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
Received on Mon Jan 02 2017 - 13:00:02 PST
