[Chimera-users] Error with partial charge calculation during minimisation

Ahir Pushpanath ahir29 at gmail.com
Wed Aug 13 08:36:54 PDT 2014

Hey there, whenever I try to do a minimisation of a ligand in presence of
protein, with a few residues selected as flexible , rest held as rigid, I
get past the adding hydrogen box, but it always has a error saying it cant
calculate partial charge for the first N-terminal residue, N atom , for
example. If I try and delete that residue, it just moves up and says it
cant do it for the second one. The PDB file seems fine, and I have opened
in Discovery studio and seen it has partial charges assigned fine. Can you
enlighten me on what maybe going wrong? I am using the latest build of

PDB is 1BW9 chain A (only one conformation chosen in multiple conformation
residue positions).
The ligand is the PPY inside.
the flexible residues are all those 5A away apart from NAD.

Dr. Ahir Pushpanath* PhD.*
Senior Biologist,
Johnson Matthey.
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