Hello Ahir, I think you are going to have to use Help->Report a Bug in Chimera and attach your structure file because I cannot reproduce your problem. When I open 1bw9 and minimize it in the daily build using all the defaults (except #conjugate gradient steps = 0) it works. If I then try again, deleting the B chain and allowing only atoms within 5 angstroms of the PPY residue to move, it also works. So it's something specific to your version of the structure or your version of Chimera… --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Aug 13, 2014, at 8:36 AM, Ahir Pushpanath <ahir29@gmail.com> wrote:

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.

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

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