ADL: Receptor file in 2016 Nature Protocols Paper

Edmund R Marinelli edmundmarinelli at gmail.com
Sat Sep 12 18:20:36 PDT 2020


The paper Computational protein-ligand docking and virtual drug screening
with the AutoDock suite , Nat Protoc. 2016 May ; 11(5): 905–919.
doi:10.1038/nprot.2016.051 is a very nice paper.  In the supplementary
material there is a receptor file  1iep_receptorH.pdb  .  As we have been
cautioned to inspect the input files, I did so.  Here are the first few
lines:

REMARK   4 XXXX COMPLIES WITH FORMAT V. 2.0
ATOM   3429  HB2 SER A 438      13.612  67.338  33.314  1.00  0.00       H  
ATOM        1  N     MET A 225      19.353  41.547  -3.887  1.00 72.26      
N  
ATOM        2  HN1 MET A 225      19.594  42.398  -3.380  1.00  0.00       
H  
ATOM        3  HN2 MET A 225      18.908  40.869  -3.268  1.00  0.00       
H

Why is Atom 3429 for SER A 438 listed as the first atom? I did notice that
atom 3429 entry is NOT listed elsewhere in the file, so there is no
duplication.  Does the order of appearance of the coordinates matter or
could conceivable all coordinates be given in a random order so long as the
data in each line are correct?  Finally, is there a detailed explanation of
all atom types and each of the fields for pdbqt files available.  



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