[Chimera-users] Minimization and dielectric choices

r charbel maroun rmaroun at gmail.com
Mon Oct 4 07:03:46 PDT 2010

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 ?



On Wed, Sep 29, 2010 at 8:54 PM, Conrad Huang <conrad at 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.AmberForceField-module.html)
> 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
>> _______________________________________________
>> Chimera-users mailing list
>> Chimera-users at cgl.ucsf.edu
>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

R. Charbel MAROUN, PhD, HDR
Neurobiologie et Pharmacologie
Centre de Psychiatrie et de
Neurosciences Broca-Sainte Anne
2ter rue d'Alésia
75014 Paris
Tél. +33 1 40 78 92 77
Fax +33 1 45 80 72 93
e-mail rmaroun at gmail.com
          charbel.maroun at inserm.fr
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