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 ---------- Forwarded message ---------- From: Francesco Pietra <chiendarret@gmail.com> Date: Mon, Nov 17, 2008 at 10:58 PM Subject: Re: [Chimera-users] carbon-chlorine bond To: Elaine Meng <meng@cgl.ucsf.edu> Hi Eleaine: Thanks. Moving Cl to columns 13 and 14, the C-Cl bond is displayed for me too.Living with the new and the old. It will be so for quite a long time. Regards francesco On Mon, Nov 17, 2008 at 7:46 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
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
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
participants (2)
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Elaine Meng -
Francesco Pietra