On Wed, Feb 28, 2024, Daniel Hall via AMBER wrote:
>
>So far residue numbers :1-54 correspond to the DNA sequence and :55-83
>correspond to the protein. I would like the protein numbering to be
>:684-712.
Amber internally starts numbering residues at 1 and incrementing with each
new residue.
If you want the "original" numbering scheme from some PDB file, use the
addPDB action in parmed. This is store the residue numbers from (say) an
input pdb file in the prmtop file. You can then write out PDB files using
those numbers, or ask some programs (like cpptraj) to use such
non-sequential numbering in various type of analyses.
...good luck....dac
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Received on Fri Mar 01 2024 - 18:00:03 PST
