From chemistry-request@ccl.net Thu Apr 4 09:52:13 1991 Date: Thu, 4 Apr 91 08:09 CDT From: Subject: BIOSYM mailer To: chemistry@ccl.net Status: R Has anyone succeeded recently in getting mail through to dibug-request@avogadro.barnard.columbia.edu? I tried earlier this week & my mail was returned by unixf.columbia (or some such) because the node allegedly does not exist... From chemistry-request@ccl.net Thu Apr 4 17:11:18 1991 Date: Sat, 30 Mar 91 15:06 CST From: MACMILLAN@iscsvax.uni.edu Subject: MM2 and NMR To: chemistry@ccl.net Status: R We are interested in modeling small peptide (<10 Amino Acids) and relating the conformations to proton NMR couplings. Would anyone have any references to MM2 modeling and proton NMR? James G. Macmillan Department of Chemistry University of Northern Iowa MACMILLAN@ISCSVAX.UNI.EDU From chemistry-request@ccl.net Thu Apr 4 17:35:35 1991 Date: Thu, 4 Apr 91 17:12 EST From: "DOUGLAS A. SMITH" Subject: MM2 and NMR To: chemistry@ccl.net, macmillan@iscsvax.uni.edu Status: R Clark Still's package MacroModel, which includes MM2, AMBER, OPLS, and will soon include MM3 (next release, version 3.5, is due out this summer and should have MM3) will allow users to calculate many couplings in the ANALYZ mode by simply touching the hydrogens of interest. The Karplus equations in the program can be limited, however, I believe (without looking at my documentation) that you can add your own equations. References are given to the literature in the program and in the documentation. I would definitely recommend against using MM2 for modeling oligoamides. MM2 has known deficiencies in reproducing hydrogen bonding. Also, the standard MM2 package does not allow you to model your compounds in solvent. AMBER or OPLS should do better with the hydrogen bonding and MacroModel (as well as other packages) will allow solvent. I prefer MacroModel, which uses a generalized Born/solvent accessible surface area algorithm rather than explicit solvent molecules. It is orders of magnitude faster and just as accurate (see JACS 1990, 112, 6127). One other warning. Most if not all molecular mechanics programs use angle independent hydrogen bonding functions, which may be a serious problem. We have been involved in modeling hydrogen bonding using MacroModel and MM3 and are preparing a paper on the comparison of AMBER, OPLS, and MM3. We have also submitted two papers on hydrogen bonding in vacuo versus CH2Cl2 on small di- and triamides in comparison with experimental data. I would like to hear more about what you are doing and would be willing to share some of our work and experiences with you. Doug Smith Assistant Professor of Chemistry The University of Toledo Toledo, OH 43606-3390 voice 419-537-2116 fax 419-537-4033 email FAX0236@UOFT02.UTOLEDO.EDU