On Thu, Sep 15, 2016, Christian Schafmeister wrote:
>
>
> I’m loading a PDB file for a large DNA/protein complex.
> The DNA residues look like what I’ve attached below.
> It contains atom names like C1*, C2*, C3*, C4* for the ribose carbons.
> The nucleic acids in files like amber/dat/leap/lib/nucleic10.lib label
> their ribose carbons as C1’, C2’, C3’, C4’
>
> (1) Are these ribose atoms equivalent? Was there a change in how ribose
> atoms are named?
The PDB changed its atom names for nucleic acids some time ago (in
going from version2 to version3). Amber's DNA/RNA leaprc file
contain addPdbAtomMap commands that allow reading in of pdb files
with the old atoms, converting them to the new ones. See, e.g.
$AMBERHOME/dat/leap/cmd/leaprc.DNA.*
Amber's output pdb files will then contain the correct (IUPAC/PDB) atom and
residue names. Your programs should do the same: we don't want to propagate
outdated nomenclature.
....dac
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Received on Fri Sep 16 2016 - 02:30:05 PDT
