Hi Conrad, Thanks for your answer. Don't worry, you needn't make a disclaim though. In my opinion, it's not a question of knowing which non-default option is more suitable for use in Chimera, but rather giving the user the choice to use the options that suit him, such as letting him choose the value of the dielectric constant, instead of forcing the value of 1, which would make minimization results useless, i.e. non realistic. It's not either a question of a full-blown MM/MD interface in Chimera, but I feel that the any decent program that does energy minimization should give the user access to steepest-descent *and* conjugate-gradient (CG) methods. Why? Because the 2nd is usually used after the 1st, given that the 1st, as the manual says, is very inefficient if the goal is to find a local minimum of the potential energy. And our purpose is to find energy minima and the conformations that are associated with. To the best of my knowledge, there is no server or free academic program doing energy minimization with these options. Introduction of the choice of dielectric constant and of CG would thus make Chimera rather complete and unique in this sense leading to an increased usage by the community of biocomputational people. Given that MMTK contains CG, what would it take to include the algorithm in Chimera ? Cheers, CM On Wed, Sep 29, 2010 at 8:54 PM, Conrad Huang <conrad@cgl.ucsf.edu> wrote:
Before I provide any answers, I have a disclaimer. I only have a rudimentary familiarity with energy minimization and molecular dynamics. I understand what force fields are and some of the algorithms used for minimization and integration, but not much about the details of force field options. My experience with MMTK is mainly playing with example scripts for the excellent documentation. So, with that in mind, here are some answers to your questions.
The code in MMTKinter uses the Amber 99 forcefield with all default arguments. THere is an "es_options" parameter that let's you control electrostatic options, but I'll be the first one to admit that I do not know which non-default option is more suitable for use in Chimera. The MMTK documentation ( http://dirac.cnrs-orleans.fr/Manuals/MMTK_reference/MMTK.ForceFields.Amber.A...) does not explicitly mention dielectric value or functional form for any of the options. The code that creates the MMTK forcefield instance is in the MMTKinter_makeUniverse method. (The MMTKinter class is actually designed so that programmers can pass force field parameters through to MMTK, but Chimera does not use this capability.)
As for why only SteepestDescentMinimizer was used, it was mainly for simplicity. The minimization options that Chimera provides is not very extensive. Our intent is to provide a tool for simple clean up of small (regions of) systems. That's why we chose to use default MMTK parameters, infinite (non-periodic) universe, steepest descent minimizer, etc. The scope of providing a full-blown MM/MD interface in Chimera is too large for us to undertake. There are just too many degrees of freedom and we currently do not have enough resources to do a proper job of it.
If you are familiar with programming MMTK, there is another way of using MMTK with Chimera. http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts/MMTK describes an approach where you can program mostly in MMTK, but display results in Chimera. Obviously, this is mainly for programmers, but it does let you get to the full power of MMTK along with visualization from Chimera.
Conrad
On 9/29/2010 8:55 AM, r charbel maroun wrote:
Hi everybody,
The value of the dielectric constant used by Chimera is 1, corresponding to calculations in vacuo. Is there not an easy way to change this value to, say 78 or to include a sigmoid function or the Generalized Born approach so as to mime the presence of the solvent ? I looked for it but couldn't find it : where in the {chimera_install_location}/share/MMMD/MMTKinter.py file can the value of the dielectric be changed ? Otherwise, how to mime implicitly the solvent ?
Also, it seems that only the Steepest descent, and not the Conjugate gradients method, for energy minimization has been implemented in Chimera. Why is this so?
It'd be so nice to have these two functionalities added as I don't know of any free academic program allowing us to do energy minimization with these options without having to parametrize every new ligand (Charmm, Namd), a painful task.
Cheers,
Charbel
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-- R. Charbel MAROUN, PhD, HDR Neurobiologie et Pharmacologie Moléculaire Centre de Psychiatrie et de Neurosciences Broca-Sainte Anne (INSERM U894) 2ter rue d'Alésia 75014 Paris FRANCE Tél. +33 1 40 78 92 77 Fax +33 1 45 80 72 93 e-mail rmaroun@gmail.com charbel.maroun@inserm.fr