Dear AMBER users,
I want to concatenate Amber trajectory from multiple parts in NC format.
The NC files and PDB file have been stripped from water and ions. Then, my
command is:
cpptraj -p 2ya8.nowater.pdb *-i cpptraj_box.txt* -y 2ya8.nc_bkp1 -y
2ya8.nc_bkp2 -y 2ya8.nc_bkp3 -y 2ya8.nc_bkp4 -y 2ya8.nc_bkp5 -y
2ya8.nc_bkp6 -y 2ya8.nc_bkp7 -y 2ya8.nc -x TEMP.nc
Where the [*cpptraj_box.txt*] file contain the following box information:
parmbox x 107.363 y 116.530 z 114.625
parmbox alpha 90.00 beta 90.00 gamma 90.00
The output of the command is:
-------------------cpptraj log starts-------------------
CPPTRAJ: Trajectory Analysis. V17.00
___ ___ ___ ___
| \/ | \/ | \/ |
_|_/\_|_/\_|_/\_|_
| Date/time: 08/12/18 13:51:11
| Available memory: 11.588 GB
Reading '2ya8.nowater.pdb' as PDB File
Determining bond info from distances.
Warning: 2ya8.nowater.pdb: Determining default bond distances from element
types.
Reading '2ya8.nc_bkp1' as Amber Trajectory
*Warning: Trajectory only contains box lengths and topology has no box
info.*
Warning: To set box angles for topology use the 'parmbox' command.
Warning: Box angle(s) <= 0.0; setting box to NONE.
Reading '2ya8.nc_bkp2' as Amber Trajectory
*Warning: Trajectory only contains box lengths and topology has no box
info.*
Warning: To set box angles for topology use the 'parmbox' command.
Warning: Box angle(s) <= 0.0; setting box to NONE.
Reading '2ya8.nc_bkp3' as Amber Trajectory
*Warning: Trajectory only contains box lengths and topology has no box
info.*
Warning: To set box angles for topology use the 'parmbox' command.
Warning: Box angle(s) <= 0.0; setting box to NONE.
Reading '2ya8.nc_bkp4' as Amber Trajectory
*Warning: Trajectory only contains box lengths and topology has no box
info.*
Warning: To set box angles for topology use the 'parmbox' command.
Warning: Box angle(s) <= 0.0; setting box to NONE.
Reading '2ya8.nc_bkp5' as Amber Trajectory
*Warning: Trajectory only contains box lengths and topology has no box
info.*
Warning: To set box angles for topology use the 'parmbox' command.
Warning: Box angle(s) <= 0.0; setting box to NONE.
Reading '2ya8.nc_bkp6' as Amber Trajectory
*Warning: Trajectory only contains box lengths and topology has no box
info.*
Warning: To set box angles for topology use the 'parmbox' command.
Warning: Box angle(s) <= 0.0; setting box to NONE.
Reading '2ya8.nc_bkp7' as Amber Trajectory
*Warning: Trajectory only contains box lengths and topology has no box
info.*
Warning: To set box angles for topology use the 'parmbox' command.
Warning: Box angle(s) <= 0.0; setting box to NONE.
Reading '2ya8.nc' as Amber Trajectory
*Warning: Trajectory only contains box lengths and topology has no box
info.*
Warning: To set box angles for topology use the 'parmbox' command.
Warning: Box angle(s) <= 0.0; setting box to NONE.
Writing 'TEMP.nc' as Amber NetCDF
*INPUT: Reading input from 'cpptraj_box.txt'*
* [parmbox x 107.363 y 116.530 z 114.625]*
*Warning: Box angle(s) <= 0.0; setting box to NONE.*
* Box: 'None' XYZ= { 107.363 116.530 114.625 } ABG= { 0.00
0.00 0.00 }*
* [parmbox alpha 90.00 beta 90.00 gamma 90.00]*
* Box: 'Orthogonal' XYZ= { 107.363 116.530 114.625 } ABG= {
90.00 90.00 90.00 }*
---------- RUN BEGIN -------------------------------------------------
PARAMETER FILES (1 total):
0: 2ya8.nowater.pdb, 7442 atoms, 474 res, box: Orthogonal, 2 mol
INPUT TRAJECTORIES (8 total):
0: '2ya8.nc_bkp1' is an AMBER trajectory, Parm 2ya8.nowater.pdb (reading
1432 of 1432)
1: '2ya8.nc_bkp2' is an AMBER trajectory, Parm 2ya8.nowater.pdb (reading
161 of 161)
2: '2ya8.nc_bkp3' is an AMBER trajectory, Parm 2ya8.nowater.pdb (reading
1054 of 1054)
3: '2ya8.nc_bkp4' is an AMBER trajectory, Parm 2ya8.nowater.pdb (reading
1432 of 1432)
4: '2ya8.nc_bkp5' is an AMBER trajectory, Parm 2ya8.nowater.pdb (reading
1431 of 1431)
5: '2ya8.nc_bkp6' is an AMBER trajectory, Parm 2ya8.nowater.pdb (reading
1221 of 1221)
6: '2ya8.nc_bkp7' is an AMBER trajectory, Parm 2ya8.nowater.pdb (reading
1400 of 1400)
7: '2ya8.nc' is an AMBER trajectory, Parm 2ya8.nowater.pdb (reading 1230
of 1230)
Coordinate processing will occur on 9361 frames.
OUTPUT TRAJECTORIES (1 total):
'TEMP.nc' (9361 frames) is a NetCDF AMBER trajectory
BEGIN TRAJECTORY PROCESSING:
*Warning: Box information present in topology but not in trajectory.*
*Warning: DISABLING BOX in topology '2ya8.nowater.pdb'!*
----- 2ya8.nc_bkp1 (1-1432, 1) -----
-------------------cpptraj log ends-------------------
My QUESTION:
*Why is "box" gets disabled even though I use the parmbox commands?*
By the way, the output united nc trajectory seems OK.
Thanks,
Dmirtt
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Received on Sun Aug 12 2018 - 04:30:02 PDT
