Hi,
Can you send me the coordinate and topology files in question
(off-list) so I can try to reproduce? Thanks,
-Dan
On Tue, Nov 6, 2018 at 10:27 AM Rosellen, Martin
<martin.rosellen.16.ucl.ac.uk> wrote:
>
> Hi,
>
> I have two crystal structures of the same protein. The first structure 156 residues, the second 159 residues. Residue 4 in the second structure is residue 1 in the first structure. I do not need the extra 3 residues from the second structure.
>
> I try to calculate rmsd values between the structures in cpptraj like this:
>
> parm first.prmtop
> trajin first.nc
> rmsd :1-156.CA :4-159.CA out rmsd.dat reftraj second.inpcrd parm second.prmtop
> go
>
> ---------- RUN BEGIN -------------------------------------------------
>
> PARAMETER FILES (1 total):
> 0: first.prmtop, 54511 atoms, 17503 res, box: Trunc. Oct., 17348 mol, 17342 solvent
>
> INPUT TRAJECTORIES (1 total):
> 0: 'first.nc' is a NetCDF AMBER trajectory, Parm first.prmtop (Trunc. Oct. box) (reading 20000 of 20000)
> Coordinate processing will occur on 20000 frames.
>
> BEGIN TRAJECTORY PROCESSING:
> .....................................................
> ACTION SETUP FOR PARM 'first.prmtop' (1 actions):
> 0: [rmsd :1-156.CA :4-159.CA out ref.dat reftraj second.inpcrd parm second.prmtop]
> Target mask: [:1-156.CA](156)
> Reference mask: [:4-159.CA](153)
> Warning: Number of atoms in target mask (156) does not equal
> Warning: number of atoms in reference mask (153).
> Warning: Setup incomplete for [rmsd]: Skipping
>
> ----------
> The reference does have 159 residues but somehow residues 157,158,159 are cut off before the mask is applied.
>
> I got it working the other way around like this, but it is not what I want:
>
> parm second.prmtop
> trajin second.nc
> strip :1-3
> rmsd :1-159.CA :1-156.CA out ref.dat reftraj first.inpcrd parm first.prmtop
> go
>
> How can I tell cpptraj to map the residue numbers correctly?
>
> cheers
> Martin
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Received on Tue Nov 06 2018 - 13:00:03 PST
