[Chimera-users] Dielectric ; Steepest descent

Conrad Huang conrad at cgl.ucsf.edu
Wed Sep 29 11:54:02 PDT 2010

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 
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.


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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> Chimera-users at cgl.ucsf.edu
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