I am pretty certain they are the same system, especially as CPPTRAJ wouldn’t run if the prmtop and nc did not have the same number of atoms.
I only generated the PDB to investigate the problem, the issue of the mixed up coordinate values is also present in the trajectory output file, which is the main thing I am trying to generate in order to perform PCA on just the CA atoms, but stripping the trajectory to just CA seems to result in coordinate values being switched. The input trajectory used in the original cpptraj script below was correct with all atoms in the correct place, but upon stripping to just CA, the coordinates for some values are outputted incorrectly in the trajectory, which I am trying to use the PDB file to demonstrate.
> > 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
Sent from Mail<
https://go.microsoft.com/fwlink/?LinkId=550986> for Windows
From: Carlos Simmerling<mailto:carlos.simmerling.gmail.com>
Sent: 27 September 2021 11:06
To: AMBER Mailing List<mailto:amber.ambermd.org>
Subject: Re: [AMBER] Co-ordinates switching in CPPTRAJ output
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
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Mon Sep 27 2021 - 03:30:02 PDT
