Hi: With CHIMERA alpha version 1.5 (build 30471 linux 64bit) and protein with H atoms added with program REDUCE: Tools -> Structure editing -> Dock prep (choice: If alternate locations keep only the highest occupancy; Add charges; write mol2) whereby I was asked to confirm residue CL- charge -1 and choose charge method AM1-BCC. getting warning: current charges are unknown for 1 non-standard atom names in otherwise standard residues. Charge 0.0 assigned to unkknown atoms. The log files reports: Charge model: AMBER ff99SB Assigning partial charges to residue CL- (net charge -1) with am1-bcc method Non-standard atom names: CYS H (CYS 55.A H, CYS 134.A H, CYS 141.A H + 39 others) Total charge for #0: -106.4198 The following residues had non-integral charges: CYS 55.A -1.2719 CYS 134.A -1.2719 CYS 141.A -1.2719 CYS 156.A -1.2719 CYS 252.A -1.2719 CYS 272.A -1.2719 CYS 276.A -1.2719 CYS 285.A -1.2719 CYS 287.A -1.2719 CYS 299.A -1.2719 CYS 307.A -1.2719 CYS 323.A -1.2719 CYS 325.A -1.2719 CYS 329.A -1.2719 CYS 55.B -1.2719 CYS 134.B -1.2719 CYS 141.B -1.2719 CYS 156.B -1.2719 CYS 252.B -1.2719 CYS 272.B -1.2719 CYS 276.B -1.2719 CYS 285.B -1.2719 CYS 287.B -1.2719 CYS 299.B -1.2719 CYS 307.B -1.2719 CYS 323.B -1.2719 CYS 325.B -1.2719 CYS 329.B -1.2719 CYS 55.C -1.2719 CYS 134.C -1.2719 CYS 141.C -1.2719 CYS 156.C -1.2719 CYS 252.C -1.2719 CYS 272.C -1.2719 CYS 276.C -1.2719 CYS 285.C -1.2719 CYS 287.C -1.2719 CYS 299.C -1.2719 CYS 307.C -1.2719 CYS 323.C -1.2719 CYS 325.C -1.2719 CYS 329.C -1.2719 As an example, the mol2 file reads for CYS 55: 877 N -27.8300 7.7310 -8.8380 N.am 55 CYS -0.4157 878 CA -28.5410 7.2460 -9.9870 C.3 55 CYS -0.0351 879 CB -27.9030 5.9690 -10.5570 C.3 55 CYS -0.2413 880 SG -26.2400 6.2310 -11.2140 S.3 55 CYS -0.8844 881 C -29.8950 6.7930 -9.5500 C.2 55 CYS 0.5973 882 O -30.0670 6.3000 -8.4370 O.2 55 CYS -0.5679 883 H -27.9010 7.1340 -8.0390 H 55 CYS 0.0000 884 HA -28.5450 8.0610 -10.7260 H 55 CYS 0.0508 885 HB2 -27.8610 5.2050 -9.7670 H 55 CYS 0.1122 886 HB3 -28.5460 5.5710 -11.3560 H 55 CYS 0.1122 ***************************** In the past I encounterd a similar problem, solving it by adding atoms with CHIMERA. This time, however, the complexity of the system suggests to use REDUCE. Thanks for suggestions. francesco pietra