Actually, I got what happened: I calculated 2 ns pH-REMD with 12 replicas,
from pH 1 to pH 12. Then, due to a reduced available walltime, I decided to
restrict my calculations to pH range 3-8 for further 20 ns, so I took the
cpin newly created by the 2 ns trajectories step as input. Unfortunately, I
didn't notice that the replicas pH values were 1 2 7 8 10 and 11.
But honestly I thought that, since I had specified the pH in the mdin, the
pH value would be adjusted to values between 3 and 8..
So what I have now is replicas with pH values equal to 1 2 7 8 10 and 11,
right? And..the keyword "solvph" in the mdin is pretty useless, isn't it?
On Mon, Jan 2, 2017 at 9:33 PM, Jason Swails <jason.swails.gmail.com> wrote:
> 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
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Jason M. Swails
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Tue Jan 03 2017 - 04:30:03 PST
