[gmx-users] Gromacs tools mistakenly change the name of atoms in coordinate files

Erik Lindahl lindahl at cbr.su.se
Wed Jun 13 19:14:55 CEST 2007

Hi Robert,

On Jun 13, 2007, at 6:48 PM, Robert Johnson wrote:

> These are all fine points. However, the question I'm asking is why do
> Gromacs tools change atoms named OXT in PDB files to O2? Of course
> there are always workarounds i.e. just simply change the atom name in
> the coordinate file. However, I was wondering if anyone knew why this
> happened. I suppose I will submit a bugzilla.

Don't bother for now :-)

This is because of a few old brain-dead choices in pdb2gmx, but we're  
working on replacing that completely, and then we'll be name-agnostic.

The only thing I can say in our defense is that most other programs  
also push their own naming convention when generation hydrogens, etc.  
For instance, charmm will rename the resname of the first/last few  
atoms in each chain to NTER/CTER.



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