Dear Amber MD users,
I am having trouble renumbering residues in the topology to match that of those assigned in UniProt. Currently the residue numbers when viewed in cpptraj are:
CPPTRAJ V18.00 - AMBER MD 18
#Res Name First Last Natom #Orig #Mol
1 DA5 1 30 30 1 1
2 DA 31 62 32 2 1
3 DT 63 94 32 3 1
....
52 DA 1613 1644 32 52 2
53 DT 1645 1676 32 53 2
54 DT3 1677 1709 33 54 2
55 LYS 1710 1733 24 55 3
56 LYS 1734 1755 22 56 3
57 PHE 1756 1775 20 57 3
...
81 ASN 2154 2167 14 81 3
82 LYS 2168 2189 22 82 3
83 LYS 2190 2212 23 83 3
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.
I have tried the following;
cpptraj
parm topol.prmtop
trajin ensemble.nc
change oresnums of :55-83 min 684 max 712
This produces the following error:
Error: No change type specified.
I am unsure how to fix this issue and any help would be greatly appreciated.
Kind regards,
Dan.
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Received on Wed Feb 28 2024 - 09:30:02 PST
