AMBER Archive (2004)

Subject: AMBER: Atomic Charge in Residue

Date: Thu Mar 11 2004 - 13:29:21 CST

('binary' encoding is not supported, stored as-is) Dear Amber Community,

When defining the charges for a new residue, how does one account for an
electron withdrawing group that is not part of the residue? Or is that
taken care of automatically when building the molecule from the residues?

Also, given that I have a pdb file that I want to make a residue from.
When I put that pdb file through antechamber, do I take off the hydrogens
for the places that will later become bonds or do I leave them on there?
This ties back in with my first question of how the different neighboring
atom will affect the charge of the atom it is bonded to.



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