[Chimera-users] Problems for mol2 with H atoms added with REDUCE

[Eric Pettersen]

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 at 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
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