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.
Thanks,
Alireza
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Received on Mon Sep 14 2009 - 11:51:15 PDT
