Hi Francesco,
Amber/Chimera expects the name of the hydrogen bonded to the backbone nitrogen in a negatively-charged cysteine to be HN (your structure has H).  I have amended the code to allow H as well, so Chimera will handle your structure "correctly" in the next daily build.
I put quotes around correctly because are you really expecting all those cysteines to be negatively charged (i.e. not involved in a disulphide bond and no hydrogen on the sulfur)?  Perhaps the CONECT records for the disulphide bonds weren't in the Reduce-generated PDB file?  If that's the case you can rectify the problem by selecting all the cysteine sulfurs ("sel :cys@sg") and then running the Build Structure tool (its "Add/Delete Bonds" tab in your current build; "Adjust Bonds" tab in a newer build) to "Add reasonable bonds between selected atoms".

--Eric

                        Eric Pettersen
                        UCSF Computer Graphics Lab
                        http://www.cgl.ucsf.edu

On Jun 10, 2010, at 11:55 AM, Francesco Pietra wrote:

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
_______________________________________________
Chimera-users mailing list
Chimera-users@cgl.ucsf.edu
http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users