CPPTRAJ: Trajectory Analysis. V16.16
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| Date/time: 03/15/17 21:50:39
| Available memory: 25.151 GB

INPUT: Reading input from 'pca.in'
  [parm ../ADP/compl_dry.prmtop [ADP]]
        Reading '../ADP/compl_dry.prmtop' as Amber Topology
  [parm ../inhibitor_002/compl_dry.prmtop [inh]]
        Reading '../inhibitor_002/compl_dry.prmtop' as Amber Topology
  [trajin ../ADP/prod1/p1_90.mdcrd parm [ADP]]
        Reading '../ADP/prod1/p1_90.mdcrd' as Amber Trajectory
  [trajin ../ADP/prod2/p2_90.mdcrd parm [ADP]]
        Reading '../ADP/prod2/p2_90.mdcrd' as Amber Trajectory
  [trajin ../ADP/prod3/p3_90.mdcrd parm [ADP]]
        Reading '../ADP/prod3/p3_90.mdcrd' as Amber Trajectory
  [trajin ../inhibitor_002/prod1/p1_90.mdcrd parm [inh]]
        Reading '../inhibitor_002/prod1/p1_90.mdcrd' as Amber Trajectory
  [trajin ../inhibitor_002/prod2/p2_90.mdcrd parm [inh]]
        Reading '../inhibitor_002/prod2/p2_90.mdcrd' as Amber Trajectory
  [trajin ../inhibitor_002/prod3/p3_90.mdcrd parm [inh]]
        Reading '../inhibitor_002/prod3/p3_90.mdcrd' as Amber Trajectory
  [rms mass first :1-316@CA,C,N,O,H]
    RMSD: (:1-316@CA,C,N,O,H), reference is first frame (:1-316@CA,C,N,O,H), mass-weighted.
        Best-fit RMSD will be calculated, coords will be rotated and translated.
  [average crdset ALL-average :1-316@CA,C,N,O,H start 1 stop 54000]
        Setting active reference for distance-based masks: 'ALL-average'
    AVERAGE: Averaging over coordinates in mask [:1-316@CA,C,N,O,H]
        Start: 1  Stop: 54000
        Saving averaged coords to set 'ALL-average'
  [createcrd ALL-trajectories]
    CREATECRD: Saving coordinates from Top compl_dry.prmtop to "ALL-trajectories"
  [run]
---------- RUN BEGIN -------------------------------------------------

PARAMETER FILES (2 total):
 0: [ADP] compl_dry.prmtop, 5121 atoms, 318 res, box: Trunc. Oct., 3 mol
 1: [inh] compl_dry.prmtop, 5118 atoms, 317 res, box: Trunc. Oct., 2 mol

INPUT TRAJECTORIES (6 total):
 0: 'p1_90.mdcrd' is an AMBER trajectory, Parm compl_dry.prmtop (Trunc. Oct. box) (reading 9000 of 9000)
 1: 'p2_90.mdcrd' is an AMBER trajectory, Parm compl_dry.prmtop (Trunc. Oct. box) (reading 9000 of 9000)
 2: 'p3_90.mdcrd' is an AMBER trajectory, Parm compl_dry.prmtop (Trunc. Oct. box) (reading 9000 of 9000)
 3: 'p1_90.mdcrd' is an AMBER trajectory, Parm compl_dry.prmtop (Trunc. Oct. box) (reading 9000 of 9000)
 4: 'p2_90.mdcrd' is an AMBER trajectory, Parm compl_dry.prmtop (Trunc. Oct. box) (reading 9000 of 9000)
 5: 'p3_90.mdcrd' is an AMBER trajectory, Parm compl_dry.prmtop (Trunc. Oct. box) (reading 9000 of 9000)
  Coordinate processing will occur on 54000 frames.

REFERENCE FRAMES (1 total):
    0: ALL-average
        Active reference frame for distance-based masks is 'ALL-average'

BEGIN TRAJECTORY PROCESSING:
.....................................................
ACTION SETUP FOR PARM 'compl_dry.prmtop' (3 actions):
  0: [rms mass first :1-316@CA,C,N,O,H]
        Target mask: [:1-316@CA,C,N,O,H](1563)
        Reference mask: [:1-316@CA,C,N,O,H](1563)
Warning: Coordinates are being rotated and box coordinates are present.
Warning: Unit cell vectors are NOT rotated; imaging will not be possible
Warning:  after the RMS-fit is performed.
  1: [average crdset ALL-average :1-316@CA,C,N,O,H start 1 stop 54000]
        Mask [:1-316@CA,C,N,O,H] corresponds to 1563 atoms.
        Averaging over 1563 atoms.
Warning: Atom selection < total # atoms, stripping parm for averaging only:
  2: [createcrd ALL-trajectories]
        Estimated memory usage (27000 frames): 1.660 GB
----- p1_90.mdcrd (1-9000, 1) -----
 0% 10%
----- p2_90.mdcrd (1-9000, 1) -----
20% 30%
----- p3_90.mdcrd (1-9000, 1) -----
40%
.....................................................
ACTION SETUP FOR PARM 'compl_dry.prmtop' (3 actions):
  0: [rms mass first :1-316@CA,C,N,O,H]
        Target mask: [:1-316@CA,C,N,O,H](1563)
Warning: Coordinates are being rotated and box coordinates are present.
Warning: Unit cell vectors are NOT rotated; imaging will not be possible
Warning:  after the RMS-fit is performed.
  1: [average crdset ALL-average :1-316@CA,C,N,O,H start 1 stop 54000]
        Mask [:1-316@CA,C,N,O,H] corresponds to 1563 atoms.
        1563 atoms will be averaged for 'compl_dry.prmtop'.
  2: [createcrd ALL-trajectories]
Error: # atoms in current topology (5118) != # atoms in coords set "ALL-trajectories" (5121)
Error: Setup failed for [createcrd]
Warning: Could not set up actions for compl_dry.prmtop: skipping.