From chemistry-request _-at-_)server.ccl.net Mon Jul 22 21:08:11 2002 Received: from web12806.mail.yahoo.com ([216.136.174.41]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g6N18Br00897 for ; Mon, 22 Jul 2002 21:08:11 -0400 Message-ID: <20020723010810.83438.qmail%!at!%web12806.mail.yahoo.com> Received: from [61.9.73.249] by web12806.mail.yahoo.com via HTTP; Mon, 22 Jul 2002 18:08:10 PDT Date: Mon, 22 Jul 2002 18:08:10 -0700 (PDT) From: amor san juan Subject: Summary: Energy minimization To: chemistry- at -ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii My question posted: -----Original Message----- From: Computational Chemistry List [mailto:chemistry-request(+ at +)ccl.net]On Behalf Of amor san juan Sent: Sunday, July 21, 2002 4:09 AM To: chemistry;at;ccl.net Subject: CCL:Energy minimization Hello, What are the good minimization algorithms for up to 150max atoms? My goal to this most stable energy conformer is to use it in docking experiment. I tried MM3 & MMFF94 algorithms built in a specific commercial software. Results showed that none of the minimized structures in synchronized with ben.pdbq distributed file in AutoDock. Im calling the attention of Autodock users, have you encountered this problem? Kindly give me a hint. I would also appreciate if someone would be considerate to give me good reading materials about energy minimization. Thanks, Amor ************************************ Hi amor san juan, I think I have suggestion for your energy minimization problem. With my experience with MM3, more than 90-100 atoms will give you a realiable structures but you really need to be very careful with the energies. I don't know which version of the MM programs you have, but in the original Allinger's program it is an option called "Stochastic Search" where you ramdomly move the atoms in the space and then minimize the energy. As a result, you can do conformational search all around the energy surphase avoiding the problem of the local minima. I have been using this option for molecules with 80-100 atoms at works very well. Once again let me tell you that the energy values of this programs are very questionable when it is applied to more than 100 atoms. If you are interested in the energies I rather will use something like semi-empirical calculation (AM1, PM3, etc). I hope this is will help you. Jorge Gonzalez -- Jorge Gonzalez Outeirino Complex Carbohydrate Research Center University of Georgia 220 Riverbend Road 30602 Athens Georgia USA e-mail: uccajgo7 /at\netscape.net Amor, EM will never synchronize with a crystal structure! Its just a theoretical adjustment of bonds and angles, and is used for refining models, and region with High B-factor. Quick summary of EM: Steepest descent; refining, requires youto be in or close to a local minimum. Conjugate Gradient: "rough" structure alternations, to rock a model hopefully in a better local minimum. Extensive reading : Leach A. (2001). Molecular Modelling: Principles and applications. 2nd Ed. Pearson Education Limited. Good luck! Sergio Good reading material, well Leach "Molecular Modelling" and Jenssen "Introduction to Computational Chemistry" are quite good. Mr James J Robinson MRSC Molecular Modeller Pharmacy and Pharmacology Dept. University of Bath Claverton Down Bath, Somerset, UK. BA2 7AY. J.J.Robinson %-% at %-% bath.ac.uk http://www.bath.ac.uk tel +44(0) 1225 384723 MM3 and MMFF94 are not minimization algorithms but force fields, i.e. they yield the energy of a given system. Your commercial program used a minimization algorithm (e.g. steepest descent, conjugate gradients, BFGS, EF) to minimize the energy (force field function) with respect to the coordinates. Thus, an answer to your question is twofold: 1, energy function You can use a force field (cheap); the rather small size of your system also would allow you to choose semiempirical MO methods, in order to take care of polarization effects. 2, minimization Because your system is that small, you should use a quasi-Newton method, like BFGS or EigenvectorFollwing. One could also think of molecular dynamics or Monte Carlo (simulated annealing) - but this depends strongly on the resources you have and the your intentions. Regards, Anselm __________________________________________________ Do You Yahoo!? Yahoo! Health - Feel better, live better http://health.yahoo.com