[gmx-users] non-standard atom names

[Stefano Meliga]

Hello,

I noticed that the command editconf -i structure.gro -o structure.pdb 
produce a pdb file in which some atom names are not standard.

In particular the delta carbon on ILE:

"CD  ILE" should be "CD1 ILE";

and the oxigens of the C-terminus

"O1" should be "O "
"O2" should be "OXT".

This is particularly annoying when GROMACS' output pdb is then used in 
input of other software, e.g. FIRST.

You might want to fix this.

Sincerely,

Stefano