I have found the problems in converting to pdbqr. Please skip this message to Chimera. francesco ---------- Forwarded message ---------- From: Francesco Pietra <chiendarret@gmail.com> Date: Sat, May 16, 2009 at 9:03 PM Subject: Verify integer/non-integer charges in mol2 To: chimera <chimera-users@cgl.ucsf.edu> Hi: I assigned Amber ff99SB charges to a proven pdb file of standard amino acids and capping groups (ACE NME), saving as mol2. Conversion to a pdbqt file with ATD (autodock tool) resulted in non-integer charge (-5...). Unless something occurred that escaped my attention, the protein has -5.00000 charge. My question: how to verify a posteriory the total charge in the Chimera-written mol2 file, in order to trace back were I have blurred things? I don't see the total in the mol2 file. Thanks francesco pietra