[Chimera-users] carbon-chlorine bond

Elaine Meng meng at cgl.ucsf.edu
Mon Nov 17 10:46:46 PST 2008

Hi Francesco,
I was going to write back that your PDB file from AMBER has the atom  
names mis-aligned so that Chimera probably thinks the chloride is a  
carbon, which would have a shorter automatic bond cutoff.  However,  
when I put those 4 lines from your message below in a file and open it  
in Chimera, the elements are correctly identified and there is already  
a C-Cl bond; only the H is unconnected.  Perhaps the characters on the  
far right were sufficient to identify element Cl.  The H is far away  
and must be bonded to something else in the complete structure.

On Nov 17, 2008, at 10:19 AM, Francesco Pietra wrote:
> Hi Elaine:
> Yes, it is a pdb file written with program ptraj (Amber) for the
> minimum energy. The chlorine atom is defined as (partial block):
> ATOM  14544 H1   AA1   341      76.488  57.341   
> 49.169                      hn
> ATOM  14545 C3   AA1   341      75.036  56.270   
> 51.132                      ca
> ATOM  14546 Cl   AA1   341      73.973  56.486   
> 49.780                      cl
> ATOM  14547 N1   AA1   341      74.619  55.535   
> 52.192                      nb
> and there are no CONECT. As you said above, prmtop/mdcrd with movie do
> show a line connecting C-Cl, but I don't know if there is another way
> to extract the minimum-energy structure than that pdb file.
> Why are all other bonds shown correctly by Chimera in the above
> situation? Why just C-Cl not?
> francesco

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