[gmx-users] A possible bug in pdb2gmx -ter (with nh2 and cooh) ?

[Markus O Kaukonen]

Dear All,

I tried to protonate the following methionine structure from
HicUp server (http://xray.bmc.uu.se/hicup)

REMARK MET Extracted from PDB file pdb1qq9.ent
REMARK MET Formula C5 H11 N1 O2 S1
REMARK MET Nr of non-hydrogen atoms   9
REMARK MET Eigen-values inertia X/Y/Z       39.2       6.8       2.5
REMARK MET Residue type MET
REMARK MET Residue name   2304
REMARK MET Original residue name (for O) $903
REMARK MET  RESOLUTION. 1.53 ANGSTROMS.
REMARK MET Also in 1.5-2.0A  :  1C21 1INN 1F4L
REMARK MET Resolution (A)    :  1.80 1.80 1.85
REMARK MET Also in 2.0-2.5A  :  1J6W 1D6S 1J6X
REMARK MET Resolution (A)    :  2.10 2.30 2.38
REMARK MET
HETATM    1  N   MET  2304      -0.292  -1.448   0.681  1.00 20.00
HETATM    2  CA  MET  2304      -0.610  -0.004   0.493  1.00 20.00
HETATM    3  C   MET  2304      -2.004   0.039  -0.050  1.00 20.00
HETATM    4  O   MET  2304      -2.588   1.087   0.023  1.00 20.00
HETATM    5  CB  MET  2304       0.338   0.646  -0.527  1.00 20.00
HETATM    6  CG  MET  2304       1.625   1.277   0.040  1.00 20.00
HETATM    7  SD  MET  2304       2.787   0.126   0.721  1.00 20.00
HETATM    8  CE  MET  2304       3.311  -0.782  -0.847  1.00 20.00
HETATM    9  OXT MET  2304      -2.567  -0.940  -0.533  1.00 20.00
REMARK MET ENDHET


with command (pdb2gmx VERSION 3.1.3)
pdb2gmx -ter -f met.pdb -o meth.pdb

with  1: Gromacs Forcefield with all hydrogens (proteins only)

and nh2 cooh terminus
 2: NH2
 2: COOH

Problem is that pdb2gmx puts oxygen atoms in cooh the output
almost on top of each other.

This problem did not arise with the same pdb file when selecting
nh3 coo terminus.

Best wishes, Markus

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