[AMBER] please, units of LENNARD_JONES_ACOEF in prmptop?

From: Jose Borreguero <borreguero.gmail.com>
Date: Tue, 13 Jul 2010 19:45:07 -0400

Dear amber users,

Are the units of LENNARD_JONES_ACOEF in prmptop (Kcal/mol * A^12) and the
units of LENNARD_JONES_BCOEF (Kcal/mol * A^6) ?

I wonder because the typical Lys - Gly salt bridge has electrostatics ~
70Kcal/mol, while only VdW ~ 2 Kcal/mol. The disparity of the energies
surprised me.
Similarly, the range of electrostatic energies between pair of residues has
a much bigger variation than the range of VdW energies. For rubredoxin in
the native state, the elec-range=[-99,80]Kcal/mol and the
VdW-range=[-6,2]Kcal/mol. Is this expected?

-Jose Borreguero
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Received on Tue Jul 13 2010 - 17:00:03 PDT
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