I am having my students model dipeptides where one residue is a phosphorylated serine or threonine. Molecular dynamics with the dibasic phosphate works fine. However, the student NMR data for their dipeptides is acquired at low pH, so I would like them to be able to model the monobasic form. Unfortunately, all my attempts at creating a monobasic form have resulted in the molecule "blowing up" in MD, first by crazily shaking the phosphate as if it wants to dislodge the proton, and then the entire molecule until it fragments. I have tried building these from scratch by various methods (e.g. those listed in http://plato.cgl.ucsf.edu/pipermail/chimera-users/2012-January/007068.html ) as well as using SwissSidechain and mutating residues. I have tried exporting as a .pdb, opening in PyMOL to make sure everything looks OK, resaving as .pdb and importing PyMOL's version. I have also used a protein from PDB that had a TPO residue assigned, and snipped it down to a dipeptide.For both this manner of construction, and for building the dipeptide from scratch with SwissSidechain, Chimera interprets SwissSidechain's TPO (pThr monobasic) and SEP (pSer monobasic) as their dibasic forms (TPO2 and SEP2 respectively). PyMOL interprets these structures with the correct level of protonation, however. Is there a known issue with Chimera and treatment of [-OPO3H]-1 groups, or have I managed to make the same error across multiple build methods? -- Dr. Geoffrey Sametz QDH 104 Department of Chemistry and Biochemistry University of Delaware sametz@udel.edu (302) 831-3621