[gmx-developers] gromacs can't recognize residue name with four letters in some cases
dong at pampas.chem.purdue.edu
Sat Aug 5 16:35:19 CEST 2006
On Sat, 2006-08-05 at 21:08 +1000, Mark Abraham wrote:
> Dongsheng Zhang wrote:
> > Dear GMX developers,
> > In my pdb file, some residues' names have four letters. When I use
> > pdb2gmx, it works fine. The output gro file shows those residues (with
> > four letters). When I use editconf -f *gro -o *pdb, gromacs can't
> > recognize those residues with four letters. All residues' names in the
> > output pdb file have only three letters. For those residues whose name
> > have four letters, the last letter has been truncated. Please check it.
> > If it is possible, could you please solve it?
> The PDB file format is only supposed to permit 3-letter residue names -
> see http://www.rcsb.org/pdb/file_formats/pdb/pdbguide2.2/part_62.html.
> Some PDB readers and writers cheat and allow four-letter residue names,
> but I doubt the best solution is to have editconf join that trend. If
> you need your residue names to be preserved, decide your own mapping
> from four-letter names to unique three-letter names and use commands like
> sed -e 's/LYSH/LYH /' -e 's/LYSP/LYP /' old.pdb > new.pdb
> Note the space - you need to replace four characters with four
> characters lest some PDB reader depend on the column numbers being right.
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