From underhil@hp.rmc.ca Tue Mar 7 11:30:35 1995 Date: Tue, 7 Mar 1995 11:07:01 -0500 To: hyperchem@hyper.com From: underhil@hp.rmc.ca (Ross Underhill) Subject: periodic boundaries Allow me to add the following to the Hyperchem wish list. I've been working on the problem of evaluating the solubility of various chemicals in polymers and liquids. To simulate the infinite liquid or solid I use periodic boundary conditions for the geometry optimization and MD runs. Obviously, to get the energy right you need the correct size cell. Unfortunately there appears to be no way to relax the size of the periodic cell other than saving the file and editting the .hin file. It would be EXTREMELY useful during these operations if the periodic cell would resize itself every now and then as part of the optimization or MD run. The algorithms to do this certainly exist and don't seem very hard to implement. Doing this by hand is extremely laborious and very inefficeint computationally because the step size is necessarily large. Any possibilities? Dr. Ross Underhill Royal Military College of Canada Kingston, Ontario (613) 541-6000 X6175 ________________________________________________________________________ From underhil@hp.rmc.ca Wed Mar 8 13:06:49 1995 Date: Wed, 8 Mar 1995 12:05:52 -0500 To: hyperchem@hyper.com From: underhil@hp.rmc.ca (Ross Underhill) Subject: .wmf converters Does anyone have a program that will convert windows metafiles (.wmf) into something a little more common? Postscript would be the most desirable end product? Dr. Ross Underhill Royal Military College of Canada Kingston, Ontario (613) 541-6000 X6175 ________________________________________________________________________ From schurro@gusun.acc.georgetown.edu Wed Mar 8 18:06:28 1995 Date: Wed, 8 Mar 1995 16:38:06 -0500 (EST) From: Oliver Schurr To: Ross Underhill Cc: hyperchem@hyper.com Subject: Re: .wmf converters Hi ross On Wed, 8 Mar 1995, Ross Underhill wrote: > Does anyone have a program that will convert windows metafiles > (.wmf) into something a little more common? Postscript would be the most > desirable end product? > > Dr. Ross Underhill > Royal Military College of Canada > Kingston, Ontario > (613) 541-6000 X6175 > You don't even need a conversion program!!! Simply past the .wmf files into Paint(brush?) and you can save it as a PCX file. Otherwise you need some commercial software like HiJack Pro. Hope this helps Oliver Schurr Department of Chemistry Georgetown University Washington, DC 20057 ________________________________________________________________________ From imcvey@scorpio.kent.edu Wed Mar 8 18:06:56 1995 From: imcvey@scorpio.kent.edu Subject: Does Hyperchem use virtual memory To: hyperchem@hyper.com Date: Wed, 8 Mar 1995 18:00:01 -0500 (EST) Cc: scabaniss@kentvm.kent.edu Dear Hyper Chemists, A question for those of you who understand the inner workings of Windows. We just purchased a pentium with 16 Mb of RAM, so I was experimenting with molecule sizes to see what the size limit is with this much memory. I found that with a relativley small windows swap file (virtual memory <10Mb) I got one size limit, and not surprisingly when I increased the swap file size >40 Mb the maximum molecule size was increased. What is confusing me however is that with the larger swap file I can get a semiempirical calculation to proceed on a molecule that was too big for the smaller swap file, BUT while the calculation on this system is in progress the hard disk remains idle, as if hyperchem is not using the swap file. What I want to know is: Why does hyperchem beleive that it has run out of memory, when it doesn't even try to use the swap file? Also if I give hyperchem a big enough molecule will it use the swap file or am I limited to using RAM only. I know that the use of virtual memory will make a calculation go very slowly, but it would be nice to have that option All suggestions/theories gladly accepted Reply to the Hyperchem list, or me if you prefer Thanks in advance, Iain. A gradual student Kent State University Kent , Ohio imcvey@scorpio.kent.edu or imcvey@en.com ________________________________________________________________________ From schurro@gusun.acc.georgetown.edu Thu Mar 9 09:33:40 1995 Date: Thu, 9 Mar 1995 09:10:40 -0500 (EST) From: Oliver Schurr To: hyperchem@hyper.com Subject: Appologies for a misdirected POST Hi Hyperchem users Yesterday I replied to the post from Ross Underhill about the .WMF converters. I did this by replying to Ross directly and CC to the hyperchem list. Now today i get 14 (!) undeliverable mail messages from all over the world that something was screwed up. I did use the address as given in the header of Ross' mail and didn't change a bit. That is going on here. I somebody else (or the whole list) got as well some of these messages I have really no clue what was going on. PS: My reply to the list shows up normally!!! Anyway, if i annoyed somebody or everybody please forgive me! Oliver Schurr Department of Chemistry Georgetown University Washington, DC 20057 ________________________________________________________________________ From polowin Thu Mar 9 10:21:20 1995 Date: Thu, 9 Mar 95 10:21:20 -0500 From: polowin (Joel Polowin) To: hyperchem Subject: Hyperchem mailing list bounce messages > From schurro@gusun.acc.georgetown.edu Thu Mar 9 09:33:40 1995 > Date: Thu, 9 Mar 1995 09:10:40 -0500 (EST) > From: Oliver Schurr > Subject: Appologies for a misdirected POST > > Yesterday I replied to the post from Ross Underhill about the .WMF > converters. I did this by replying to Ross directly and CC to the > hyperchem list. Now today i get 14 (!) undeliverable mail messages from > all over the world that something was screwed up. I was under the impression that the software that manages the mailing list monitored bounce messages and automatically performed cleanups of addresses that fail repeatedly. I may have been mistaken in this. At any rate, I'll be cleaning the thing up manually. I apologize for the inconvenience. Some of those messages seem to be warnings from our mail service provider that it couldn't connect immediately to a recipient's machine, and that it would keep trying. I'm not sure what can be done about that at the moment. This message will serve as a test, I think: I'll be recording the addresses of bounce messages for further checking. Regards, Joel ------------ Joel Polowin, Ph.D. Manager, Scientific Support Email to: polowin@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 ________________________________________________________________________ From owner-hyperchem Thu Mar 9 16:47:08 1995 Date: Thu, 9 Mar 1995 13:40:12 -0500 From: Joel Polowin To: hyperchem@hyper.com Subject: Re: Mail List Bounces > From jstucker@gar.st.usm.edu Thu Mar 9 12:38:53 1995 > From: "Stacy Tucker" > Date: Thu, 9 Mar 1995 11:43:40 -0800 > To: polowin@hyper.com > Subject: Mail List Bounces > > I wanted to report that I have also experienced problems similar problems. > These errors occured after my initial posting to the list. At that time I > assumed I my technique was in error, but maybe it wasn't. Just wanted to > report a similar occurence. No, it wouldn't be anything that you had done incorrectly. The real bounce messages (unlike the mail-handler's warnings about delayed connections) happen because a recipient's address no longer exists. This may be because s/he has changed accounts (or simply lost the old account), or that a mail server has been renamed -- something along those lines. You folks will probably have seen occasional messages requesting unsubscription which are sent to the entire group, instead of to hyperchem-request. In fact, we get more of them sent to the group than to the proper channel... and a substantial proportion of them are sent from accounts other than the ones that we've actually got on the list, presumably because the address we've got has had its mail forwarded. The mail handler isn't smart enough to handle that. When one or both addresses are arbitrary number/letter combinations, instead of names, the list administrator usually isn't smart enough to handle it either. :-) I'd like to warn everyone on the list that we're in the middle of changing our mail service around, as part of bringing up a home page (and other changes). Mail service may be a bit chancy for a few days. Regards, Joel ------------ Joel Polowin, Ph.D. Manager, Scientific Support Email to: polowin@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 ________________________________________________________________________ From owner-hyperchem Thu Mar 9 18:31:15 1995 Date: Thu, 9 Mar 1995 14:11:29 -0500 From: "Edmund C. Lam" To: hyperchem Subject: FYI for users on the HyperChem mailing list... Hypercube in the process of setting some Internet resources. Our Web site will be: http://www.hyper.com Our FTP site will be: ftp://ftp.hyper.com Demo and support files will be open to anonymous FTP. These new internet address should begin to propagate out to the 'VOID' within the week. Mail to hyper.com has also been changed. Please advise us of delivery problems by phoning us at 1-800-960-1871 and ask for Edmund. ________________________________________________________________________ From owner-hyperchem Mon Mar 13 15:15:13 1995 Date: Mon, 13 Mar 1995 16:58:42 +0000 (GMT) From: KANEPCHEM <94970459@vax1.dcu.ie> Subject: sodium ion radii To: hyperchem@hyper.com Dear HyperChemers, I am studying the interaction of metal ions with calixarenes. To do this I have attempted to create new atom types corresponding to metal ions of different radii, according to the instructions given on page 144 of the Computational Chemistry manual. However when I attempted to click Build/Compile Type Rules (step 3) I received a STOP message saying that "there is an error in line 73 of the mmptyp.txt file". The following is part of the modified mmptyp.txt file, containing two new entries for the new sodium atom types : sd1 22.990 73. Na SODIUM ZERO NINE FIVE A sd2 22.990 74. Na SODIUM ONE FIVE ZERO A fe2 55.847 61. Fe IRON (II) fe3 55.847 62. Fe IRON (III) ni2 58.710 63. Ni NICKEL (II) ni3 58.710 64. Ni NICKEL(III) co2 58.933 65. Co COBALT (II) co3 58.933 66. Co COBALT (III) The following is part of the modified chem.rul file, containing two new entries for the new sodium atom types : Na: ; sodium+ radius is 0.95 A =SD1. ; numerical type 73 ; sodium+ radius is 1.50 A ; =SD2. ; numerical type 74 Fe: ; Iron (II) ; =FE2. ; numerical type 61 ; Iron (III) =FE3. ; numerical type 62 Co: ; Cobalt (II) =CO2. ; numerical type 65 ; Cobalt (III) ; =CO3. ; numerical type 66 In both cases the entries for iron, cobalt and nickel are included for comparison purposes. Thanks in advance for suggestions. Regards, Paddy Kane ________________________________________________________________________ From owner-hyperchem Wed Mar 15 06:49:42 1995 From: Wolfgang=Ziche@rz.hu-berlin.de Date: Mon, 13 Mar 95 12:34:43 MET To: hyperchem@hyper.com I have by now been working some weeks with HyperChem (version 4) and have discovered several snags: 1. Calculating parts of molecules by semiempirical methods (using the Extend to sp3 command) is thwarted by the following message: "Error message received from node = 0: Capping atom # with atomic number ##: the slater exponent of s orbital is less than or equal to zero, please check your parameter file (am1_1.abp, mndo_1.abp, mindo3_1.abp, zindos_1.abp)." The parameter for the slater exponent (column 8 for am1_1.abp, mndo_1.abp, mindo3_1.abp, column 2 for zindos_1.abp), however, is positive in all .abp files. PM3 and ZINDO1 work without problems. This error obviously does not impair the results obtained with AM1 for "whole" molecules. 2. For users of non-english EXCEL versions: the macros supplied by Hypercube are translated by EXCEL, except for the "row" and "column" variables. This must be done by hand. 3. Do you also accept questions concerning HyperNMR? Wolfgang ________________________________________________________________________ From owner-hyperchem Wed Mar 15 11:18:15 1995 Date: Wed, 15 Mar 1995 13:48:48 UTC+0100 From: "Jose G. de la Campa" Subject: About amides To: hyperchem@www.hyper.com I am trying to calculate some rotational barriers around the HN-CO bond by AM1. I need to know if Hyperchem uses the same system that MOPAC, where it is neccesary to say if you want to make a molecular mechanics correction (MMOK) or if you do not want to make it NOMM. As Hyperchem does not ask anything I should like to now if the molecular mechanics correction is included or not. I suppose it is not included, but I am not sure. Thanks for any help. Jose Gonzalez de la Campa Instituto de Polimeros, Madrid, Spain ________________________________________________________________________ From owner-hyperchem Wed Mar 15 16:54:05 1995 Date: Wed, 15 Mar 95 14:57:34 -0500 From: polowin@hyper.hyper.com (Joel Polowin) To: hyperchem@hyper.hyper.com Subject: Re: About amides > Date: Wed, 15 Mar 1995 13:48:48 UTC+0100 > From: "Jose G. de la Campa" > Subject: About amides > > I am trying to calculate some rotational barriers around the HN-CO bond > by AM1. I need to know if Hyperchem uses the same system that MOPAC, > where it is neccesary to say if you want to make a molecular mechanics > correction (MMOK) or if you do not want to make it NOMM. As Hyperchem > does not ask anything I should like to now if the molecular mechanics > correction is included or not. I suppose it is not included, but I am > not sure. By default, HyperChem does not make a molecular mechanics correction. If you wish to make such a correction, you can -- for example -- select a torsional angle, assign a name to that selection, and then apply a restraint to that named selection, where the angle and force constant are the values indicated in the dialog box. Then you would do the AM1 calculation. The MOPAC correction uses a (1-cos(x-x_0))^2 correction, I think; our restraints use (x-x_0)^2. They are approximately the same for small (x-x_0). Regards, Joel ------------ Joel Polowin, Ph.D. Manager, Scientific Support Email to: polowin@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 ________________________________________________________________________ From owner-hyperchem Wed Mar 15 17:01:47 1995 Date: Wed, 15 Mar 95 14:04:16 -0500 From: polowin@hyper.hyper.com (Joel Polowin) To: hyperchem@hyper.com Subject: Missing parameters, mixed mode calculations > From: Wolfgang=Ziche@rz.hu-berlin.de > Date: Mon, 13 Mar 95 12:34:43 MET > To: hyperchem@hyper.com > Status: RO > > 1. Calculating parts of molecules by semiempirical methods (using the Extend > to sp3 command) is thwarted by the following message: > "Error message received from node = 0: Capping atom # with atomic number ##: > the slater exponent of s orbital is less than or equal to zero, please check > your parameter file (am1_1.abp, mndo_1.abp, mindo3_1.abp, zindos_1.abp)." > The parameter for the slater exponent (column 8 for am1_1.abp, mndo_1.abp, > mindo3_1.abp, column 2 for zindos_1.abp), however, is positive in all .abp > files. PM3 and ZINDO1 work without problems. This error obviously does not > impair the results obtained with AM1 for "whole" molecules. The problem here lies with the "capping atoms", which aren't completely parameterized in all cases. For example, when I load in the structure of aspartame and select the ring atoms (plus the attached CH2 by the Extend to sp3 command) and try to minimize it with AM1, I get the error message reported above. Capping atom 15 with atomic number 6:, etc. There isn't a trivial solution to this. The way of solving the problem is to edit the parameter file -- am1_1.abp, for example. The file begins with the complete parameter sets for "real" atoms, and then has the parameters for capping atoms. The capping atoms are indicated by negative "atomic numbers" in the first column. What you'd need to do is to copy the parameters for the real atom to the line for the capping atom -- in this case, the line for atomic #6 to the line for #-6. Then recompile the parameters. The reason that we haven't done this ourselves is that the parameters were optimized for complete molecular systems, and published, etc. We don't guarantee that the behaviour will be entirely correct for partial systems, since those parameters would then be used in ways that may not be quite appropriate. > 2. For users of non-english EXCEL versions: the macros supplied by Hypercube > are translated by EXCEL, except for the "row" and "column" variables. This > must be done by hand. Since we don't have a non-English version of Excel here, I'm not quite sure what you're referring to. It doesn't surprise me that the regular macro commands would be translated automatically; I would imagine that they might be stored in tokenized form, and that when a file is read into Excel those tokens are expanded in the local language. Must the variables be translated in order to get the macro to work, or is the translation necessary only for convenient use in another language? > 3. Do you also accept questions concerning HyperNMR? Certainly. Regards, Joel ------------ Joel Polowin, Ph.D. Manager, Scientific Support Email to: polowin@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 ________________________________________________________________________ From owner-hyperchem Wed Mar 15 18:39:21 1995 Date: Wed, 15 Mar 95 16:50:36 -0500 From: polowin@hyper.hyper.com (Joel Polowin) To: hyperchem@www.hyper.com Subject: Re: About amides > Date: Wed, 15 Mar 1995 13:48:48 UTC+0100 > From: "Jose G. de la Campa" > Subject: About amides > > I am trying to calculate some rotational barriers around the HN-CO bond > by AM1. I need to know if Hyperchem uses the same system that MOPAC, > where it is neccesary to say if you want to make a molecular mechanics > correction (MMOK) or if you do not want to make it NOMM. As Hyperchem > does not ask anything I should like to now if the molecular mechanics > correction is included or not. I suppose it is not included, but I am > not sure. By default, HyperChem does not make a molecular mechanics correction. If you wish to make such a correction, you can -- for example -- select a torsional angle, assign a name to that selection, and then apply a restraint to that named selection, where the angle and force constant are the values indicated in the dialog box. Then you would do the AM1 calculation. The MOPAC correction uses a (1-cos(x-x_0))^2 correction, I think; our restraints use (x-x_0)^2. They are approximately the same for small (x-x_0). Regards, Joel ------------ Joel Polowin, Ph.D. Manager, Scientific Support Email to: polowin@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 ________________________________________________________________________ From owner-hyperchem Wed Mar 15 19:01:04 1995 Date: Wed, 15 Mar 95 16:49:43 -0500 From: polowin@hyper.hyper.com (Joel Polowin) To: hyperchem@www.hyper.com Subject: Missing parameters, mixed mode calculations > From: Wolfgang=Ziche@rz.hu-berlin.de > Date: Mon, 13 Mar 95 12:34:43 MET > To: hyperchem@hyper.com > Status: RO > > 1. Calculating parts of molecules by semiempirical methods (using the Extend > to sp3 command) is thwarted by the following message: > "Error message received from node = 0: Capping atom # with atomic number ##: > the slater exponent of s orbital is less than or equal to zero, please check > your parameter file (am1_1.abp, mndo_1.abp, mindo3_1.abp, zindos_1.abp)." > The parameter for the slater exponent (column 8 for am1_1.abp, mndo_1.abp, > mindo3_1.abp, column 2 for zindos_1.abp), however, is positive in all .abp > files. PM3 and ZINDO1 work without problems. This error obviously does not > impair the results obtained with AM1 for "whole" molecules. The problem here lies with the "capping atoms", which aren't completely parameterized in all cases. For example, when I load in the structure of aspartame and select the ring atoms (plus the attached CH2 by the Extend to sp3 command) and try to minimize it with AM1, I get the error message reported above. Capping atom 15 with atomic number 6:, etc. There isn't a trivial solution to this. The way of solving the problem is to edit the parameter file -- am1_1.abp, for example. The file begins with the complete parameter sets for "real" atoms, and then has the parameters for capping atoms. The capping atoms are indicated by negative "atomic numbers" in the first column. What you'd need to do is to copy the parameters for the real atom to the line for the capping atom -- in this case, the line for atomic #6 to the line for #-6. Then recompile the parameters. The reason that we haven't done this ourselves is that the parameters were optimized for complete molecular systems, and published, etc. We don't guarantee that the behaviour will be entirely correct for partial systems, since those parameters would then be used in ways that may not be quite appropriate. > 2. For users of non-english EXCEL versions: the macros supplied by Hypercube > are translated by EXCEL, except for the "row" and "column" variables. This > must be done by hand. Since we don't have a non-English version of Excel here, I'm not quite sure what you're referring to. It doesn't surprise me that the regular macro commands would be translated automatically; I would imagine that they might be stored in tokenized form, and that when a file is read into Excel those tokens are expanded in the local language. Must the variables be translated in order to get the macro to work, or is the translation necessary only for convenient use in another language? > 3. Do you also accept questions concerning HyperNMR? Certainly. Regards, Joel ------------ Joel Polowin, Ph.D. Manager, Scientific Support Email to: polowin@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 ________________________________________________________________________ From owner-hyperchem Thu Mar 16 08:56:44 1995 From: "Gregor Fels" To: hyperchem@hyper.com Date: Thu, 16 Mar 1995 11:19:06 GST Subject: conformational search Dear HyperChemists does anybody know wether there is a way of setting a "through space constrain" within the ChemPlus conformational search modul (two atoms within the same molecule that are far apart)? Gregor Dr. Gregor Fels Universitaet-GH-Paderborn FB 13-Org. Chemie Warburgerstr. 100 D-33098 Paderborn, Germany Tel. 0049-5251-602181/Fax -603245 EMail GF@chemie.uni-paderborn.de ________________________________________________________________________ From owner-hyperchem Thu Mar 16 14:14:46 1995 From: Piotr Skurski Subject: Symmetry To: hyperchem@hyper.com Date: Thu, 16 Mar 95 16:33:29 MET Cc: piotr@ewa.chem.univ.gda.pl I am carrying out some calculations for molecular systems which posses high symmetry. How can I use symmetry in HyperChem ? Piotr Skurski, M.Sc. Department of Chemistry University of Gdansk e-mail: piotr@ewa.chem.univ.gda.pl ________________________________________________________________________ From owner-hyperchem Thu Mar 16 18:33:23 1995 Date: Thu, 16 Mar 95 16:07:14 -0500 From: polowin@hyper.hyper.com (Joel Polowin) To: hyperchem@www.hyper.com Subject: Re: Symmetry > From: Piotr Skurski > Subject: Symmetry > Date: Thu, 16 Mar 95 16:33:29 MET > > I am carrying out some calculations for molecular systems > which posses high symmetry. > How can I use symmetry in HyperChem ? HyperChem allows one to perform a number of symmetry-related operations, such as inversions and reflections. However, if you are asking if the calculations take advantage of assumed or defined structural symmetries, that is something that we don't do. This allows us to get a more accurate result, at the potential cost of some speed. Regards, Joel ------------ Joel Polowin, Ph.D. Manager, Scientific Support Email to: polowin@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 ________________________________________________________________________ From owner-hyperchem Thu Mar 16 18:45:50 1995 Date: Thu, 16 Mar 95 16:08:27 -0500 From: polowin@hyper.hyper.com (Joel Polowin) To: hyperchem@www.hyper.com Subject: Re: conformational search > From: "Gregor Fels" > Date: Thu, 16 Mar 1995 11:19:06 GST > Subject: conformational search > > does anybody know wether there is a way of setting a "through space > constrain" within the ChemPlus conformational search modul (two atoms > within the same molecule that are far apart)? I am not certain if this answers your question, but: Before you perform the conformational search, you can apply structural restraints in the usual way, to fix distances, angles, and torsions. (You select the atoms defining the distance/angle/torsion; use Select/Name to apply a name to the selection; use Setup/Restraints to set the feature and force constant.) These restraints do not require that atoms be bonded; you could apply a distance restraint to far-apart atoms on one molecule, or even on two different molecules. Although the changes in the torsional angles due to the conformational search may initially move the restrained features away from the specified values, they will return to the desired positions during the structural optimization. (It may be that the other structural changes would prevent that return by getting in the way, but then the resulting optimized structure would have a very high energy and would be rejected by the searcher.) Regards, Joel ------------ Joel Polowin, Ph.D. Manager, Scientific Support Email to: polowin@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 ________________________________________________________________________ From owner-hyperchem Fri Mar 17 14:40:40 1995 From: "Jens Spanget-Larsen" Organization: Roskilde Universitetscenter To: hyperchem@hyper.com Date: Fri, 17 Mar 1995 17:30:27 +0100 Subject: Isotopes in HyperChem Dear HyperChem'ers! I would like to know, if it is possible to investigate isotope effects with HyperChem. For example, is it possible to substitute a hydrogen atom with a deuterium atom and study the influence on the calculated vibrational frequencies? Yours, Jens >--< _________________________________ _________________________________ | | | | Jens Spanget-Larsen | Phone: +45 46757711 | | Associate Professor, dr.scient. | - direct: +45 46757781 * 2710 | | Department of Chemistry (17.2) | - private: +45 42840320 | | Roskilde University | Fax: +45 46757721 [Dept.] | | RUC, P.O. Box 260 | - +45 46757401 [RUC] | | DK-4000 Roskilde, Denmark | Internet: JSL@mmf.ruc.dk | |_________________________________|_________________________________| ________________________________________________________________________ From owner-hyperchem Fri Mar 17 14:42:36 1995 Date: Fri, 17 Mar 95 08:52:10+020 From: chemjps@eagle.uovs.ac.za (JP Steynberg) To: hyperchem@hyper.com Upgrading costs Can anyone give me information regarding the following: 1. I currently have Release 3 of HYPERCHEM. What is the cost of upgrading to Release 4. I also want to obtain a second copy of Release 4, and what will be the cost of this. This is for academic use. 2. Are there any versions of HYPERCHEM available yet for UNIX workstations or for Windows NT and where can one obtain more information to this regard. Thank you Dr. JP Steynberg ________________________________________________________________________ From owner-hyperchem Fri Mar 17 18:32:41 1995 Date: Fri, 17 Mar 95 15:28:48 -0500 From: polowin@hyper.hyper.com (Joel Polowin) To: hyperchem@www.hyper.com Subject: Re: upgrading costs, etc. > Date: Fri, 17 Mar 95 08:52:10+020 > From: chemjps@eagle.uovs.ac.za (JP Steynberg) > To: hyperchem@hyper.com > > 1. I currently have Release 3 of HYPERCHEM. What is the cost of > upgrading to Release 4. I also want to obtain a second copy of > Release 4, and what will be the cost of this. This is for > academic use. The suggested academic price to upgrade from v.3 to v.4 of HyperChem is US$195; the academic price of a new copy of v.4 is US$995. If you send a note to info@hyper.com, we can put you in touch with a local distributor for local purchasing arrangements; or you can order directly from us. > 2. Are there any versions of HYPERCHEM available yet for UNIX > workstations or for Windows NT and where can one obtain more > information to this regard. The current version of HyperChem is a 32-bit application that will run under Windows NT as is. The only special requirement is the need to use a port driver so that the software can find the hardware lock. We supply that driver at no additional charge to those who tell us that they wish to run under NT when they order the software, or for the cost of shipping to those who want the driver later. We can also send the driver by E-mail, and it's available for download from our ftp site, ftp.hyper.com, directory /pub/patch . As for UNIX workstations, our current major project is a new release for SGI stations, which we hope to have out in a few more months. For now, all that we can offer are the back-end computational modules, which allow a PC running HyperChem to off-load the molecular mechanics and/or semi-empirical calculations to a network-linked UNIX machine. The platforms that we currently support are: Silicon Graphics IRIX 4.0 to 4.0.5F and 5.2; IBM AIX 3.2.5 and 4.0; DEC OSF/AXP 1.2 . We can run on DEC Alpha NT and USF but not on a DEC VAX. Regards, Joel ------------ Joel Polowin, Ph.D. Manager, Scientific Support Email to: polowin@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 ________________________________________________________________________ From owner-hyperchem Sat Mar 18 14:51:05 1995 Date: Sat, 18 Mar 1995 15:10:24 +0000 (GMT) From: KANEPCHEM <94970459@vax1.dcu.ie> Subject: Parameters for metal ions / MMPNBD.txt file To: hyperchem@hyper.com Hi HyperChemers, I am interested in modelling in the inter action of calixarenes with metal ions, especially those of group 1. To those of you who read my recent message about my difficulties in creating new atom types for sodium, you may be interested to know that I eventually succeeded by modifying the chem.rul and mmptyp.txt files with Microsoft Word, whereas I had previously used Notepad. Can anyone tell me why I failed with the latter. More importantly, I need suitable values for the rstar and eps variables so that I can modify the MMPNBD.TXT file. I would be very grateful if any could supply me with such values for group ions or suggest a simple method (because I am a simple sort of a person !!!!!!!!!!!!!!!!!!) for obtaining them. Regards, Paddy Kane P.S. I know that I am a day late, but anyway, happy St. Paddy's Day. ________________________________________________________________________ From owner-hyperchem Sat Mar 18 18:14:16 1995 From: Howard.Shertzer@UC.Edu Date: Sat, 18 Mar 1995 15:53:01 -0500 (EST) Subject: Basic Computational Texts To: hyperchem@hyper.COM I recently asked if there were basic textbooks in computational chemistry that were not exceptionally mathematical. I recieved a few responses, indicating that there were few texts in this area that might be used to supplement the Hyperchem Manual. One suggestion, by 4 different users, was: Hehre et al. "Experiments in Computational Organic Chemistry", published by Wavefunction (fax 714-955-2118 Phone 714-955-2120). This features a hands-on tutorial. Cost is $15. The other suggestion was: "Computational chemistry using the PC", by DW Rogers (VCH). ________________________________________________________________________ From owner-hyperchem Mon Mar 20 14:14:57 1995 Date: Mon, 20 Mar 95 10:17:16 -0500 From: polowin@hyper.hyper.com (Joel Polowin) To: hyperchem@www.hyper.com Subject: Re: Isotopes in HyperChem > From: "Jens Spanget-Larsen" > Date: Fri, 17 Mar 1995 17:30:27 +0100 > Subject: Isotopes in HyperChem > > I would like to know, if it is possible to investigate isotope > effects with HyperChem. For example, is it possible to substitute > a hydrogen atom with a deuterium atom and study the influence on the > calculated vibrational frequencies? I'm afraid that it is not possible with the current version of HyperChem; the calculation methods are hard-wired in the program and cannot be worked around. We plan to include isotope effects in the next version of HyperChem, which we expect to release later this year. Regards, Joel ------------ Joel Polowin, Ph.D. Manager, Scientific Support Email to: polowin@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 ________________________________________________________________________ From owner-hyperchem Tue Mar 21 14:01:16 1995 Date: Tue, 21 Mar 1995 15:19:17 GMT To: hyperchem@hyper.com From: tadrury@liverpool.ac.uk (Adam Drury) Subject: Snapshot File Editor Dear All, About a year or so ago, there was some talk on this list about a utility called CINECHEM which converted HyperChem Version 2 snapshot files (and HIN Files) into a format which can be read by 3D Studio. I have a copy of this utility, and it seems to work fine with version 2 of HyperChem. However, version 3 and above uses a completely different file format for the snapshot files, and hence a snapshot file editor program was passed to me by HyperCube (beta test version) in order to convert snapshot files from Version 3 to Version 2, which could then be used with CINECHEM and consequently 3D studio. Unfortunately, I have not had much success with this beta test utility. I therefore have a number of questions:- (i) Is there a release version of the Snapshot File Editor available anywhere ? (To buy or as public domain) (ii) Has CINECHEM ever been updated in order to cope with the change in file format ? (iii) Does anyone know of any other utilities to convert HIN and SNP files into a format which can be read by 3D Studio ? Thanks in advance Adam Drury ------------------------------------------------------------------------ Adam Drury CTI Centre for Chemistry Department of Chemistry University of Liverpool P.O. Box 147 Liverpool L69 3BX ENGLAND Tel : 0151-794-3523 Fax : 0151-794-3586 E-mail : tadrury@uk.ac.liverpool ________________________________________________________________________ From owner-hyperchem Tue Mar 21 15:03:52 1995 Date: Tue, 21 Mar 1995 17:13:08 +0100 (MET) From: Andrzej Szyczewski To: hyperchem@hyper.com Hallo, I am a new user of HyperChem and therefore i have some problems on the start: FIRST: How to calculate EPR HYPERFINE SPLITTINGS from data ontained by INDO or MINDO/3 (as well as unpaired electron density)? For example MOPAC give hyperfine splittings with other data together. SECOND: What about the order of alpha and beta orbitals? The order is: alpha1, alpha2, alpha3 ... or alpha1 alpha2 alpha3 . . Thank you in advance Andrzej Szyczewski Dr.Andrzej Szyczewski Institute of Physics A.Mickiewicz University Umultowska 85 61-614 Poznan/ Poland e-mail aszy@phys.amu.edu.pl ________________________________________________________________________ From owner-hyperchem Tue Mar 21 20:49:16 1995 Date: Tue, 21 Mar 1995 20:35:18 -0300 (BST) From: Edecio C Neto Subject: molecular modeling of antigenic peptides To: hyperchem@hyper.com I am an immunologist dealing with molecular mimicry between antigenic peptides derived from non-related proteins. I would like to get in touch with anybody using HYPERCHEM for molecular modeling/dinamics of short peptides (6-30 residues or higher). Edecio Cunha-Neto, M.D., Ph.D. ________________________________________________________________________ From owner-hyperchem Mon Mar 27 18:03:00 1995 Date: Mon, 27 Mar 1995 13:19:00 -0500 From: Matthew.Harbowy@tjlus.sprint.com To: hyperchem@hyper.com Subject: ab initio on Hyperchem? March 27 C&E news, back cover, says that Hyperchem now has Ab Initio. Any info on an upgrade for us v.3 users? matt harbowy thomas j. lipton ________________________________________________________________________ From owner-hyperchem Tue Mar 28 17:16:29 1995 Date: Tue, 28 Mar 95 11:10:27 -0500 From: polowin@hyper.hyper.com (Joel Polowin) To: hyperchem@hyper.com Subject: Re: ab initio on Hyperchem? > Date: Mon, 27 Mar 1995 13:19:00 -0500 > From: Matthew.Harbowy@tjlus.sprint.com > Subject: ab initio on Hyperchem? > > March 27 C&E news, back cover, says that Hyperchem now has Ab Initio. > > Any info on an upgrade for us v.3 users? The new versions will not be ready for another couple of months. (The "NOW!" part of "NOW! with Ab Initio" is a bit premature, at least as far as buying the product goes...) We will accept orders for the new version; we expect to ship the new Windows version in 60 to 90 days, the new SGI version in 90 to 120 days. The new version will be on display at the ACS meeting in Anaheim in the first week of April. As far as pricing goes, suggested retail prices for the Windows version as of April 1 will be as follows, given in $US, commercial (acedemic): Release 4.5 for Windows, standalone: 2,595 (1,295) network, 1 license 2,595 (1,295) 5 license 10k (5k) 10 license 18k (9k) 25 license 30k (15k) 50 license 40k (20k) unlimited 60k (30k) Extra rel. 4.5 for Windows manual set 350 (175) Release 4 to 4.5 update 795 (495) 3 4.5 1,095 (650) 2 4.5 1,595 (895) 3 to 4 update 395 (195) 2 4 995 (495) Update of N non-networking to N-license network version of v. 4.5: free Regards, Joel ------------ Joel Polowin, Ph.D. Manager, Scientific Support Email to: polowin@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 ________________________________________________________________________ From owner-hyperchem Tue Mar 28 20:29:45 1995 From: "Dr. Steven Desjardins" Organization: Washington & Lee University To: hyperchem@hyper.com Date: Tue, 28 Mar 1995 12:10:56 EDT Subject: ab initio Is it true that a new release of hyperchem is available with ab initio methods? Is this in the PC version, and, if so, what are the details, e.g., price, methods, basis sets, etc.? ________________________________________________________________________ From owner-hyperchem Wed Mar 29 02:23:46 1995 Date: Wed, 29 Mar 1995 10:58:26 +1000 To: hyperchem@hyper.com From: bromrd92@octarine.cc.adfa.oz.au (Marcus Bromet) Subject: HyperChem V.4 and Cyclodextrins My name is Marcus Bromet. As part of my Honours year in Chemistry I am attempting to use HyperChem Version 4 (for Microsoft Windows) to model an alpha, beta and gamma cyclodextrin, and then energy minimise using the AMBER force field. Once this has been completed I aim to model cyclodextrins for complexing with specific compounds, and then verify my results with actual lab results. My first query is regarding the (SELECT PARAMETERS) option located under the (SETUP) menu bar. In Version 4 this option gives the user the ability to select the parameters of "AMBER", "AMBER2", and "AMBER3". Could anyone explain the relevant differences for each of these force fields, and as such which field is more often used for complex molecules (such as cyclodextrins). My second query relates to the actual values of the Amber force fields as described by HyperChem. I would like to verify the parameters specified within the AMBER force field (as supplied by HyperChem), with known literature values. Consequently I need to find a listing of the values supplied within the data files of the HyperChem directory. If anyone knows the exact location and name of such files could they please advise me. Finally, it is of interest to me anyone who is involved in the modelling of cyclodextrins, and I would be very eager to hear of success or failure with either your computerized modelling or practical lab results. With Thanks Marcus Bromet, Chemistry Department, University College (UNSW) Australian Defence Force Academy, CANBERRA ACT 2600 Australia voice: +61 6 2688943(w)/2688922(h) fax:+61 6 2688002 e-mail:bromrd92@octarine.adfa.oz.au ________________________________________________________________________ From owner-hyperchem Wed Mar 29 12:55:50 1995 From: "Fabri Marsicano" Organization: CHEMISTRY - WITS UNIVERSITY To: hyperchem@hyper.com Date: Wed, 29 Mar 1995 16:41:02 GMT + 2:00 Subject: Stretch-bend term in the MM+ force field Dear Hyperchemers, We have recently developed a set of MM2(87) force field parameters for various first-row transition metal ions, and ligand donor atoms, for use in the modelling of metal-ligand complexes. In view of the close similarity of the MM+ and MM2(87) force fields for saturated systems, we are currently trying to transplant our force field into Hyperchem Version 4 in order to make use of Hyperchem's superior graphical features. We are relatively new users of Hyperchem. We have defined appropriate new atom types and made appropriate entries in the mmp*.txt files. We would like to be able to "switch off" the stretch-bend term in the MM+ force field specifically for interactions involving the new metal ions, because we find that this term causes instability during energy minimisation in MM2 (and presumably also in Hyperchem). Can anyone please tell us : 1) How does Hyperchem determine whether and what stretch-bend constant is to be used for any particular atom ? Is this done using atomic weights specified in mmptyp.txt, or by using element types, or in some other way ? 2)Does the MM+ force field use a value of 0 for the stretch-bend constant for Ge (as done in MM2(87)) ? 3)Is there any way of changing (e.g., switching off) the stretch-bend constant that is used for any atom ? One final question of a more general nature. Is it possible in Hyperchem to obtain a breakdown of the total steric energy in terms of stretching, bending, torsion, etc. contributions (as is possible, e.g., in Alchemy or MM2) ? This would help a lot in trouble-shooting. If you can help with any of these points, please contact us. FABRI MARSICANO ________________________________________________________________________ From owner-hyperchem Wed Mar 29 16:20:43 1995 Date: Wed, 29 Mar 95 12:08:47 -0500 From: polowin@hyper.hyper.com (Joel Polowin) To: hyperchem@www.hyper.com Subject: Re: HyperChem V.4 and Cyclodextrins > Date: Wed, 29 Mar 1995 10:58:26 +1000 > From: bromrd92@octarine.cc.adfa.oz.au (Marcus Bromet) > Subject: HyperChem V.4 and Cyclodextrins > > My first query is regarding the (SELECT PARAMETERS) option located under > the (SETUP) menu bar. In Version 4 this option gives the user the ability > to select the parameters of "AMBER", "AMBER2", and "AMBER3". Could anyone > explain the relevant differences for each of these force fields, and as > such which field is more often used for complex molecules (such as > cyclodextrins). I think I'd best leave it to people who actually use AMBER for their work to explain their preferences. Anyone..? > My second query relates to the actual values of the Amber force fields as > described by HyperChem. I would like to verify the parameters specified > within the AMBER force field (as supplied by HyperChem), with known > literature values. Consequently I need to find a listing of the values > supplied within the data files of the HyperChem directory. If anyone knows > the exact location and name of such files could they please advise me. The files should be in the same directory that HyperChem itself is in; filenames should be 'amber*.*' and 'am89a*.*', as described in Appendix B of the reference manual. The specific file names are also listed in CHEM.INI; this is how HyperChem knows what files to use when it compiles the parameter sets. The parameters were taken from the literature; see the references cited on page 161 of _Computational Chemistry_ or page 401 of the _Reference_ manual. Regards, Joel ------------ Joel Polowin, Ph.D. Manager, Scientific Support Email to: polowin@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 ________________________________________________________________________ From owner-hyperchem Wed Mar 29 20:57:59 1995 Date: Wed, 29 Mar 95 18:00:24 -0500 From: polowin@hyper.hyper.com (Joel Polowin) To: hyperchem@www.hyper.com Subject: Re: Stretch-bend term in the MM+ force field > From: "Fabri Marsicano" > Date: Wed, 29 Mar 1995 16:41:02 GMT + 2:00 > > 1) How does Hyperchem determine whether and what stretch-bend > constant is to be used for any particular atom ? Is this done using > atomic weights specified in mmptyp.txt, or by using element types, or > in some other way ? The stretch-bend term is described on pages 158-159 of _Computational Chemistry_. Stretch-bend terms are defined when the central atom is in the first or second periodic row (after H and He), and taken to be zero otherwise. This is determined by element, not by atom type. (I tested this: drew dimethyl ether in HyperChem, turned on the log file, and ran a single-point calculation. The list of terms included a C-O-C stretch-bend term. Changed the O to a Ge but did not recompute the atom types. Single-point calculation reports a bend term for the C4-O2-C4 angle (since the Ge still had an atom type of O2) but no stretch-bend term. Recompute atom types, changing the Ge to type GE; single-point calculation again reports a bend term but not a stretch- bend term for the C4-GE-C4 angle.) > 2)Does the MM+ force field use a value of 0 for the stretch-bend > constant for Ge (as done in MM2(87)) ? Yes. > 3)Is there any way of changing (e.g., switching off) the stretch-bend > constant that is used for any atom ? I think not; according to the manual, "The stretch-bend force constants are incorporated into the program and you cannot modify them." > One final question of a more general nature. Is it possible in > Hyperchem to obtain a breakdown of the total steric energy in terms > of stretching, bending, torsion, etc. contributions (as is possible, > e.g., in Alchemy or MM2) ? This would help a lot in trouble-shooting. Yes. While HyperChem is NOT running -- this is very important -- you edit the file CHEM.INI with any text editor that works with plain text files without adding formatting characters or other similar surprises. The lines you want are in the "[HyperChem]" block of information, probably near the end of the block. They specify values for "MechanicsPrintLevel" and "QuantumPrintLevel"; the higher the value, the more information you get. If you set MechanicsPrintLevel to 6 or higher, save the file, and start HyperChem, then open a log file and do a single-point MM+ calculation on a structure, the log file will contain a detailed list of each energy interaction, the force constant used, the deviation from the minimum-energy conformation for that interaction, and the resulting energy term. Regards, Joel ------------ Joel Polowin, Ph.D. Manager, Scientific Support Email to: polowin@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 ________________________________________________________________________ From owner-hyperchem Thu Mar 30 04:43:42 1995 Date: Thu, 30 Mar 1995 02:05:23 -0500 (EST) From: "William T. Winter" To: Joel Polowin Cc: hyperchem@www.hyper.com Subject: Re: HyperChem V.4 and Cyclodextrins > My first query is regarding the (SELECT PARAMETERS) option located under > the (SETUP) menu bar. In Version 4 this option gives the user the ability > to select the parameters of "AMBER", "AMBER2", and "AMBER3". Could anyone > explain the relevant differences for each of these force fields, and as > such which field is more often used for complex molecules (such as > cyclodextrins). Actually the best Amber parameters to use for this type structure are those developed by Homans ( see Biochemistry v.29; 9110 (1990) You can add these in your self using any text editor to extend the forcefield or you can buy the add-on program Chemplus from hyperchem for about $500US I believe. I was a beta tester of this package for Hyperchem and found it to be a useful addition for polysaccharides and oligosaccharides. The "saccharide builder" is particularly nice feature analaous to the peptide and nucleic acid builders in Hyperchem itself. > > My second query relates to the actual values of the Amber force fields as > described by HyperChem. I would like to verify the parameters specified > within the AMBER force field (as supplied by HyperChem), with known > literature values. Consequently I need to find a listing of the values > supplied within the data files of the HyperChem directory. If anyone knows > the exact location and name of such files could they please advise me. The best place to see the parameters is in the ascii files with names like AM.... . TXT and if you have a conventional installation of the program these reside in the directory \hyper. We use hyperchem extensively for visualizing polysaccharides modeled in other programs and are also using it to produce starting models of the chemical repeat units in such polymers. In general I am quite satisfied with the results of this approach. =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= Dr. William T. Winter Phone: (315)470-6876 315 Baker Lab FAX: (315)470-6856 SUNY-ESF Internet: wtwinter@mailbox.syr.edu Syracuse, NY 13210-2786 ________________________________________________________________________ From owner-hyperchem Thu Mar 30 05:56:58 1995 From: "GRAHAM WILLS-JOHNSON" Organization: RMIT Applied Physics To: hyperchem@hyper.com Date: Thu, 30 Mar 1995 17:22:46 EST-10 Subject: Chem.ini settings An aside to recent exchanges on the stretch-bend term: There is an alternative to editing Chem.ini settngs which is much more flexible and immediate... The appropriate messages written into a script can be used to alter things like quantum-print-level at will during a run (for example to avoid getting repeats of info into your log file if a vibrational analysis is to be performed after an optimization). In fact I have sometimes thought I should write myself a RESET.SCR to avoid the surprises I sometimes get after the weekend when I am doing some very different sort of job and last Friday has vanished into a complete haze. Graham Wills-Johnson ________________________________________________________________________ From owner-hyperchem Thu Mar 30 14:32:52 1995 Date: Thu, 30 Mar 95 10:50:13 -0500 From: polowin@hyper.hyper.com (Joel Polowin) To: hyperchem@www.hyper.com Subject: Re: AMBERS parameters > Thanks Joel for your e-mail and references for literature values. I have > the both papers from Weiner and Kollman (1984, Am. Chem. Soc. & 1986 J. > Comp. Chem.). These are the references as supplied on p161(Computational > Chemistry) and p401 (Reference Manual) - these references cover "AMBER2" > parameters and "AMBER3" parameters. However in the (SELECT PARAMETERS) > option in HyperChem there is also an "AMBERS" set of parameters. The > manuals make no reference as to where this series of variable came from - > could you please advise? > A second point is that in the AMBERTYP.TXT file the last eleven > (11) entries have been modified by a reference (1990, Biochem.). This > reference is written by HOMANS, S.W. and is titled "A Molecular Mechanical > Force Field for the Conformational Analysis of Oligosaccharides". No > mention of this paper is made within the reference manuals and I suspected > that "AMBERS" may have incorporated HOMANS values, with the "S" standing > for "sugars" - is this assumption wrong, and should I use a different force > field for the minimization of cyclodextrins? I'd missed that point. Yes, the AMBERS version is from the paper by Homans. The parameters were added for polysaccharides when ChemPlus was released, with its "Sugar Builder" module; that happened after the HyperChem version 4 manuals were finalized, so no references to that version of the force field are in them. I'll have to fix that for the next version of the manuals. I'll admit to relative ignorance on the subject of polysaccharides. The discussion of the Sugar Builder in the ChemPlus manual leads me to think that the Homans parameters would be appropriate for a structure like a cyclodextrin, but I don't want to use the Voice Of Authority to tell you that AMBERS is better for your purposes than the other AMBER force fields. Regards, Joel ------------ Joel Polowin, Ph.D. Manager, Scientific Support Email to: polowin@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 ________________________________________________________________________ From owner-hyperchem Fri Mar 31 14:21:54 1995 Date: Fri, 31 Mar 1995 09:18:01 -0600 (CST) From: Jerry Stacy Tucker Sender: Jerry Stacy Tucker Reply-To: Jerry Stacy Tucker Subject: Error Messages To: Hyperchem Discussion I have a question concerning an error message I received after solvating a protein. I created a periodic box about the protein and initiated my calculations. In a few moments, I received an error that "two or more atoms are in the same position." Is there a way to correct this problem? Since the error message did not appear until after I began using water molecules in my calculations, I believe they're the cause of the error. Can I simply find the offending water molecule and remove it? Thanks for any help or suggestions. Stacy Tucker E-mail: jstucker@whale.st.usm.edu University of Southern Mississippi Department of Chemistry and Biochemistry ________________________________________________________________________ From owner-hyperchem Fri Mar 31 15:52:17 1995 Date: Fri, 31 Mar 1995 17:58:39 +0000 (GMT) From: KANEPCHEM <94970459@vax1.dcu.ie> Subject: macrocycles and internal rotation To: hyperchem@hyper.com Dear HyperChemers, I am using molecular mechanics to study the structure of calixarenes, a class of macrocycle. Calixarenes consist of 4 to 14 benzene rings, joined by -CH2- bridges to form one big ring. I wish to know how to rotate a benzene ring andany groups attached through an angle of for example 20 degrees, about the axis containing the atoms in the benzene ring where the which are bonded to the -CH2- groups. Currently, I am trying to do this by attempting to create a plane containing the aforementioned two atoms which would make an angle of 10 degrees with the benzene ring and then I could REFLECT the NAMED SELECTION of the benzene ring and the attached groups through this plane. However I don't know how to create such a plane. Another idea is to CONSTRAIN two atoms in benzene rings on opposite sides of the large ring to finish at a certain distance from each other at the end off a geometry optimization. However I am at a loss as to how I place such a a constrai int on the optimization. Would the Conformational Search option ChemPlus be o any use Thanks in advance for any responses, which I'll summarise and mail.