[gmx-users] non-standard atom names
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.
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