From jkl@ccl.net Fri Aug 16 11:15:55 1991 To: chemistry@ccl.net Subject: Modeling software from UofToledo Date: Fri, 16 Aug 91 11:15:51 EDT From: jkl@ccl.net Status: R Programs are now available from Professor Douglas A. Smith at the University of Toledo: FITIT version 3.0 is a question and answer driven file format conversion program. It will read output files from MacroModel (formatted, unformatted, and DUMPCT), MM2, MM3, MOPAC and AMPAC and convert them to input files for MacroModel, MM2, MM3, MOPAC, AMPAC, XDRAW and ARKMOD. Other interfaces, such as to Gaussian 88/9x are under development. XDRAW version 1.1 is an X11 compatible version of the popular DRAW program, written by Maj. D. Storch of the USAF. XDRAW runs on any UNIX or VMS machine, and can be displayed across a network to any X-windowing environment. BOLTZMAN version 1.0 is designed to calculate ratios of components and DDG values of a collection of molecules. To get more information on how to obtain this software, retrieve the file toledo.note from our archives. Send one line message: send toledo.note from chemistry to oscpost@ccl.net or OSCPOST@OHSTPY.BITNET, and the file toledo.note will be automatically forwarded to you via e-mail. Jan Labanowski jkl@ccl.net From chemistry-request@ccl.net Fri Aug 16 15:02:59 1991 Date: Fri, 16 Aug 91 14:51:38 EDT From: Karthik Iyer To: chemistry@ccl.net Subject: Shell Model Status: R Dear Netters, I am using the Shell model, wherein each atom is treated as consisting of a shell, representing the electrons, and a core representing the nucleus, for simulating certain crystals. Do any of you have experience with this model. If so, I would like to get in touch with you and clarify some of the doubts I have at present. Thank you in advance, Karthik Iyer From chemistry-request@ccl.net Fri Aug 16 16:36:24 1991 From: Dongchul Lim Subject: conformational study of protein with CHEM-X To: CHEMISTRY@ccl.net Date: Fri, 16 Aug 91 16:24:39 EDT Status: R One of my friends asked me this question but I thought it is more appropriate to post it on this news group. Here's what he asked: Byoung Choi writes: > > Recently I found a paper talking about conformation of nodularin which is one of > my biosynthesis project compounds and is a cyclic pentapeptide (MW 824). > They did calculation using this program in vacuo and suggested a conformer. > However, this conformer is quite contradictory to our experimental data such as > NOE and other NMR expts. So I wonder first how much this program is reliable for > this kind of compound and what is this program mainly for? Is there any better > program available for this kind of compound? Also, one of the reason why these > data are quite contradictory each other might be because calculation is done in > vacuo. So they must neglect solvent effect. We did NMR measurement in MeOH. > Do you think it is possible and easy to calculate conformation in water or MeOH > solution? Also do you think is there any better program available to do calculation studies? > Do you think we can do calculation with an assistance of our experimental data? > -Dongchul Lim- lim@rani.chem.yale.edu From chemistry-request@ccl.net Fri Aug 16 16:59:29 1991 Date: Fri, 16 Aug 1991 16:49 EDT From: "DOUGLAS A. SMITH" Subject: Re: conformational study of protein with CHEM-X To: lim@rani.chem.yale.edu Status: R There are probably many sources of error in the calculation, but your friend has mentioned the two I would be most concerned with - problems with the CHEM-X force field and lack of solvent. Many programs could do what he wants and probably better. MacroModel from Clark Still at Columbia University would be one choice. It allows for full searching of conformational space by several different methods, has three de facto standard force fields (MM2, AMBER, and OPLS - MM3 is due in the next version around Jan. '92), and can handle solvation via explicit solvent molecules or via the GB/SA continuum method (see Still's papers: JACS 1990, 112, 6127, and JACS 1991, 113, 1454). Of the commercial packages, I would suggest BIOGRAF, from Molecular Simulations (Bill Goddard's company). It conatins the AMBER, MM2, and CHARMM force fields as well as Goddard's DREIDING general purpose force field (J. Phys. Chem. 1990, 94, 8897), handles solvation through explicit treatment of interactions, and most importantly (in my mind) calculates charges on atoms dynamically, that is, as a function of the conformation of the molecule and the polarization effects of neighboring atoms (Goddard, J. Phys. Chem. 1991, 95, 1008). 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