[gmx-developers] 4-letter residue codes in PDB files

Justin MacCallum justin.maccallum at me.com
Thu Mar 11 00:25:31 CET 2010

> Unless PDB with 4-letter residue names is required for some external 
> program, choosing to write .gro files would circumvent the problem. This 
> approach should be preferred where possible, rather than add to the 
> chaos of standards-incompatible pseudo-PDB-format there is out there.
> Mark

This is indeed the case. I'm working with external programs that require PDB files. As it stands, if I take a pdb file and run it through gromacs and my external utility, I then have to edit the file before gromacs will accept it again. Ideally gromacs should be willing to eat its own output.


Justin MacCallum
Post Doctoral Fellow
Department of Pharmaceutical Chemistry
University of California San Francisco

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