From bioinfo.ernet.in!deva@bioinfo.ernet.in Fri Jun 9 02:33:21 1995 Received: from sangam.ncst.ernet.in for bioinfo.ernet.in!deva@bioinfo.ernet.in by www.ccl.net (8.6.10/930601.1506) id CAA22471; Fri, 9 Jun 1995 02:32:21 -0400 Received: from bioinfo.UUCP (uucp@localhost) by sangam.ncst.ernet.in (8.6.12/8.6.6) with UUCP id MAA18247 for chemistry@ccl.net; Fri, 9 Jun 1995 12:02:18 +0530 Received: from bioinfo.UUCP by iucaa (4.1/SMI-4.1) id AA21666; Fri, 9 Jun 95 11:59:58+050 Received: by bioinfo.bioinfo.ernet.in (5.x/SMI-SVR4) id AA22029; Fri, 9 Jun 1995 11:58:30 -0500 Date: Fri, 9 Jun 1995 11:58:30 -0500 From: deva@bioinfo.ernet.in (Deva ) Message-Id: <9506091658.AA22029@bioinfo.bioinfo.ernet.in> To: chemistry@ccl.net Subject: Molec.Mechanics in torsion angle space. Dear Netters, Is there any public domain software to molecular mechanics calculations, using only torsion angles as variables? If not can anyone give me references where such calculations were carried out? Thanks. Devapriya Choudhury Bioinformatics Centre, University of Poona Pune, Maharashtra 411 007 INDIA e-mail deva@bioinfo.ernet.in From sanja@indigo.irb.hr Fri Jun 9 03:33:23 1995 Received: from indigo.irb.hr for sanja@indigo.irb.hr by www.ccl.net (8.6.10/930601.1506) id DAA23072; Fri, 9 Jun 1995 03:26:27 -0400 Received: by indigo.irb.hr (940816.SGI.8.6.9/930416.SGI.AUTO) for CHEMISTRY@ccl.net id JAA08058; Fri, 9 Jun 1995 09:27:23 -0700 From: "sanja" Message-Id: <9506090927.ZM8056@indigo.irb.hr> Date: Fri, 9 Jun 1995 09:27:13 -0700 X-Mailer: Z-Mail (3.2.0 26oct94 MediaMail) To: CHEMISTRY@ccl.net Subject: summary-scaling vibrational frequencies Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Hi, Here is the summary of the responses answering my question about scaling calculated vibrational frequencies. Original question was: > I am interested in scaling vibration frequencies calculated at the >MP2/6-31G** level. Should I use the scaling factor of 0.9427, proposed by >J.A. Pople et.al for the MP2/6-31G* calculated frequencies. I am not sure >how much this scaling factor is sensitive to the difference in the basis sets. >Every comment is wellcome. > > Thanx, > Sanja and the answers ... *************************************************************************** Hello, this is a reply to your posting on the CCL about scaling factors. I believe it is most important to consider what molecule, cluster, or other system of particles you are calculating. If there is an experimental ir available, this should be used to develope your own set of scaling factors. These results can be compared with "standard" published scaling factors. This is not a very difficult task. One reason to support the calculation of one's own set of scaling factors is that different scaling factors are sometimes needed even within a range of stretching frequencies (free OH, as opposed to H-bonded OH stretches) as well as a set for bending frequencies. (Burke, Krishnan, and Jensen, Chem Ph Let., vol206,p293(1993); vol217,p311(1994), as only one example (water clusters)). There are quite a few discussions in the literature about this subject, and I expect you will get many more replies to your question. Luke Anthony Burke tel:609-225-6158 Department of Chemistry fax:609-225-6506 Rutgers University e-mail: Camden, NJ 08102 burke@camden.rutgers.edu USA *************************************************************************** Since HF frequencies are only approximate, I'd recommend a less precise scaling factor. O.9 is good for HF/6-31G* or HF/DZP frequencies. Dave Ewing John Carroll University ewing@jcvaxa.jcu.edu There is some data that DFT frequencies might not need much scaling. DFT might be much faster than MP2 for this....The DFT method of choice is ? Regards, John -- John M. McKelvey email: mckelvey@Kodak.COM Computational Science Laboratory phone: (716) 477-3335 2nd Floor, Bldg 83, RL Eastman Kodak Company Rochester, NY 14650-2216 -- *************************************************************************** Dear Sanja, Probably the best way to obtain a scaling factor, which is certainly better than a generic scaling factor for a particular level of theory, is to perform another ab initio calculation at the same level of theory on an analogous molecule for which the vibrational frequencies are known. One can then apply the scaling factor which best suits the known molecule to the molecule in question. Yours sincerely, Ryan ************************************* * Dr Ryan P.A. Bettens, * * Department of Physics, * * 174 West 18th Ave., * * Columbus, OH 43210-1106, * * U.S.A. * * * * email: BETTENS@MPS.OHIO-STATE.EDU * * Phone: (614) 292 4492 * ************************************* *************************************************************************** The original poster asked about scaling factors to be applied to mp2/6-31g** calculated frequencies. He asked if our mp2/6-31g* scaling factor is applicable and if the scalinf factor varies with basis set. Our work in this area, which is nearing completion, indicates that the mp2 level of theory is not particularly sensitive to basis set in predicting frequencies. While the 6-31g** basis set was not studied, we have data for the 6-311g** basis set. The appropriate scaling factor for the mp2 level of theory with this basis set is 0.9496 (with about the same overall RMS error as wefound for the mp2/6-31g* level of theory). We have actually studied a very extensive range of methods (including DFT) with various basis sets. If readers would like further information then please contact me. Hi, Here is the summary of the responses answering my question about scaling calculated vibrational frequencies. Original question was: > I am interested in scaling vibration frequencies calculated at the >MP2/6-31G** level. Should I use the scaling factor of 0.9427, proposed by >J.A. Pople et.al for the MP2/6-31G* calculated frequencies. I am not sure >how much this scaling factor is sensitive to the difference in the basis sets. >Every comment is wellcome. > > Thanx, > Sanja and the answers ... *************************************************************************** Hello, this is a reply to your posting on the CCL about scaling factors. I believe it is most important to consider what molecule, cluster, or other system of particles you are calculating. If there is an experimental ir available, this should be used to develope your own set of scaling factors. These results can be compared with "standard" published scaling factors. This is not a very difficult task. One reason to support the calculation of one's own set of scaling factors is that different scaling factors are sometimes needed even within a range of stretching frequencies (free OH, as opposed to H-bonded OH stretches) as well as a set for bending frequencies. (Burke, Krishnan, and Jensen, Chem Ph Let., vol206,p293(1993); vol217,p311(1994), as only one example (water clusters)). There are quite a few discussions in the literature about this subject, and I expect you will get many more replies to your question. Luke Anthony Burke tel:609-225-6158 Department of Chemistry fax:609-225-6506 Rutgers University e-mail: Camden, NJ 08102 burke@camden.rutgers.edu USA *************************************************************************** Since HF frequencies are only approximate, I'd recommend a less precise scaling factor. O.9 is good for HF/6-31G* or HF/DZP frequencies. Dave Ewing John Carroll University ewing@jcvaxa.jcu.edu There is some data that DFT frequencies might not need much scaling. DFT might be much faster than MP2 for this....The DFT method of choice is ? Regards, John -- John M. McKelvey email: mckelvey@Kodak.COM Computational Science Laboratory phone: (716) 477-3335 2nd Floor, Bldg 83, RL Eastman Kodak Company Rochester, NY 14650-2216 -- *************************************************************************** Dear Sanja, Probably the best way to obtain a scaling factor, which is certainly better than a generic scaling factor for a particular level of theory, is to perform another ab initio calculation at the same level of theory on an analogous molecule for which the vibrational frequencies are known. One can then apply the scaling factor which best suits the known molecule to the molecule in question. Yours sincerely, Ryan ************************************* * Dr Ryan P.A. Bettens, * * Department of Physics, * * 174 West 18th Ave., * * Columbus, OH 43210-1106, * * U.S.A. * * * * email: BETTENS@MPS.OHIO-STATE.EDU * * Phone: (614) 292 4492 * ************************************* *************************************************************************** The original poster asked about scaling factors to be applied to mp2/6-31g** calculated frequencies. He asked if our mp2/6-31g* scaling factor is applicable and if the scalinf factor varies with basis set. Our work in this area, which is nearing completion, indicates that the mp2 level of theory is not particularly sensitive to basis set in predicting frequencies. While the 6-31g** basis set was not studied, we have data for the 6-311g** basis set. The appropriate scaling factor for the mp2 level of theory with this basis set is 0.9496 (with about the same overall RMS error as wefound for the mp2/6-31g* level of theory). We have actually studied a very extensive range of methods (including DFT) with various basis sets. If readers would like further information then please contact me. Hope this is of some assistance, Kind Regards, Anthony P. Scott Research Officer Computational Chemistry Group Research School of Chemistry Australian National University Canberra, ACT, Australia Thanx to you all who replyed to my question. Sanja Hope this is of some assistance, Kind Regards, Anthony P. Scott Research Officer Computational Chemistry Group Research School of Chemistry Australian National University Canberra, ACT, Australia Thanx to you all who replyed to my question. Sanja -- *~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~* Sanja Sekusak e-mail: sanja@indigo.irb.hr Rudjer Boskovic Institute phone: (385-1) 46 10 89 HR-41001 Zagreb, CROATIA fax: (385-1) 27 26 48 *~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~* From srheller@nalusda.gov Fri Jun 9 10:18:28 1995 Received: from cliff.nalusda.gov for srheller@nalusda.gov by www.ccl.net (8.6.10/930601.1506) id KAA27395; Fri, 9 Jun 1995 10:17:10 -0400 Received: from origin.nalusda.gov by cliff.nalusda.gov (4.1/SMI-4.1) id AA26840; Fri, 9 Jun 95 10:17:04 EDT Received: by origin.nalusda.gov (5.x/SMI-SVR4) id AA20290; Fri, 9 Jun 1995 10:12:35 -0400 Date: Fri, 9 Jun 1995 10:12:34 -0400 (EDT) From: "Stephen R. Heller" To: jcicshelp , chemistry@ccl.net, chminf-l@iubvm.ucs.indiana.edu, orgchem@extreme.chem.rpi.edu, spectrscpy@aol.com Subject: New Chemical Concepts Web Site Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII 9 June, 1995 I have been asked to pass on the information that Chemical Concepts GmbH (Weinheim, Germany) has developed a WWW site which is now available. It is http://www.vchgroup.de/cc/ The Chemical Concepts WWW site has information on their spectral databases, search software, and analysis software. More information can be obtained by contacting them at info@cc.vchgroup.de Steve Heller, USDA, ARS, Plant Genome Program Bldg. 005, Room 337 Beltsville, MD 20705-2350 E-Mail: srheller@nalusda.gov Phone: 301-504-6055 FAX: 301-504-6231 From raeker@saturn.kent.edu Fri Jun 9 10:33:34 1995 Received: from saturn.kent.edu for raeker@saturn.kent.edu by www.ccl.net (8.6.10/930601.1506) id KAA27273; Fri, 9 Jun 1995 10:08:24 -0400 Received: by saturn.kent.edu (AIX 3.2/UCB 5.64/4.03) id AA12473; Fri, 9 Jun 1995 08:58:30 -0500 Date: Fri, 9 Jun 1995 08:58:29 -0500 (CDT) From: "Todd J. Raeker" To: chemistry@ccl.net Subject: Potentials for modeling biomolecules. Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello! My name is Leon Gardner and I am a new Ph.D. student at Kent State. I am interested in computational chemistry, specifically computational biochemistry. I don't have an account on this mailing list yet, so my advisor has let me use his account. Right now I am interested in finding out the latest developments in potentials for modeling proteins, hopefully above molecular mechanics. Any references as to where I could find such potentials would be very helpful. I am not sure which direction my research will take yet, but I am interested in artificial photosynthesis, biosensors, and biomolecular materials. If anyone has information about developments in this field, that would also be greatly appreciated. I am glad to be part of this group, and hopefully it will not be too long before I can help someone out there with their project. Here is my email address: gardner@saturn.kent.edu Thank you for your attention. Leon Dr. Todd J. Raeker | Department of Chemistry raeker@saturn.kent.edu | Kent State University Phone (216)-672-2986 | Kent, OH 44242-0001 From hinsenk@ERE.UMontreal.CA Fri Jun 9 16:03:31 1995 Received: from condor.CC.UMontreal.CA for hinsenk@ERE.UMontreal.CA by www.ccl.net (8.6.10/930601.1506) id PAA05166; Fri, 9 Jun 1995 15:57:31 -0400 Received: from eole.ERE.UMontreal.CA (eole.ERE.UMontreal.CA [132.204.10.20]) by condor.CC.UMontreal.CA with ESMTP id PAA28450 (8.6.11/IDA-1.6); Fri, 9 Jun 1995 15:55:32 -0400 Received: from cyclone.ERE.UMontreal.CA by eole.ERE.UMontreal.CA (950221.405.SGI.8.6.10/5.17) id PAA13404; Fri, 9 Jun 1995 15:55:31 -0400 Received: by cyclone.ERE.UMontreal.CA (950221.405.SGI.8.6.10/5.17) id PAA24973; Fri, 9 Jun 1995 15:50:02 -0400 Date: Fri, 9 Jun 1995 15:50:02 -0400 From: hinsenk@ERE.UMontreal.CA (Hinsen Konrad) Message-Id: <199506091950.PAA24973@cyclone.ERE.UMontreal.CA> To: deva@bioinfo.ernet.in CC: chemistry@ccl.net In-reply-to: <9506091658.AA22029@bioinfo.bioinfo.ernet.in> (deva@bioinfo.ernet.in) Subject: Re: CCL:Molec.Mechanics in torsion angle space. Is there any public domain software to molecular mechanics calculations, using only torsion angles as variables? If not can anyone give me references where such calculations were carried out? I can send you a preprint of an article by myself and G. Kneller, in which we present a simulation method suitable for a large range of constrained systems. As an example we compare several constraint models for a simple alpha-helix, among them one with only torsional angles (i.e. phi/psi-angles). Another work on simulations in these variables is L.M. Rice and A.T. Br\"unger, Proteins {\bf 19}, 277~(1994) ------------------------------------------------------------------------------- Konrad Hinsen | E-Mail: hinsenk@ere.umontreal.ca Departement de chimie | Tel.: +1-514-343-6111 ext. 3953 Universite de Montreal | Fax: +1-514-343-7586 C.P. 6128, succ. 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