Hi amber users,
I performed REMD simulations using AMBER10. I would like to filter
temperature trajectory. I have now AMBER12 so trying to extract with this
version. Earlier I filtered few temperatures from the same trajectories.
It worked at that time. Now I want to filter all the sixteen temperatures
and getting the problem. It is the version problem?
Could anybody suggest why am I getting such message in spite of having
that temperature. I tried with all the sixteen temperatures. However
getting the same message.
I pasted the messages I got when I ran the ptraj program.
I will appreciate your help.
Thank you.
Sunita
======================================================
PTRAJ: Processing input from "STDIN" ...
PTRAJ: trajin remd_0.4ns.mdcrd.001 remdtraj remdtrajtemp 281.85
Checking coordinates: remd_0.4ns.mdcrd.001
REMDTRAJ: Using specified file as lowest replica: remd_0.4ns.mdcrd.001
REMDTRAJ: Frames at 281.850000 K will be processed.
REMDTRAJ: Scanning for other REMD files.
REMDTRAJ: Found 1 replica traj files.
PTRAJ: trajin remd_0.8ns.mdcrd.001 remdtraj remdtrajtemp 281.85
Checking coordinates: remd_0.8ns.mdcrd.001
REMDTRAJ: Using specified file as lowest replica: remd_0.8ns.mdcrd.001
REMDTRAJ: Frames at 281.850000 K will be processed.
REMDTRAJ: Scanning for other REMD files.
REMDTRAJ: Found 1 replica traj files.
PTRAJ: trajin remd_1.2ns.mdcrd.001 remdtraj remdtrajtemp 281.85
Checking coordinates: remd_1.2ns.mdcrd.001
REMDTRAJ: Using specified file as lowest replica: remd_1.2ns.mdcrd.001
REMDTRAJ: Frames at 281.850000 K will be processed.
REMDTRAJ: Scanning for other REMD files.
REMDTRAJ: Found 1 replica traj files.
PTRAJ: trajin remd_1.6ns.mdcrd.001 remdtraj remdtrajtemp 281.85
Checking coordinates: remd_1.6ns.mdcrd.001
REMDTRAJ: Using specified file as lowest replica: remd_1.6ns.mdcrd.001
REMDTRAJ: Frames at 281.850000 K will be processed.
REMDTRAJ: Scanning for other REMD files.
REMDTRAJ: Found 1 replica traj files.
PTRAJ: trajin remd_2.0ns.mdcrd.001 remdtraj remdtrajtemp 281.85
Checking coordinates: remd_2.0ns.mdcrd.001
REMDTRAJ: Using specified file as lowest replica: remd_2.0ns.mdcrd.001
REMDTRAJ: Frames at 281.850000 K will be processed.
REMDTRAJ: Scanning for other REMD files.
REMDTRAJ: Found 1 replica traj files.
PTRAJ: trajout output_remd_281.85.mdcrd
remd_0.4ns.mdcrd.001: 200 frames.
remd_0.8ns.mdcrd.001: 200 frames.
remd_1.2ns.mdcrd.001: 200 frames.
remd_1.6ns.mdcrd.001: 200 frames.
remd_2.0ns.mdcrd.001: 200 frames.
PTRAJ: Successfully read the input file.
Coordinate processing will occur on 1000 frames.
Summary of I/O and actions follows:
INPUT COORDINATE FILES
File (remd_0.4ns.mdcrd.001) is an AMBER REMD (new format) trajectory
with 200 sets
Replica processing by temperature will occur.
1 files total (First index is 001), frames at 281.850000 K will be used.
File (remd_0.8ns.mdcrd.001) is an AMBER REMD (new format) trajectory
with 200 sets
Replica processing by temperature will occur.
1 files total (First index is 001), frames at 281.850000 K will be used.
File (remd_1.2ns.mdcrd.001) is an AMBER REMD (new format) trajectory
with 200 sets
Replica processing by temperature will occur.
1 files total (First index is 001), frames at 281.850000 K will be used.
File (remd_1.6ns.mdcrd.001) is an AMBER REMD (new format) trajectory
with 200 sets
Replica processing by temperature will occur.
1 files total (First index is 001), frames at 281.850000 K will be used.
File (remd_2.0ns.mdcrd.001) is an AMBER REMD (new format) trajectory
with 200 sets
Replica processing by temperature will occur.
1 files total (First index is 001), frames at 281.850000 K will be used.
OUTPUT COORDINATE FILE
File (output_remd_281.85.mdcrd) is an AMBER trajectory
NO ACTIONS WERE SPECIFIED
Processing AMBER REMD trajectory (new format)
REMDTRAJ: Opening files remd_0.4ns.mdcrd.001 -> remd_0.4ns.mdcrd.001
Done.
1%
REMDTRAJ: Final repTemp value read= 285.390000, set 3
Could not find target 281.850000 in any of the replica trajectories.
Check that all replica trajectory files were found and that
none of the trajectories are corrupted (e.g. missing a temperature).
ptrajProcessInputCoordinates(): Target replica temperature not found in
traj! 100%
Processing AMBER REMD trajectory (new format)
REMDTRAJ: Opening files remd_0.8ns.mdcrd.001 -> remd_0.8ns.mdcrd.001
Done.
REMDTRAJ: Final repTemp value read= 303.770000, set 1
Could not find target 281.850000 in any of the replica trajectories.
Check that all replica trajectory files were found and that
none of the trajectories are corrupted (e.g. missing a temperature).
ptrajProcessInputCoordinates(): Target replica temperature not found in
traj! 100%
Processing AMBER REMD trajectory (new format)
REMDTRAJ: Opening files remd_1.2ns.mdcrd.001 -> remd_1.2ns.mdcrd.001
Done.
REMDTRAJ: Final repTemp value read= 339.880000, set 1
Could not find target 281.850000 in any of the replica trajectories.
Check that all replica trajectory files were found and that
none of the trajectories are corrupted (e.g. missing a temperature).
ptrajProcessInputCoordinates(): Target replica temperature not found in
traj! 100%
Processing AMBER REMD trajectory (new format)
REMDTRAJ: Opening files remd_1.6ns.mdcrd.001 -> remd_1.6ns.mdcrd.001
Done.
REMDTRAJ: Final repTemp value read= 339.880000, set 1
Could not find target 281.850000 in any of the replica trajectories.
Check that all replica trajectory files were found and that
none of the trajectories are corrupted (e.g. missing a temperature).
ptrajProcessInputCoordinates(): Target replica temperature not found in
traj! 100%
Processing AMBER REMD trajectory (new format)
REMDTRAJ: Opening files remd_2.0ns.mdcrd.001 -> remd_2.0ns.mdcrd.001
Done.
REMDTRAJ: Final repTemp value read= 339.880000, set 1
Could not find target 281.850000 in any of the replica trajectories.
Check that all replica trajectory files were found and that
none of the trajectories are corrupted (e.g. missing a temperature).
ptrajProcessInputCoordinates(): Target replica temperature not found in
traj! 100%
PTRAJ: Successfully read in 2 sets and processed 2 sets.
Dumping accumulated results (if any)
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Received on Sat Feb 08 2014 - 04:00:03 PST
