Hi,
Try adding 'topresnum' to your 'trajout' command (e.g. 'trajout
MyStruc_Reordered.pdb topresnum') to use topology residue numbering
instead of the PDB residue numbering (which is intentionally not
reordered).
-Dan
On Fri, May 26, 2023 at 12:31 PM Matthew Guberman-Pfeffer via AMBER
<amber.ambermd.org> wrote:
>
> Dear AMBER community,
>
> I noticed that the fixatomorder keyword in CPPTRAJ doesn’t renumber the residue IDs. For example, the below CPPTRAJ input fixes the atom ordering so residue 775 in my structure comes immediately after residue 258 to which it is bonded. However, the residue ID remains 775.
>
> parm MyStruc.prmtop
> trajin min.rst7
> fixatomorder parmout MyStruc_Reordered.prmtop
> trajout MyStruc_Reordered.pdb
> run
> quit
>
> If I pass the re-ordered prmtop and rst7 to ambpdb, the residue IDs get corrected.
>
> It would be nice if CPPTRAJ could update the residue IDs after correcting the atom ordering.
>
> Best,
> Matthew
>
>
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Received on Tue May 30 2023 - 11:30:02 PDT
