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

Eric Pettersen pett at cgl.ucsf.edu
Wed Aug 13 10:47:16 PDT 2014

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 Pettersen
                        UCSF Computer Graphics Lab

On Aug 13, 2014, at 8:36 AM, Ahir Pushpanath <ahir29 at 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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> Chimera-users at cgl.ucsf.edu
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