Summary: Energy minimization

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
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