Date: Thu, 27 Feb 1997 12:02:11 -0600 From: David_DeBerry@radian.com (David DeBerry) Subject: how to set up a nonaqueous solvent box? >Would someone post a few details on how to set up a "nonaqueous" >solvent solvation box? I see how to calculate the number of molecules >in the instruction manual, but I am not sure how to then "get >started," create a box, add 100+ molecules, equilibrate, etc. > >Using Hyperchem 5.0 Hi David and HyperChemists, Once the periodic box has been created, and the water molecules emptied (using Select All and Delete) the question is how to get many solvent molecules back into the box. It is possible to create a solvent molecule, select it, paste, and then use the translation tools to position the "pasted" solvent molecule back in the box but of course that gets rather tedious for the number of molecules you suggest, even if you use the multiple selections tool to do several molecules at a time. We suggest a script file which will do multiple merges, and displace the solvent molecule by a certain amount each time. This does not need to do a very fancy placement of molecules. Once you have placed as many molecules as you want in the cell, you might want to do a geometry optimization to distribute the molecules better before doing a molecular dynamics run. (This is fun to watch; use Display/Sticks/ Perspective and rotate the periodic box before doing Geometry Optimize with a simple MM potential.) The appended sample script, "box.tcl" should be placed in the same folder as the sample HyperChem file, "benzene.hin". To run this script, open it from the "Script" menu item. This is just one suggestion; other newsgroup readers might have Excel macros which make a better initial guess ... ? In any event, once you get a reasonable box of solvent, save the hin file for re-use. Regards, Victoria ------------ Victoria Barclay, Ph.D. Manager, Scientific Support Email to: barclay@hyper.com WWW: http://www.hyper.com Hypercube Inc, 7-419 Phillip St, Waterloo, Ont, Canada N2L 3X2 (519)725-4040 Info requests to: info@hyper.com Support questions to: support@hyper.com Email group: Send "subscribe hyperchem" to hyperchem-request@hyper.com OR "unsubscribe hyperchem" ... ------------------ box.tcl ------------------------------ TclOnly hcExec "solvate-system-in-this-box 20,20,20" hcExec "menu-select-select-all" hcExec "delete-selected-atoms" hcExec "menu-select-molecules" hcExec "merge-file benzene.hin" set NumCell 2 set nummol 1 set i 0 while {$i < $NumCell} { incr i set xx [expr $i* 2] set j 0 while {$j < $NumCell} { incr j set yy [expr $j *2] set k 0 while {$k < $NumCell} { incr k set zz [expr $k *2] hcExec "merge-file benzene.hin" incr nummol hcExec "select-atom 1 $nummol" hcExec "translate-selection $xx $yy $zz" hcExec "select-none" } } } Reminder to HyperChem newsgroup subscribers: To unsubscribe: Send e-mail to hyperchem-owner@hyper.com ^^^^^ and in the body of the message, type 'unsubscribe'. To subscribe: Send e-mail to hyperchem-owner@hyper.com ^^^^^ and in the body of the message, type 'subscribe'. To post a message: Send e-mail to hyperchem@hyper.com with the posting in the body of the message. General note about posting: 1. - Don't unsubscribe/subscribe by posting to the general newsgroup. If you have trouble with these operations, send e-mail to support@hyper.com with a description of the problem. 2. - Please give your posting an appropriate title. 3. - Don't append really long text; this is often broken up by some mail applications. 4. - Don't append MIME, binhex, or any non-human-readable file; this is confusing to and/or may be broken up by some mail applications. 5. - Do make the subject of general interest to HyperChem users. Re: 3 and 4: If you would like to make a program/HIN file/non-text file available to other subscribers, please contact support@hyper.com and request that the file be made available via our ftp site. We welcome newsgroup discussion by HyperChem users. Please share your comments, suggestions, work-arounds, questions and answers! The newsgroup postings are available for perusal at our web site-- http://www.hyper.com/Support/view_mail.html From barclay Mon Mar 3 13:23:39 1997 To: hyperchem@hyper.com Subject: non-aqueous solvent in box Status: O >Date: Thu, 27 Feb 1997 12:02:11 -0600 >From: David_DeBerry@radian.com (David DeBerry) >Subject: how to set up a nonaqueous solvent box? > >Would someone post a few details on how to set up a "nonaqueous" >solvent solvation box? I see how to calculate the number of molecules >in the instruction manual, but I am not sure how to then "get >started," create a box, add 100+ molecules, equilibrate, etc. > >Using Hyperchem 5.0 Hi David and HyperChemists, Once the periodic box has been created, and the water molecules emptied (using Select All and Delete) the question is how to get many solvent molecules back into the box. It is possible to create a solvent molecule, select it, paste, and then use the translation tools to position the "pasted" solvent molecule back in the box but of course that gets rather tedious for the number of molecules you suggest, even if you use the multiple selections tool to do several molecules at a time. We suggest a script file which will do multiple merges, and displace the solvent molecule by a certain amount each time. This does not need to do a very fancy placement of molecules. Once you have placed as many molecules as you want in the cell, you might want to do a geometry optimization to distribute the molecules better before doing a molecular dynamics run. (This is fun to watch; use Display/Sticks/ Perspective and rotate the periodic box before doing Geometry Optimize with a simple MM potential.) The appended sample script, "box.tcl" should be placed in the same folder as the sample HyperChem file, "benzene.hin". To run this script, open it from the "Script" menu item. This is just one suggestion; other newsgroup readers might have Excel macros which make a better initial guess ... ? In any event, once you get a reasonable box of solvent, save the hin file for re-use. Regards, Victoria ------------ Victoria Barclay, Ph.D. Manager, Scientific Support Email to: barclay@hyper.com WWW: http://www.hyper.com Hypercube Inc, 7-419 Phillip St, Waterloo, Ont, Canada N2L 3X2 (519)725-4040 Info requests to: info@hyper.com Support questions to: support@hyper.com Email group: Send "subscribe hyperchem" to hyperchem-request@hyper.com OR "unsubscribe hyperchem" ... ------------------ beginning of box.tcl ------------------------------ TclOnly hcExec "solvate-system-in-this-box 20,20,20" hcExec "menu-select-select-all" hcExec "delete-selected-atoms" hcExec "menu-select-molecules" hcExec "merge-file benzene.hin" set NumCell 2 set nummol 1 set i 0 while {$i < $NumCell} { incr i set xx [expr $i* 2] set j 0 while {$j < $NumCell} { incr j set yy [expr $j *2] set k 0 while {$k < $NumCell} { incr k set zz [expr $k *2] hcExec "merge-file benzene.hin" incr nummol hcExec "select-atom 1 $nummol" hcExec "translate-selection $xx $yy $zz" hcExec "select-none" } } } ------------------ end of box.tcl ------------------------------ From barclay Mon Mar 3 13:27:02 1997 To: hyperchem-request@hyper.com Status: O unsubscribe From barclay Mon Mar 3 13:31:41 1997 To: hyperchem-request@hyper.com Status: O unsubscribe hyperchem From barclay Mon Mar 3 13:37:46 1997 To: hyperchem-request@hyper.com Status: O subscribe hyperchem From barclay Mon Mar 3 13:40:44 1997 To: hyperchem@hyper.com Subject: newsgroup info Status: O Reminder to HyperChem newsgroup subscribers: To unsubscribe: Send e-mail to hyperchem-request@hyper.com ^^^^^^^ and in the body of the message, type 'unsubscribe hyperchem'. To subscribe: Send e-mail to hyperchem-request@hyper.com ^^^^^^^ and in the body of the message, type 'subscribe hyperchem'. To post a message: Send e-mail to hyperchem@hyper.com with the posting in the body of the message. General notes about posting: 1. - Don't unsubscribe/subscribe by posting to the general newsgroup. If you have trouble with these operations, send e-mail to support@hyper.com with a description of the problem. Note that the "unsubscribe" address is the same as the "subscribe" address you are given in the "Getting Started" manual. 2. - Please give your posting an appropriate title. 3. - Don't append really long text; this is broken up by some mail applications. 4. - Don't append MIME, binhex, uuencoded, or any non-human-readable file; this causes indigestion in some mail applications. 5. - Do make the subject of general interest to HyperChem users. Re: 3 and 4: If you would like to make a program/HIN file/non-text file available to other subscribers, please contact support@hyper.com and request that the file be made available via our ftp site. We welcome newsgroup discussion by HyperChem users. Please share your comments, suggestions, work-arounds, questions and answers! An archive of newsgroup postings is available for perusal at our web site-- http://www.hyper.com/Support/view_mail.html From barclay Wed Mar 5 15:19:14 1997 To: hyperchem@hyper.com Subject: ChemPlus 1.6 Status: O TO HYPERCHEM RELEASE 5 USERS Hypercube is pleased to announce ChemPlus 1.6 is now available. ChemPlus 1.6 is an upgrade of ChemPlus 1.5. It is designed to operate seamlessly with HyperChem release 5. It does not otherwise extend the functionality of ChemPlus 1.5. Pricing information: ChemPlus 1.6 is a free upgrade, if you have ChemPlus 1.5 and HyperChem 5.0 or 5.01. We only ask you to cover the shipping and handling costs by pre-payment of $US 20. If you are currently purchasing or upgrading to HyperChem 5, and have an existing copy of ChemPlus 1.5, you may upgrade to ChemPlus 1.6 at no extra charge. How to order: There are three ways - (1) at the time of purchase of HyperChem 5.0, request the ChemPlus upgrade. The shipping and handling fee for ChemPlus 1.6 will be waived. (2) request the ChemPlus 1.6 upgrade separately. The shipping and handling costs of $US 20 must be pre-paid. (3) if you do not have ChemPlus 1.5, you can order ChemPlus 1.6 for the regular price of ChemPlus 1.5. All orders must include the following: - serial number for ChemPlus 1.5 - serial number for HyperChem 5. "Do I need ChemPlus 1.6?" If you have HyperChem release 4 or 4.5, no. Even on the Windows 95 or Windows NT 4 platform, ChemPlus 1.5 communicates well with older versions of HyperChem. If you have HyperChem 5, there are some "glitches" in accessing ChemPlus 1.5 modules but they can mainly be overcome by following the instructions at http://www.hyper.com/Support/Faq/faq15.html However, the interaction between HyperChem 5 and ChemPlus is not as smooth as what we would like it, and thus we are offering the upgrade to ChemPlus 1.6. Before March 27, send your order to: Hypercube, Inc., 419 Phillip St., Waterloo, ONT N2L 3X2 Canada After March 27, send your order to: Hypercube, Inc., 1115 NW 4th St., Gainesville, FL 32601 USA From barclay Fri Mar 7 17:48:20 1997 To: hyperchem@hyper.com Subject: linux HyperChem; dealer info Status: O >Date: Thu, 6 Mar 1997 08:38:22 +0530 (IST) >From: Kangueane P > >Hi, >I would like to know the price of Hyperchem 5.01 and is it portable onto >linux. If there are agents in India can you send me their email address. >This is rather urgent. >Gautam Hi Gautam and HyperChemists, No, HyperChem is not available for linux. The information on HyperChem distributors can be found on our web site. Point your browser to: http://www.hyper.com/Dealers (and in this case, select india.html). In general we recommend going through your local dealer because normally they offer "first-line support"; and you don't have the same customs, duties, and shipping fees arrangements to make as when you order through Hypercube, Inc. Regards, Victoria ------------ Victoria Barclay, Ph.D. Manager, Scientific Support Email to: barclay@hyper.com WWW: http://www.hyper.com/ Hypercube Inc, 419 Phillip St, Waterloo, Ont, Canada N2L 3X2 (519)725-4040 Info requests to: info@hyper.com Support questions to: support@hyper.com Email group: Send "subscribe hyperchem" (or "unsubscribe hyperchem") to hyperchem-request@hyper.com; please do not send such administrative messages to the group itself. >Subject: DDE and Visual Basic >Date: Mon, 10 Mar 97 13:32:36 -0500 >From: Gonzalo Hernandez > >-- [ From: Gonzalo Hernandez * EMC.Ver #2.5.02 ] -- > >Hi there, >I'm using Visual Basic 4.0 to make some applications to use HyperChem via >DDE, but i couldn't stablished a connection with HC because i don't know >what Item i should specify in the command line. In more detail, when you try >to do a DDE betwen two applications in Visual Basic you should specify three >properties: >LinkTopic (your source application, in this case HyperChem|System), LinkMode >(the mode of connection), and LinkItem that its a specific item within your >source application (for example a celd in Excel). >The question is, which is the LinkItem property for HyperChem? >There is antoher way to do it? >Can someone send me an example? Hi Gonzalo and HyperChemists, Nice to read of another user who is merging the power of Visual Basic with HyperChem. The best example for you might be the one which appears at the end of "Getting Started" (Lesson 15 for release 4/4.5 or Lesson 18 for release 5). There, in the section "Entering Visual Basic Code" is an example where the LinkItem is "total-energy." This could have been any one of hundreds of HyperChem messages, for example, "version", "atom-count", etc. These are described in Chapter 10 of the "Reference Manual" where there is a detailed list of the multitude of HyperChem messages available. Your query indicates the next version of "Getting Started" would be more helpful if it included a specific pointer to Chapter 10 for possible HyperChem messages to include; I'll take note of that. Regards, Victoria ------------ Victoria Barclay, Ph.D. Manager, Scientific Support Email to: barclay@hyper.com WWW: http://www.hyper.com/ Hypercube Inc, 419 Phillip St, Waterloo, Ont, Canada N2L 3X2 (519)725-4040 Info requests to: info@hyper.com Support questions to: support@hyper.com Email group: Send "subscribe hyperchem" (or "unsubscribe hyperchem") to hyperchem-request@hyper.com; please do not send such administrative messages to the group itself. From barclay Tue Mar 11 13:28:16 1997 To: hyperchem@hyper.com Subject: DDE and Visual Basic Status: O >Subject: DDE and Visual Basic >Date: Mon, 10 Mar 97 13:32:36 -0500 >From: Gonzalo Hernandez > >-- [ From: Gonzalo Hernandez * EMC.Ver #2.5.02 ] -- > >Hi there, >I'm using Visual Basic 4.0 to make some applications to use HyperChem via >DDE, but i couldn't stablished a connection with HC because i don't know >what Item i should specify in the command line. In more detail, when you try >to do a DDE betwen two applications in Visual Basic you should specify three >properties: >LinkTopic (your source application, in this case HyperChem|System), LinkMode >(the mode of connection), and LinkItem that its a specific item within your >source application (for example a celd in Excel). >The question is, which is the LinkItem property for HyperChem? >There is antoher way to do it? >Can someone send me an example? Hi Gonzalo and HyperChemists, Nice to read of another user who is merging the power of Visual Basic with HyperChem. The best example for you might be the one which appears at the end of "Getting Started" (Lesson 15 for release 4/4.5 or Lesson 18 for release 5). There, in the section "Entering Visual Basic Code" is an example where the LinkItem is "total-energy." This could have been any one of hundreds of HyperChem messages, for example, "version", "atom-count", etc. These are described in Chapter 10 of the "Reference Manual" where there is a detailed list of the multitude of HyperChem messages available. Your query indicates the next version of "Getting Started" would be more helpful if it included a specific pointer to Chapter 10 for possible HyperChem messages to include; I'll take note of that. Regards, Victoria ------------ Victoria Barclay, Ph.D. Manager, Scientific Support Email to: barclay@hyper.com WWW: http://www.hyper.com/ Hypercube Inc, 419 Phillip St, Waterloo, Ont, Canada N2L 3X2 (519)725-4040 Info requests to: info@hyper.com Support questions to: support@hyper.com Email group: Send "subscribe hyperchem" (or "unsubscribe hyperchem") to hyperchem-request@hyper.com; please do not send such administrative messages to the group itself. From barclay Tue Mar 11 13:30:21 1997 To: hyperchem@hyper.com Subject: logging out Status: O >Date: Thu, 6 Mar 1997 23:17:16 -0500 (EST) >From: Phil Tavernier > >Question for subscribers: I just began using Hyperchem on a Silicon >Graphics computer running irix 5.3. My question is this, I would like to >run hyperchem calculations while I am not actively logged into the computer >(similar to Spartan which allows jobs to run unattended). However, >whenever I logout of the workstation, my jobs are killed automatically on >hyperchem. What can I do to change this besides spending many lonely >night looking at the computer screen waiting for jobs to finish? Hi Phil and HyperChemists, HyperChem calculations involve backend/frontend communication. If you logout you kill the frontend portion, and the backend would have nowhere to send its results to. That is why the design of HyperChem does not permit jobs to run when you are not logged on. However, there's no requirement that you actually be "looking at the computer screen waiting for jobs to finish"... :-) If you start a logfile for the job, you can read all the results from it later. Regards, Victoria ------------ Victoria Barclay, Ph.D. Manager, Scientific Support Email to: barclay@hyper.com WWW: http://www.hyper.com/ Hypercube Inc, 419 Phillip St, Waterloo, Ont, Canada N2L 3X2 (519)725-4040 Info requests to: info@hyper.com Support questions to: support@hyper.com Email group: Send "subscribe hyperchem" (or "unsubscribe hyperchem") to hyperchem-request@hyper.com; please do not send such administrative messages to the group itself. >From: Gerardo Burton >Subject: Network lock > >Hello Victoria >A couple of months ago I sent this problem to Joel who said he would try = >and find out some more info on the license server operation. I would = >appreciate if you could take a look at this problem, we are running = >HyperChem 5.0 with a network lock (1 license): According to what I can find, this is on Win 95 with a Novell xx server and IPX/SPX protocol--is this correct? (Fill in 'xx'.) >If the license timeout is set to a shorter time than the calculation = >length, the license server will not release the license unless someone = >else requests one after the timeout has occurred, Unfortunately this may = >happen inadvertently, either because the calculation takes longer than = >expected or because the calculation ended but the user was not there to = >save the results before the license timed out. In any case, the new user = >takes over the license unaware of the situation and leaves the former = >calculation running (or waiting) in an unlicensed window. A similar = >situation will result if the computer where the license server is = >running has a problem and needs to be rebooted. We've tested the = >situation and apparently the unlicensed window continues to run and = >operate normally, even new calculations may be started without = >reengaging the license. However, ocassionally, the unlicensed window = >will check for its license and if it has been lost the only option is to = >exit and the calculation is lost. Also under normal conditions but with = >"heavy network traffic" a window may lose its license (it happened once = so far). In all these cases there is no message to the user informing = >that the license has been lost until you try to open a menu and the only = >option is to exit without being able to save the results. We couldn't = >find a way of forcing HC to reconnect or recheck the license (unless you = >exit and restart). Overall the system appears somewhat = >unpredictable/unstable. > >The license timeout has a maximun limit of 60 minutes although Joel gave = >me a workaround to this bug by editing the registry and putting a = >timeout of up to 65000 minutes. Although this may help it will tie up = >the license even after the calculation has ended, and until the first = >user closes the window in his machine. Are there any ways of avoiding = >these problems? > > A much safer alternative would be that the calculation be stopped if = >the license is lost and allowed to continue once the license is = >reestablished, with the option of saving the intermediate result. We = >have another program with a similar protection system (Wibu key) which = >operates in this way. I have a few additional questions to throw at you: (hope you don't mind): what Network protocol settings do you have toggled on in your File/Preferences settings? Have you been able to download winmon.exe from our ftp site and run it to verify the machines accessing the server? We have been able to sort out a couple of related HyperChem 5 network problems since the date you posted this, so I hope we can get to the bottom of this problem as well. Thanks in advance for any information you can provide. Regards, Victoria ------------ Victoria Barclay, Ph.D. Manager, Scientific Support Email to: barclay@hyper.com WWW: http://www.hyper.com Hypercube Inc, 7-419 Phillip St, Waterloo, Ont, Canada N2L 3X2 (519)725-4040 Info requests to: info@hyper.com Support questions to: support@hyper.com Email group: Send "subscribe hyperchem" to hyperchem-request@hyper.com Latest upgrade for ChemPlus available; e-mail me for info CHEMPLUS 1.6 Hypercube is pleased to announce ChemPlus 1.6 is now available. ChemPlus 1.6 is an upgrade of ChemPlus 1.5. It is designed to operate seamlessly with HyperChem release 5. It does not otherwise extend the functionality of ChemPlus 1.5. Pricing information: ChemPlus 1.6 is a free upgrade, if you have ChemPlus 1.5 and HyperChem 5.0 or 5.01. We only ask you to cover the shipping and handling costs by pre-payment of $US 20. If you are currently purchasing or upgrading to HyperChem 5, and have an existing copy of ChemPlus 1.5, you may upgrade to ChemPlus 1.6 at no extra charge. How to order: There are three ways - (1) at the time of purchase of HyperChem 5.0, request the ChemPlus upgrade. The shipping and handling fee for ChemPlus 1.6 will be waived. (2) request the ChemPlus 1.6 upgrade separately. The shipping and handling costs of $US 20 must be pre-paid. (3) if you do not have ChemPlus 1.5, you can order ChemPlus 1.6 for the regular price of ChemPlus 1.5. All orders must include the following: - serial number for ChemPlus 1.5 - serial number for HyperChem 5. "Do I need ChemPlus 1.6?" If you have HyperChem release 4 or 4.5, no. Even on the Windows 95 or Windows NT 4 platform, ChemPlus 1.5 communicates well with older versions of HyperChem. If you have HyperChem 5, there are some "glitches" in accessing ChemPlus 1.5 modules but they can mainly be overcome by following the instructions at http://www.hyper.com/Support/Faq/faq15.html However, the interaction between HyperChem 5 and ChemPlus is not as smooth as what we would like it, and thus we are offering the upgrade to ChemPlus 1.6. Before March 27, send your order to: Hypercube, Inc., 419 Phillip St., Waterloo, ONT N2L 3X2 Canada After March 27, send your order to: Hypercube, Inc., 1115 NW 4th St., Gainesville, FL 32601 USA From barclay Mon Mar 17 11:56:27 1997 To: hyperchem@hyper.com Subject: HISTORY Status: O >Date: Mon, 17 Mar 97 11:08:27 >From: "Alasdair Elliot" >Subject: HISTORY > >Hi, >The development of smart programmes such as Hyperchem are relatively >new as is the concept of molecular modelling (I think). >Can anyone give me any dates or ref. sources on the development of >this field? >Incidentally my area is design of organic dyestuff molecules if >anyone out there is also interested in this field. > Many Thanks >Alexander Elliot Hi Alexander and HyperChemists, _Reviews in Computational Chemistry_ ed. by K.B. Lipkowitz and D. B. Boyd (VCH Publishers, New York, 1990) would likely be a good place to start. It contains nine reviews on aspects of computational chemistry and molcular modelling by various experts. This book is part of a series which make for some interesting browsing. As well, there are other references which you may find pertinent in the preface to the _Computational Chemistry_ manual which comes with HyperChem. Regards, Victoria ------------ Victoria Barclay, Ph.D. Manager, Scientific Support Email to: barclay@hyper.com WWW: http://www.hyper.com/ Hypercube Inc, 419 Phillip St, Waterloo, Ont, Canada N2L 3X2 (519)725-4040 Info requests to: info@hyper.com Support questions to: support@hyper.com Email group: Send "subscribe hyperchem" (or "unsubscribe hyperchem") to hyperchem-request@hyper.com; please do not send such administrative messages to the group itself. From barclay Tue Mar 18 11:29:34 1997 To: hyperchem-request@hyper.com Subject: Re: APPROVE hyperchem Status: O approve PASSW0RD unsubscribe hyperchem Thorsten Rohde rohde@ochhades.chemie.uni-karlsruhe.de From barclay Mon Mar 24 11:29:04 1997 To: hyperchem@hyper.com, J.P.M.LANGEVELD@id.dlo.nl Subject: Sybyl coordinates Status: O >From: J.P.M.LANGEVELD@id.dlo.nl >Date: Fri, 21 Mar 1997 15:28:45 +0000 (GMT) >Subject: protein assembly into icosaeder > >I would like to >build icosaedral structures from one viral protein subunit, of which I >have the coordinates, with the Sybyl software we have. Until now we >have not found any indication how to assemble this in your software, >but it would be of great use to us if you could help me to solve this >problem. I include an answer in a copy of this message to you >from a colleague in the UK who also >thinks we should be able to do this with your software. HyperChem will accept as input (or create, upon output) MOL2 files, which is the format used by many programs from Tripos Associates including the Sybyl application. Regards, Victoria ------------ Victoria Barclay, Ph.D. Manager, Scientific Support Email to: barclay@hyper.com WWW: http://www.hyper.com/ Hypercube Inc, 419 Phillip St, Waterloo, Ont, Canada N2L 3X2 (519)725-4040 Info requests to: info@hyper.com Support questions to: support@hyper.com Email group: Send "subscribe hyperchem" (or "unsubscribe hyperchem") to hyperchem-request@hyper.com; please do not send such administrative messages to the group itself. From barclay Mon Mar 24 11:38:23 1997 To: hyperchem@hyper.com Subject: Re: AMBER 4.1 Status: O >From ross@cgl.ucsf.EDU Fri Mar 21 14:20:13 1997 >Subject: Re: AMBER 4.1 > >I don't know how Hyperchem works, but in the new ff, the >atom types are different, so in the amber progs themselves, >we have to load different residue templates so that the atoms >are typed properly. Bill, you make a good point. If there are new atom types, this must also be taken into account. The treatment of these types can be set in HyperChem via the "chem.rul" file (using a text editor and taking care to follow the clause structure outlined in Appendix F). After changing "chem.rul" you would have to use Build/Compile Type Rules. The "ambertyp.txt" file would have to be changed to include the new type. Then all the associated files for bending, hydrogen bonding, bond stretching, etc. would have to be modified. After altering the Parameter files, then you must choose the parameter set (using Setup/Select Parameter Set) and then compile the parameter set (using Select/Compile Parameter Set). So, this is a little involved but is tractable. On the other hand, if AMBER 4.1 implements some completely new and different the functional forms of the force field, then it cannot be implemented by changing parameters and modifying type rules. Laurence Lavelle kindly forwarded to me the AMBER web-site-- http://www.amber.ucsf.edu/amber/amber.html --and from what I can see (an admittedly cursory look) there are more types in AMBER 4.1, and there is also a description of the residue fitting you mention but no changes to the functional forms per se. Laurence's suggestion to include this most recent version of the popular AMBER force-field in our next release has been put on the request list. Regards, Victoria ------------ Victoria Barclay, Ph.D. Manager, Scientific Support Email to: barclay@hyper.com WWW: http://www.hyper.com/ Hypercube Inc, 419 Phillip St, Waterloo, Ont, Canada N2L 3X2 (519)725-4040 Info requests to: info@hyper.com Support questions to: support@hyper.com Email group: Send "subscribe hyperchem" (or "unsubscribe hyperchem") to hyperchem-request@hyper.com; please do not send such administrative messages to the group itself. From barclay Tue Mar 25 09:52:47 1997 To: hyperchem@hyper.com Subject: re: optimising large systems Status: O >Date: Mon, 24 Mar 1997 12:03:41 +0000 >From: Richy C > >When using MM+ to optimise a large system (say 1000 atoms) using >hyperchem 5.01. After some time (usually less than 100 cycles) the >system is effectively eliminated to leave one or two connected atoms, >why is this? and can anyting be done to prevent this? >Yours, > Richard Carney (Leeds University) Hmmm... this does not sound too healthy. You don't indicate whether there is a sensitivity to MM+ options settings or which algorithm for geometry optimization is chosen. Could you please ftp your HIN file to the "incoming" sub-directory at ftp.hyper.com so we can take a look at it? Regards, Victoria ------------ Victoria Barclay, Ph.D. Manager, Scientific Support Email to: barclay@hyper.com WWW: http://www.hyper.com/ Hypercube Inc, 419 Phillip St, Waterloo, Ont, Canada N2L 3X2 (519)725-4040 Info requests to: info@hyper.com Support questions to: support@hyper.com Email group: Send "subscribe hyperchem" (or "unsubscribe hyperchem") to hyperchem-request@hyper.com; please do not send such administrative messages to the group itself.