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.
Cheers,
Erik
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