Use the command "ncdump -h" (to get the header information) for each of the
trajectories.
Do they all have the same number of frames?
Another suggestion is to use the "ensemble" command in cpptraj, which will
analyze all replicas in the same run.
HTH,
Jason
On Mon, Jan 2, 2017 at 3:31 PM, Elisa Pieri <elisa.pieri90.gmail.com> wrote:
> Dear Amber people,
>
> I have 6 pH-REMD .nc trajectory files (from tappo.003 to tappo.008). I used
> this script (which already worked fine several times with other systems):
>
> for ph in 3 4 5 6 7 8
> do
> cat > cpptraj.in << mamihlapinatapai
> parm tappo.parm7
> trajin tappo.003 remdtraj remdtrajtemp ${ph}.00
> autoimage
> trajout tappo_${ph}.pdb
> mamihlapinatapai
> cpptraj tappo.parm7 cpptraj.in
> rm -f cpptraj.in
> done
>
> For some reason, tappo_7.pdb and tappo_8.pdb were perfectly done, while the
> files for the other pH values where empty. If I used cpptraj interactively,
> this is what I get:
>
> > parm tappo.parm7
> Reading 'tappo.parm7' as Amber Topology
> > trajin tappo.003 remdtraj remdtrajtemp 5.00
> Found 6 replicas.
> Reading 'tappo.003' as Amber NetCDF
> > autoimage
> AUTOIMAGE: To box center based on center of mass, anchor is first
> molecule.
> > trajout tappo_5.pdb
> Writing 'tappo_5.pdb' as PDB
> > go
> ---------- RUN BEGIN -------------------------------------------------
>
> PARAMETER FILES (1 total):
> 0: tappo.parm7, 31941 atoms, 9611 res, box: Trunc. Oct., 9386 mol, 9379
> solvent
>
> INPUT TRAJECTORIES (1 total):
> 0: REMD trajectories (6 total), lowest replica 'tappo.003' (reading 20000
> of 20000)
> Looking for frames at 5.00 K
> Coordinate processing will occur on 20000 frames.
>
> OUTPUT TRAJECTORIES (1 total):
> 'tappo_5.pdb' (20000 frames) is a PDB file
>
> BEGIN TRAJECTORY PROCESSING:
> .....................................................
> ACTION SETUP FOR PARM 'tappo.parm7' (1 actions):
> 0: [autoimage]
> Original box is truncated octahedron, turning on 'familiar'.
> Anchor molecule is 1
> The following molecules are fixed to anchor: 2
> 9384 molecules are mobile.
> Warning: For PDB with MODEL, box coords for first frame only will be
> written to CRYST1.
> Warning: No PDB space group specified.
> ----- tappo.003 (1-20000, 1) -----
> Error: Target replica not found. Check that all replica trajectories
> Error: were found and that the target temperature or indices are valid
> Error: for this ensemble.
>
> Read 0 frames and processed 0 frames.
>
> The mdout files do not mention any error. Unfortunately, I'm working in
> remote and I don't have the chance to visually check the trajectories (the
> files are huge). I don't get what is wrong: the .nc files have all the same
> dimension, so I'm supposing they are fine. Why some pH values are OK and
> some others are not? And why cpptraj says "Found 6 replicas." before
> processing and "Target replica not found" after?
>
> Elisa
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>
--
Jason M. Swails
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Received on Mon Jan 02 2017 - 13:00:03 PST
