[Chimera-users] Write Amber/GAFF atom types

[Francesco Pietra]

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