Force on multiple atoms in ABF

From: Mert Gür (gurmert_at_gmail.com)
Date: Sun May 24 2009 - 11:26:16 CDT

Dear all,
Is it possible to apply the Adaptive Biasing Force on multiple atoms as it
can be done in Steered Molecular Dynamics? (I can select multiple SMD atoms
that are going to be pulled)

If yes how?

As much as I know I have only 2 selection options in ABF calculations
:distance or distance-com. Both of which are applied only at one location.

This problem is keeping me busy since the binding binding site in
protein-ligand binding can have more then one residue. So how can I define
the reaction coordinate by just selecting one residue ? In SMD I solved this
problem by selecting all the Calfa atoms of the ligand's residues as SMD
atoms.

Thanks in advance!

Mert

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