AMBER Archive (2009)

Subject: [AMBER] Dummy atoms and MM-PBSA

From: Alireza Shaneh (
Date: Fri Sep 04 2009 - 11:48:16 CDT

Hello All,

I want to calculate the binding free energy of my complex, consisting of a MG2+
ion. Rather than spheric ion, I've defined the geometrical representation of
the ion in which the octahedral nodes are dummy atoms with zero radii (cationic
dummy set). Using MM-PBSA, I tried to calculate the binding free energy, but I
got the following message from the mm-pbsa script:

=>> Calculating energy / entropy contributions
    Calc contrib for ./output/output_com.crd.1
        Calc MM/GB/SAS
        Generate PDB
        Center PDB
        Calc PBSA
        Generate PQR
        No radius found for LP 5797 in residue MD6 314

LP is the lone pair atom with no radius. I was hoping if anybody in the
community has an experience knowing this problem and offers a suggestion.



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