[gmx-users] order of atoms in pdb-file

[Mr.Sridhar]

Dear gromacs users,

I faced this problem while running g_chi.

I wanted to calculate the the number of violations of ramachandran angles
of the structures in trajectory file.
The program outputs residue wise files of violations, that was fine. but
there were error messages saying

"No chi1 & chi2 angle for ALA356 "

and so on for almost all residues.

When I observed one of the pdb file of one of the snapshots(I worte it
with trjconv), I found that the order of atoms (backbone and sidechain
atoms) in residues does not match the standard pdb format. For example,

#############order in gromacs pdb file################################
ATOM   4754  N   VAL   469      52.310  49.270  35.790  1.00  0.00
ATOM   4755  H   VAL   469      51.440  49.270  35.300  1.00  0.00
ATOM   4756  CA  VAL   469      53.460  48.600  35.170  1.00  0.00
ATOM   4757  CB  VAL   469      53.170  47.120  34.910  1.00  0.00
ATOM   4758  CG1 VAL   469      54.410  46.380  34.390  1.00  0.00
ATOM   4759  CG2 VAL   469      52.690  46.340  36.140  1.00  0.00
ATOM   4760  C   VAL   469      53.740  49.280  33.840  1.00  0.00
ATOM   4761  O   VAL   469      52.960  49.690  32.980  1.00  0.00

###############order in a standard pdb file##############################
ATOM    219  N   VAL A  60      19.146  69.476  49.828  1.00 43.93
ATOM    220  CA  VAL A  60      18.468  69.172  51.091  1.00 39.04
ATOM    221  C   VAL A  60      17.398  68.085  51.001  1.00 40.95
ATOM    222  O   VAL A  60      17.209  67.353  51.969  1.00 36.94
ATOM    223  CB  VAL A  60      17.888  70.420  51.791  1.00 39.98
ATOM    224  CG1 VAL A  60      18.437  71.732  51.199  1.00 38.84
ATOM    225  CG2 VAL A  60      16.378  70.406  51.791  1.00 39.59


Is this the reason for error message in g_chi ?

When I checked the starting pdb file I used for running dynamics it
contained the same order as that given by gromacs (above).

Does this affect the analysis of other properties or the dynamics run
itself ?

Waiting for your suggessions.


sridhar.