Are you certain that the prmtop and nc are the same system? You generated
the trajectory via md using the stripped.file.prmtop?
On Mon, Sep 27, 2021, 4:50 AM Annabelle Hartt <ah16287.bristol.ac.uk> wrote:
> Sorry. I have generated this PDB from the 1st frame of the output
> trajectory so that I could see what was going on using this:
> parm <stripped.file>.prmtop
> trajin <output traj file>.nc 1 1
> autoimage
> rms first
> trajout <pdbfile>.pdb
> run
>
> By the coordinates in the wrong column, I mean that CPPTRAJ seems to
> somehow be mixing up the X, Y and Z coordinate values and printing the
> Z-coordinate value in place of X, the X-coordinate in place of Y and Y
> coordinate in place of Z. If you look at the values in the PDB file for
> residues 127-131 this is shown as the X should be ~60/70 but instead this
> is in the place of the Z coordinate.
>
> ________________________________
> From: Daniel Roe <daniel.r.roe.gmail.com>
> Sent: 24 September 2021 16:20
> To: AMBER Mailing List <amber.ambermd.org>
> Subject: Re: [AMBER] Co-ordinates switching in CPPTRAJ output
>
> Hi,
>
> First, it's not clear what you mean by coordinates being in the wrong
> column. Also, how are you generating the PDB? There is no PDB output
> in the cpptraj input you posted as far as I can tell.
>
> -Dan
>
> On Fri, Sep 24, 2021 at 10:37 AM Annabelle Hartt <ah16287.bristol.ac.uk>
> wrote:
> >
> > Hi,
> >
> > I have been trying to run a CPPTRAJ script to generate a trajectory with
> just CA atoms using the following script:
> > parm <name>.prmtop
> > trajin nowaters/<name>_nowaters.nc
> > autoimage
> > rms first .CA
> > average crdset AVG
> > run
> > rms ref AVG .CA
> > # strip and output results.
> > strip !.CA outprefix CA
> > trajout CA_traj/<name>_CA.nc
> > run
> > clear all
> >
> > However this was resulting in output trajectories where the X, Y and Z
> co-ordinates were sometimes in the wrong column as demonstrated by residues
> 127-131 in this section of a pdb file :
> > ATOM 123 CA GLN 123 68.309 29.110 1.473 1.00 0.00
> C
> > ATOM 124 CA LEU 124 66.353 31.970 -0.226 1.00 0.00
> C
> > ATOM 125 CA ARG 125 67.566 34.771 -2.529 1.00 0.00
> C
> > ATOM 126 CA ASP 126 67.312 38.488 -2.652 1.00 0.00
> C
> > ATOM 127 CA SER 127 35.179 -2.383 68.197 1.00 0.00
> C
> > ATOM 128 CA LYS 128 37.592 0.697 68.026 1.00 0.00
> C
> > ATOM 129 CA SER 129 40.316 -1.856 66.986 1.00 0.00
> C
> > ATOM 130 CA SER 130 11.099 79.441 67.583 1.00 0.00
> C
> > ATOM 131 CA ASP 131 14.290 80.687 69.232 1.00 0.00
> C
> > ATOM 132 CA LYS 132 72.574 38.092 -1.012 1.00 0.00
> C
> > ATOM 133 CA SER 133 70.558 35.313 0.680 1.00 0.00
> C
> > ATOM 134 CA VAL 134 68.398 34.435 3.699 1.00 0.00
> C
> >
> > I have not been able to figure out what has caused this – but thought
> there may be an issue in CPPTRAJ?
> >
> > Many thanks,
> > Annabelle
> > _______________________________________________
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Mon Sep 27 2021 - 03:30:02 PDT
