[gmx-users] converting all-atom pdb to cg.pdb

[Francesco Pietra]

Does the atom2cg_v2.1.awk require the indication of the subunit (A, B,
C, etc) in the pdb file of a multimeric protein?

From

ATOM      1  N   LEU     1     153.242  64.673  95.851  0.00  0.00           N
ATOM      2  CA  LEU     1     154.534  64.963  95.169  0.00  0.00           C
ATOM      3  CB  LEU     1     155.257  66.191  95.767  0.00  0.00           C
ATOM      4  CG  LEU     1     156.589  66.550  95.065  0.00  0.00           C
ATOM      5  CD1 LEU     1     156.406  66.834  93.574  0.00  0.00           C
ATOM      6  CD2 LEU     1     157.222  67.770  95.727  0.00  0.00           C
ATOM      7  C   LEU     1     155.425  63.717  95.081  0.00  0.00           C
ATOM      8  O   LEU     1     155.371  63.026  94.063  0.00  0.00           O
ATOM      9  N   SER     2     156.233  63.409  96.105  0.00  0.00           N

I get

ATOM      2  BN0 LEU  154.534      64.963  95.169   0.000  0.00  0.00
ATOM      4  SC1 LEU  156.589      66.550  95.065   0.000  0.00  0.00
ATOM     10  BN0 SER  157.124      62.235  96.094   0.000  0.00  0.00

i.e., weird residue numbers.

In another case (coming from AMBER, where the subunit indication is
omitted) with the subunit indicated, the residue numbers in the cg
file are correct. I don't see any other difference between the two
starting files. Or should I look for a different cause.

thanks

francesco pietra
.......