Andrew,
> Can you please say why I can't just measure bond lengths and
> dihedral angles parameters in the PDB structure which I want to use
> for MD. This will just fix the already existing parameters and that
> is what I need. Why I should gather or calculate prceise bond length
> and angle parameters if the PDB data already measured by X-ray
> analysis? The bond energies and VdW radii I can get from the papers,
> yes.
You can get equilibrium values for bonds & angles from small
crystallographic structures, Yes. Dihedrals do not have equilibrium
values. Force constants for bonds and angles and dihedral parameters
can be obtained from fitting to a QM profile.
regards, Francois
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Received on Tue Nov 24 2009 - 06:30:02 PST
