CPPTRAJ: Trajectory Analysis. V15.00 ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 07/29/16 23:06:47 | Available memory: 56684.6 MB INPUT: Reading Input from file rmsd_all.in [parm WT.prmtop] Reading 'WT.prmtop' as Amber Topology [parm GFP.prmtop] Reading 'GFP.prmtop' as Amber Topology [parm MIC.prmtop] Reading 'MIC.prmtop' as Amber Topology [parm mCherry.prmtop] Reading 'mCherry.prmtop' as Amber Topology [trajin WT.mdcrd 1 100 parm WT.prmtop] Reading 'WT.mdcrd' as Amber Trajectory [trajin GFP.mdcrd 1 100 parm GFP.prmtop] Reading 'GFP.mdcrd' as Amber Trajectory [trajin MIC.mdcrd 1 100 parm MIC.prmtop] Reading 'MIC.mdcrd' as Amber Trajectory [trajin mCherry.mdcrd 1 100 parm mCherry.prmtop] Reading 'mCherry.mdcrd' as Amber Trajectory [reference WT.mdcrd 1 parm WT.prmtop [wt]] Reading 'WT.mdcrd' as Amber Trajectory Warning: Reference has 50100 frames, only reading frame 1 [reference GFP.mdcrd 1 parm GFP.prmtop [gfp]] Reading 'GFP.mdcrd' as Amber Trajectory Warning: Reference has 50100 frames, only reading frame 1 [reference MIC.mdcrd 1 parm MIC.prmtop [mic]] Reading 'MIC.mdcrd' as Amber Trajectory Warning: Reference has 50008 frames, only reading frame 1 [reference mCherry.mdcrd 1 parm mCherry.prmtop [mch]] Reading 'mCherry.mdcrd' as Amber Trajectory Warning: Reference has 50100 frames, only reading frame 1 [rms WT ref [wt] :1-88@C,CA,N,O out rmsd.dat] Reference mask: [:1-88@C,CA,N,O](352) RMSD: (:1-88@C,CA,N,O), reference is "WT.mdcrd" (:1-88@C,CA,N,O), with fitting. [rms GFP ref [gfp] :1-330@C,CA,N,O out rmsd.dat] Reference mask: [:1-330@C,CA,N,O](1320) RMSD: (:1-330@C,CA,N,O), reference is "GFP.mdcrd" (:1-330@C,CA,N,O), with fitting. [rms MIC ref [mic] :1-131@C,CA,N,O out rmsd.dat] Reference mask: [:1-131@C,CA,N,O](524) RMSD: (:1-131@C,CA,N,O), reference is "MIC.mdcrd" (:1-131@C,CA,N,O), with fitting. [rms mCherry ref [mch] :1-345@C,CA,N,O out rmsd.dat] Reference mask: [:1-345@C,CA,N,O](1380) RMSD: (:1-345@C,CA,N,O), reference is "mCherry.mdcrd" (:1-345@C,CA,N,O), with fitting. ---------- RUN BEGIN ------------------------------------------------- PARAMETER FILES: 0: 'WT.prmtop', 1460 atoms, 88 res, box: Trunc. Oct., 1 mol, 100 frames 1: 'GFP.prmtop', 5226 atoms, 330 res, box: Trunc. Oct., 1 mol, 100 frames 2: 'MIC.prmtop', 2088 atoms, 131 res, box: Trunc. Oct., 1 mol, 100 frames 3: 'mCherry.prmtop', 5419 atoms, 345 res, box: Trunc. Oct., 1 mol, 100 frames INPUT TRAJECTORIES: 0: 'WT.mdcrd' is an AMBER trajectory, Parm WT.prmtop (Trunc. Oct. box) (reading 100 of 50100) 1: 'GFP.mdcrd' is an AMBER trajectory, Parm GFP.prmtop (Trunc. Oct. box) (reading 100 of 50100) 2: 'MIC.mdcrd' is an AMBER trajectory, Parm MIC.prmtop (Trunc. Oct. box) (reading 100 of 50008) 3: 'mCherry.mdcrd' is an AMBER trajectory, Parm mCherry.prmtop (Trunc. Oct. box) (reading 100 of 50100) Coordinate processing will occur on 400 frames. REFERENCE FRAMES (4 total): 0: 'WT.mdcrd', frame 1 1: 'GFP.mdcrd', frame 1 2: 'MIC.mdcrd', frame 1 3: 'mCherry.mdcrd', frame 1 Active reference frame for distance-based masks is 0 TIME: Run Initialization took 0.0000 seconds. BEGIN TRAJECTORY PROCESSING: ..................................................... ACTION SETUP FOR PARM 'WT.prmtop' (4 actions): 0: [rms WT ref [wt] :1-88@C,CA,N,O out rmsd.dat] Target mask: [:1-88@C,CA,N,O](352) 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: [rms GFP ref [gfp] :1-330@C,CA,N,O out rmsd.dat] Target mask: [:1-330@C,CA,N,O](352) Warning: Number of atoms in target mask (352) does not equal Warning: number of atoms in reference mask (1320). Warning: Setup failed for [rms GFP ref [gfp] :1-330@C,CA,N,O out rmsd.dat]: Skipping 2: [rms MIC ref [mic] :1-131@C,CA,N,O out rmsd.dat] Target mask: [:1-131@C,CA,N,O](352) Warning: Number of atoms in target mask (352) does not equal Warning: number of atoms in reference mask (524). Warning: Setup failed for [rms MIC ref [mic] :1-131@C,CA,N,O out rmsd.dat]: Skipping 3: [rms mCherry ref [mch] :1-345@C,CA,N,O out rmsd.dat] Target mask: [:1-345@C,CA,N,O](352) Warning: Number of atoms in target mask (352) does not equal Warning: number of atoms in reference mask (1380). Warning: Setup failed for [rms mCherry ref [mch] :1-345@C,CA,N,O out rmsd.dat]: Skipping ----- WT.mdcrd (1-100, 1) ----- 0% 10% 20% 30% 40% 51% 61% 71% 81% 91% 100% Complete. Warning: Active reference has only 1460 atoms, parm 'GFP.prmtop' has 5226. Warning: Parm will only have reference coordinates for the first 1460 atoms (distance-based masks only). ..................................................... ACTION SETUP FOR PARM 'GFP.prmtop' (4 actions): 0: [rms WT ref [wt] :1-88@C,CA,N,O out rmsd.dat] Target mask: [:1-88@C,CA,N,O](352) 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: [rms GFP ref [gfp] :1-330@C,CA,N,O out rmsd.dat] Target mask: [:1-330@C,CA,N,O](1320) 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. 2: [rms MIC ref [mic] :1-131@C,CA,N,O out rmsd.dat] Target mask: [:1-131@C,CA,N,O](524) 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. 3: [rms mCherry ref [mch] :1-345@C,CA,N,O out rmsd.dat] Target mask: [:1-345@C,CA,N,O](1320) Warning: Number of atoms in target mask (1320) does not equal Warning: number of atoms in reference mask (1380). Warning: Setup failed for [rms mCherry ref [mch] :1-345@C,CA,N,O out rmsd.dat]: Skipping ----- GFP.mdcrd (1-100, 1) ----- 0% 10% 20% 30% 40% 51% 61% 71% 81% 91% 100% Complete. Warning: Active reference has only 1460 atoms, parm 'MIC.prmtop' has 2088. Warning: Parm will only have reference coordinates for the first 1460 atoms (distance-based masks only). ..................................................... ACTION SETUP FOR PARM 'MIC.prmtop' (4 actions): 0: [rms WT ref [wt] :1-88@C,CA,N,O out rmsd.dat] Target mask: [:1-88@C,CA,N,O](352) 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: [rms GFP ref [gfp] :1-330@C,CA,N,O out rmsd.dat] Target mask: [:1-330@C,CA,N,O](524) Warning: Number of atoms in target mask (524) does not equal Warning: number of atoms in reference mask (1320). Warning: Setup failed for [rms GFP ref [gfp] :1-330@C,CA,N,O out rmsd.dat]: Skipping 2: [rms MIC ref [mic] :1-131@C,CA,N,O out rmsd.dat] Target mask: [:1-131@C,CA,N,O](524) 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. 3: [rms mCherry ref [mch] :1-345@C,CA,N,O out rmsd.dat] Target mask: [:1-345@C,CA,N,O](524) Warning: Number of atoms in target mask (524) does not equal Warning: number of atoms in reference mask (1380). Warning: Setup failed for [rms mCherry ref [mch] :1-345@C,CA,N,O out rmsd.dat]: Skipping ----- MIC.mdcrd (1-100, 1) ----- 0% 10% 20% 30% 40% 51% 61% 71% 81% 91% 100% Complete. Warning: Active reference has only 1460 atoms, parm 'mCherry.prmtop' has 5419. Warning: Parm will only have reference coordinates for the first 1460 atoms (distance-based masks only). ..................................................... ACTION SETUP FOR PARM 'mCherry.prmtop' (4 actions): 0: [rms WT ref [wt] :1-88@C,CA,N,O out rmsd.dat] Target mask: [:1-88@C,CA,N,O](352) 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: [rms GFP ref [gfp] :1-330@C,CA,N,O out rmsd.dat] Target mask: [:1-330@C,CA,N,O](1320) 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. 2: [rms MIC ref [mic] :1-131@C,CA,N,O out rmsd.dat] Target mask: [:1-131@C,CA,N,O](524) 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. 3: [rms mCherry ref [mch] :1-345@C,CA,N,O out rmsd.dat] Target mask: [:1-345@C,CA,N,O](1380) 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. ----- mCherry.mdcrd (1-100, 1) ----- 0% 10% 20% 30% 40% 51% 61% 71% 81% 91% 100% Complete. Read 400 frames and processed 400 frames. TIME: Trajectory processing: 1.0161 s TIME: Avg. throughput= 393.6675 frames / second. ACTION OUTPUT: DATASETS: 8 data sets: [wt]:1 "Cpptraj Generated trajectory " (reference), size is 1 'WT.mdcrd', refindex 0 (1460 atoms) [gfp]:1 "Cpptraj Generated trajectory " (reference), size is 1 'GFP.mdcrd', refindex 1 (5226 atoms) [mic]:1 "Cpptraj Generated trajectory " (reference), size is 1 'MIC.mdcrd', refindex 2 (2088 atoms) [mch]:1 "Cpptraj Generated trajectory " (reference), size is 1 'mCherry.mdcrd', refindex 3 (5419 atoms) WT "WT" (double, rms), size is 400 GFP "GFP" (double, rms), size is 400 MIC "MIC" (double, rms), size is 400 mCherry "mCherry" (double, rms), size is 400 DATAFILES: rmsd.dat (Standard Data File): WT GFP MIC mCherry ---------- RUN END --------------------------------------------------- TIME: Total execution time: 1.5358 seconds. -------------------------------------------------------------------------------- To cite CPPTRAJ use: Daniel R. Roe and Thomas E. Cheatham, III, "PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data". J. Chem. Theory Comput., 2013, 9 (7), pp 3084-3095.