[gmx-users] non-standard atom names

Stefano Meliga smeliga at gmail.com
Tue Oct 20 19:03:28 CEST 2009


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.



More information about the gromacs.org_gmx-users mailing list