Thanks for the files. I think I know what's going on now.
I should have asked before, but what version of cpptraj are you using.
When I use your input and files, I actually get an error message:
```
[rmsd :1-156.CA :4-159.CA out rmsd.dat reftraj 1d7p.inpcrd parm 1d7p.prmtop]
Loading reference trajectory '1d7p.inpcrd'
Error: Topology '1d7p.prmtop' not found.
Error: No topology found for reftraj 1d7p.inpcrd. Ensure topologies are loaded.
Error: Could not initialize action [rmsd]
```
The problem is that 'parm' in the 'rmsd' command is referring to a
topology that has not yet been loaded. Now I don't have your complete
input so I'm not sure that if in the original instance you had
specified the missing topology on the command line, but it's possible
that if you're using an older version of cpptraj that this error was
not properly trapped and it was using the wrong topology to set up the
reference mask. Using your original input as a template, add a 'parm
second.prmtop' after your 'parm first.prmtop' and see if that fixes
your input. Also, if you're using an older (<v18) version of cpptraj I
recommend you upgrade.
Hope this helps,
-Dan
On Tue, Nov 6, 2018 at 3:59 PM Daniel Roe <daniel.r.roe.gmail.com> wrote:
>
> 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
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
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Received on Wed Nov 14 2018 - 16:00:02 PST
