Hi Francesco, I believe that correct PDB format includes atom names with the element symbol right-justified in 13-14. So if the element symbol is one character (C,N,O,H,...) it should appear in column 14. If the element is two characters (CL,CA,FE,...) it should appear in columns 13-14. The exception to this rule is if a hydrogen name has four characters, it begins at 13. This is the pattern observed in the current (remediated) PDB files from RCSB and other wwPDB sites. <http://remediation.wwpdb.org/documentation/format32/sect9.html#ATOM> <http://remediation.wwpdb.org/documentation/format32/sect9.html#HETATM> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/pdbintro.html#erro...
Best, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Nov 18, 2008, at 12:18 AM, Francesco Pietra wrote:
Elaine: In the fear that docking and MD had been carried out with C in place of Cl for the ligand, I checked all. OK, correct for Cl.
I noticed that when all atom names are left-justifies in column 13, Chimera reports the structures correctly.When all atom names are left-justified in column 14, Chimera does not report Cl correctly.
I writing pdb files, the various programs in DOCK/Amber are not well consistent (although I did not carry out a thorough search). Dock6 writes the final pose pdb for receptor+ligand by left-justifying all atom names in column 13. Amber behaves differently according to which internal program is used.
francesco