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