[gmx-users] Chlorine in PDBs

az adam.zalewski at mail.com
Fri Jul 24 10:27:41 CEST 2015


Could someone enlighten me what are the "correct" (Gromacs-wise) atom 
type and PDB column numbers for a chlorine substituent in a ligand ? I 
use a MOE-written PDBs as MD input (Amber99SB), and if a chlorine is 
present, its written as CL (both letters uppercase) in the 13th and 14th 
column. Now when feeding that to acpype, the output PDB has a CL again, 
but shifted to columns 14 and 15 and with a C in the last element 
column. Seeing how this is similar to how box ions are written, I gave 
it no heed, but now PDBs saved from a completed trajectory, display the 
CL as a carbon in VMD, Chimera, or MOE. I can obviously edit that but 
I'd like to be sure if my CLs are being treated as chlorines during the MD.

Input line:    HETATM 2166 CL   PXN     0      -7.547  -4.598 6.977  
1.00  0.00          CL
Post-acpype:    ATOM     26  CL  PXN Z   1      -7.547  -4.598 6.977  
1.00  0.00           C
Post-MD:        ATOM   2147  CL  PXN B 169       2.196   0.709 5.879  


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