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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri May 26 2023 - 09:30:02 PDT
