[gmx-users] atom name in pdb converted by editconf (gmx4)

[Jian Zou]

Hi,

I found that when the output format from editconf (gmx4) is PDB, atom
name like H5'1 will be changed to 1H5'. For other four-character atom
name like ABCD, editconf works properly.

example: editconf -f a.pdb -o b.pdb
============= a.pdb ==================
ATOM      1  P    DT     1      -1.848   4.613   1.141  1.00  0.00
ATOM      2  O1P  DT     1      -2.880   4.343   2.135  1.00  0.00
ATOM      3  O2P  DT     1      -0.455   4.129   1.433  1.00  0.00
ATOM      4  O5'  DT     1      -2.282   4.044  -0.246  1.00  0.00
ATOM      5  C5'  DT     1      -3.668   4.059  -0.487  1.00  0.00
ATOM      6 H5'1  DT     1      -3.929   4.396  -1.500  1.00  0.00
ATOM      7 H5'2  DT     1      -4.303   4.601   0.280  1.00  0.00
============= b.pdb ==================
ATOM      1  P    DT     1       1.100   4.615   1.808  1.00  0.00
ATOM      2  O1P  DT     1       2.094   4.346   2.840  1.00  0.00
ATOM      3  O2P  DT     1       1.393   4.130   0.416  1.00  0.00
ATOM      4  O5'  DT     1      -0.287   4.047   2.242  1.00  0.00
ATOM      5  C5'  DT     1      -0.528   4.063   3.628  1.00  0.00
ATOM      6 1H5'  DT     1      -1.541   4.400   3.889  1.00  0.00
ATOM      7 2H5'  DT     1       0.239   4.606   4.263  1.00  0.00

editconf in gmx3 works fine in the above situation.


Regards,

Jian