Hello!
Please make sure you have the latest version of CPPTRAJ. The 'change'
command has been updated many times recently.
Rodrigo.
On Wed, Feb 28, 2024 at 10:19 AM Daniel Hall via AMBER
<amber.ambermd.org> wrote:
>
> 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 - 09:30:03 PST
