[gmx-developers] Off-by-one error in pbd2gmx

[Lieven Buts]

  While creating a GRO file and topology from a PDB file
with "pdb2gmx -f hr.pdb -o hr.gro -p hr.top -dummy hydrogens"
and the GROMOS96 43a1 force field I got the following 
warnings:

WARNING: atom CD is missing in residue LEU 26 in the pdb file
WARNING: atom CE is missing in residue LEU 26 in the pdb file
WARNING: atom NZ is missing in residue LEU 26 in the pdb file
WARNING: atom CE is missing in residue TYR 42 in the pdb file
WARNING: atom NZ is missing in residue TYR 42 in the pdb file
WARNING: atom OD1 is missing in residue PHE 50 in the pdb file
WARNING: atom OD2 is missing in residue PHE 50 in the pdb file
WARNING: atom CG is missing in residue ASN 99 in the pdb file
WARNING: atom OD1 is missing in residue ASN 99 in the pdb file
WARNING: atom ND2 is missing in residue ASN 99 in the pdb file


  In the PDB file lysine 25 is indeed missing its CD, CE and NZ
atoms, but the program is reporting leucine 26, the next residue
in the chain. Likewise for the other residues.

  I figure there is some kind of off-by-one error in the
functions "missing_atoms" or "name2type" in src/kernel/pdb2top.c.


-- 
Lieven Buts
Vrije Universiteit Brussel