From E702BS@FRCCSC21.bitnet Fri Sep 25 02:51:35 1992 Date: Fri, 25 Sep 92 08:15 FST From: "BIOSTRUCTURE SA" To: "Computer Chemistry List" Subject: GROMOS, AMBER, BOSS, CADPAC... Do you know that you can get GROMOS, AMBER, BOSS, CADPAC from us? ------------------------------------------------------------------------------- BIOSTRUCTURE S.A. Parc d'Innovation-Bat. Euclide F-67400 Illkirch, FRANCE Phone : (33) 88 67 98 00 Fax: (33) 88 67 98 01 ------------------------------------------------------------------------------- From RWOODS@VAX.MOLECULAR-BIOPHYSICS.OXFORD.AC.UK Fri Sep 25 09:02:00 1992 Date: Fri, 25 Sep 92 9:02 GMT From: RWOODS@VAX.MOLECULAR-BIOPHYSICS.OXFORD.AC.UK To: CHEMISTRY Subject: Gaussian/Mopac Differences In reference to the differences noted in the AM1 etc. results as calculated by MOPAC or Gaussian I would suggest comparing results calculated with the Gaussian "Standard Orientation" coordinates. All of the Gaussian programs reorient the input geometry to a "Standard Orientation", if there is a problem with rotational variations this should correct it. Robert J. Woods Glycobiology Institute University of Oxford South Parks Road Oxford, OX1 3QU From B_DUKE@DARWIN.NTU.EDU.AU Fri Sep 25 18:25:23 1992 Date: Fri, 25 Sep 1992 18:25:23 GMT From: B_DUKE@DARWIN.NTU.EDU.AU (Brian Duke) Subject: rotational invarience To: chemistry@ccl.net > Mark Thompson write: >ok...so I tried two different orientations in MOPAC 6.0 using formaldehyde. >No matter how I place the x,y,z coordinates, the program rotates the molecule >into some "standard" orientation before performing the calculation. >Putting two different orientations into MOPAC actually generates the >exact same set of cartesian coordinates used internally for the calculation. >I would like to run these calcs using the absolute coordinates I type in. >Is this possible?...can anyone help me with this? Am I building the data >deck incorrectly? Does it have to be formaldehyde? Try a molecule with no symmetry, if all you want to do is test out rotational invarience. Regards, Brian Salter-Duke (Brian Duke) School of Chemistry and Earth Sciences, Northern Territory University GPO Box 40146, Casuarina, NT 0811, Australia. Phone 089-466702 FAX 089-410460 E-mail B_DUKE@DARWIN.NTU.EDU.AU From E702BS@FRCCSC21.bitnet Fri Sep 25 06:51:34 1992 Date: Fri, 25 Sep 92 12:17 FST From: "BIOSTRUCTURE SA" To: "Computer Chemistry List" Subject: Reply to Comments about Mail We are glad to answer to some comments legitimely gone through the cc-list: PRO-SIMULATE is an interface and tool-box intended to run GROMOS, AMBER or BOSS: W.v.Gunsteren and W.L.Jorgensen are part of the scientific board of BIOSTRUCTURE S.A. which is distributing GROMOS and BOSS. AMBER is a natural extension to this explaining why we established working relationships with P.Kollman and provide this code. PRO-QUANTUM is an interface and tool-box intended to run CADPAC, MOPAC and Extended-Huckel code: R. Amos is therefore also part of our scientific collaborators and helping our development team to offer a good front-end to his ab-initio package. MOPAC or MOPAC-Clones or EH codes are rather easily integrated into a consistent environment... We are sorry that this could generate agressivity, and will not ad any further comments, but in fact today you could imagine setting-up easily a calculation with GROMOS (or any clone of it) using first data from a MOPAC geometry optimization with charges obtained through a Single-Point calculation with CADPAC... Setting up the whole process should not take you more than the time for drawing and clicking the system. For the people interessed we offer them to contact some of our customers. Thank you. From E702BS@FRCCSC21.bitnet Fri Sep 25 08:51:35 1992 Date: Fri, 25 Sep 92 14:17 FST From: "BIOSTRUCTURE SA" To: "Computer Chemistry List" Subject: Email We apologize again for the "commercial" side of the messages and will provide from now on ONLY scientific informations. ------------------------------------------------------------------------------- BIOSTRUCTURE S.A. Parc d'Innovation-Bat. Euclide F-67400 Illkirch, FRANCE Phone : (33) 88 67 98 00 Fax: (33) 88 67 98 01 E-mail: E702BS@FRCCSC21.BITNET ------------------------------------------------------------------------------- From jkl@ccl.net Fri Sep 25 07:41:29 1992 Date: Fri, 25 Sep 1992 11:41:29 -0400 From: jkl@ccl.net To: chemistry@ccl.net Subject: List abuse Dear Netters, So we have flame on the list. Many people send mail also to me. Please remember this: DO NOT PUNISH THE INNOCENT --- PUNISH THE OFFENDER... I want to remind you that I do not censor the list. Please remember, DO NOT SEND HATE MAIL TO THE LIST --- you only worsen the situation. DO NOT SEND THE HATE MAIL TO ME EITHER --- I am as helpless as you are. SEND HATE MAIL TO ABUSERS !!! I decided for the first time in the history of this list to block access to the list of somebody, namely E702BS@FRCCSC21.bitnet. I feel that I may do it, since E702BS@FRCCSC21.bitnet is not a subscriber. However, I do not want to be a policeman. You can exert more pressure than I can. Imagine someone getting 1200 pieces of mail on a single day saying how bad he/she is. Believe me, it would work... Jan Labanowski Ohio Supercomputer Center jkl@ccl.net From DSMITH@uoft02.utoledo.edu Tue Sep 25 08:38:20 1992 Date: 25 Sep 1992 12:38:20 -0400 (EDT) From: "DR. DOUGLAS A. SMITH, UNIVERSITY OF TOLEDO" Subject: Re: MOPAC and charges To: CUNDARIT%MEMSTVX1.BITNET@OHSTVMA.ACS.OHIO-STATE.EDU Tome Cundari writes: > A colleague of mine is researching the metabolites of various >psychoactive drugs using theory and experiments. He is using MOPAC to >compare the geometry of various metabolite structures, and from their >electronic structure try to predict potential reactivity. Since the >most pertinent reactions are charge-controlled, he would like to know which >of the various MOPAC Hamiltonians (AM1, PM3, MNDO) is most suitable for >calculating Mulliken atomics charges. Of course, there are philosophical >problems with using the Mulliken versus the other schemes, but we want to >keep it simple here. I have seen much discussion about one of the MOPAC >Hamiltonians giving spurious results for nitrogen compounds (which these >molecules have), and I don't remember which, if any, was the offending >culprit. Thanks. The problem is not which Hamiltonian and parameter set gives the best charges, but which one will give you the best optimization, i.e. which one gives correct or nearly correct answers where correct is defined as in agreement with reality and/or high level ab initio calculations. If there are aromatic amine nitrogens in the compound, use AM1 - the other methods fail. The reference you want is J. Comp. Chem. 1992, 13, 640. The paper is by Smith, Ulmer and Gilbert, and compared the three methods for aromatic amines. Doug Smith Assistant Professor of Chemistry The University of Toledo Toledo, OH 43606-3390 voice 419-537-2116 fax 419-537-4033 email dsmith@uoft02.utoledo.edu From GBENT@UCONNVM.UCONN.EDU Fri Sep 25 10:21:54 1992 Date: Fri, 25 Sep 92 15:21:54 EST From: Gary Bent Subject: DFT for excited states To: chemistry@ccl.net Dear Netters: I recently had a chance to use the program DMOL for a few days. I had just finished calculating the first excited state of HClCO (A" symmetry) at the gro und state (A' symmetry) optimized geometry to determine the vertical excitation energy. I had used Gaussian 90 at several different levels with CCSD with the triplets correction giving a value close to the experimental. For the heck of it, I calculated the same thing with DMOL. It gave a value better than any of the other methods. That surprised me because I had heard that DFT methods can't be trusted to do excited states. So am I just lucky in this case? Can someone give me some references on the problems or successes one might expect when calculating exci ted states with density functional theory? From chemistry-request@ccl.net Fri Sep 25 23:38:00 1992 Date: 25 Sep 92 10:14:43 U From: "Barbara Graham" Subject: CDA New-Special Offer for 1 To: CHEMISTRY@ccl.net Subject: Time:9:27 AM OFFICE MEMO CDA New-Special Offer for 1993 Date:9/25/92 Chemical Design Automation News, is the first and only industry publication to cover the CAMD community. Now, for a limited time only, CDA News is extending a special offer to new subscribers for the 1993 calendar year. To learn more, please contact CDA News Business Manager, P. J. Bolis, by phone: 617-890-2888, x264, or by FAX: 617-890-8694. --- Administrivia: This message is automatically appended by the mail exploder. CHEMISTRY@ccl.net: --- everyone CHEMISTRY-REQUEST@ccl.net: --- coordinator OSCPOST@ccl.net: send help from chemistry Anon. ftp: www.ccl.net --- From chemistry-request@ccl.net Fri Sep 25 23:47:19 1992 Date: Fri, 25 Sep 92 15:28:08 -2300 From: marchi@cecaix.cecam.fr (Massimo Marchi) To: E702BS%FRCCSC21.BITNET@OHSTVMA.ACS.OHIO-STATE.EDU, chemistry@ccl.net Subject: Re: Reply to Comments about Mail Will somebody (jkl) stop this inappropriate use of the mail list to blatantly advertise commercial products!! I suggest to delete the sender access to the list. Either that or delete me from the list. In either case, goodbye. mm --- Administrivia: This message is automatically appended by the mail exploder. CHEMISTRY@ccl.net: --- everyone CHEMISTRY-REQUEST@ccl.net: --- coordinator OSCPOST@ccl.net: send help from chemistry Anon. ftp: www.ccl.net ---