Hi,
Since trajectories typically carry the "correct" box coordinates, any
time there is a discrepancy between box info from a topology and box
info from a trajectory, cpptraj defaults to the latter. So just
replace 'parmbox' with 'box' (which overrides trajectory box info) and
you should be good.
Hope this helps,
-Dan
On Sun, Aug 12, 2018 at 7:04 AM Dmitry Suplatov <genesup.gmail.com> wrote:
>
> 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 Mon Aug 20 2018 - 11:30:03 PDT
