_Guide/bpeq.html for blood pressure measuring devices...