[gmx-users] charge atoms

[Justin A. Lemkul]

cesteban at unsl.edu.ar wrote:
> Hi All
> I am trying to analyze the dynamics of polymer of GlcN residues using
> ffG53a6 force field.
> I made a new building block in .rtp file, but I haven´t the charge of some
> atoms.
> Which is the best procedure to obtein new charges?

For some general information, refer here:

http://wiki.gromacs.org/index.php/Parameterization

With empirical force fields like Gromos96, a reasonable starting point is to 
identify similar functional groups from other molecules (those that have been 
parameterized already), and apply them to your molecule.

The extent of the validation is up to you, but rigorous verification of the 
parameters typically involves some sort of free energy calculations.  I have 
seen several instances in the literature where investigators have molecules that 
are very similar to existing compounds in the force field, and they have skipped 
the validation steps.  Whether or not that is acceptable is up to you...

-Justin

> Someone has experience about this?
> Any help would be appreciated
> Carmen
> 
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-- 
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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