[EMAIL PROTECTED] 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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--
========================================
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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