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

Berk Hess hess at cbr.su.se
Wed Mar 10 10:02:34 CET 2010


Gromacs does allow 4 letter residue names in pdb files, but apparently
not everywhere then.

I have fixed this issue for Amber with an automatic residue name to rtp
entry translation file
in git master.
But the question is now if we may want to store the real residue names
in the topology (and thus
for all purposes), instead of the rtp entry name as we do now.
We could then add a comment line in the top file for every residue that
would give its rtp entry.
The disadvantage would be that you can no longer see the protonation
state of a residue
from its residue name.


Justin MacCallum wrote:
> Hi,
> As you may know, using the ffamber port of the Amber forcefields requires that the terminal residue codes are transformed by prepending an 'N' or a 'C' for the N- and C-Terminal residue, respectively. I.e., THR -> NTHR. The PDB routines in gromacs appear to be able to read PDB files containing these residue codes without any problems. However, they are not able to write PDBs with four-letter residue codes. Instead, the residue name is truncated to three characters, i.e, NTHR -> NTH. This can be annoying when trying to use tools such as pdb2gmx and editconf to prepare files. In particular, I am using the gromacs tools in a scripted way and the output PDB file from mdrun cannot be used as input for another simulation without hacking the PDB file to fix the termini names each time.
> Attached is a simple patch that allows for four-letter residue names in PDB files. This has not been tested extensively, but appears to work.
> ------------------------------------------------------------------------
> Cheers,
> Justin
> --
> Justin MacCallum
> Post Doctoral Fellow

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