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. Elaine 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