AMBER: universal recognition of chemicals

From: Ioana Cozmuta <>
Date: Mon, 26 Apr 2004 15:15:55 -0700 (PDT)

Hi amber users,

Is there a way to make amber recognize and build automatically a topology
for any given chemical? What would be the limitations?

To my knowledge amber recognizes residues and will not build a topology
file if the structure does not match one that exists in its library.
Is there a way to shortcut the "residue recognition" and use the atom
types, bond, angles and torsions defined by default in the force field?

Thank you,

Ioana Cozmuta, PhD
Research Scientist
Eloret Corporation
Mail Stop 230-3
NASA AMES Research Center
Moffet Field, CA 94035-1000
Phone: (650) 604-0993

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Received on Mon Apr 26 2004 - 23:53:00 PDT
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