Resetting modules to system default. Reseting $MODULEPATH back to system default. All extra directories will be removed from $MODULEPATH. CPPTRAJ: Trajectory Analysis. V18.00 ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 07/10/21 12:38:36 | Available memory: 23.378 GB INPUT: Reading input from 'STDIN' [parm ../../../01_6DDE_BU72/rep1/01_6DDE_BU72_nowater.prmtop [BU72]] Reading '../../../01_6DDE_BU72/rep1/01_6DDE_BU72_nowater.prmtop' as Amber Topology Radius Set: modified Bondi radii (mbondi) [parm ../02_6DDE_BU72_PAM_nowater.prmtop [BU72_PAM]] Reading '../02_6DDE_BU72_PAM_nowater.prmtop' as Amber Topology Radius Set: modified Bondi radii (mbondi) [trajin ../../../01_6DDE_BU72/rep1/01_6DDE_BU72_nowater.dcd 1 100000 parm [BU72]] Reading '../../../01_6DDE_BU72/rep1/01_6DDE_BU72_nowater.dcd' as Charmm DCD Version >= 22; assuming shape matrix is stored. Warning: Trajectory box type is 'Orthogonal' but topology box type is 'None'. Warning: Setting topology box information from trajectory. [trajin ../02_6DDE_BU72_PAM_nowater.dcd 1 100000 parm [BU72_PAM]] Reading '../02_6DDE_BU72_PAM_nowater.dcd' as Charmm DCD Version >= 22; assuming shape matrix is stored. Warning: Trajectory box type is 'Orthogonal' but topology box type is 'None'. Warning: Setting topology box information from trajectory. [rms first :972-1252&!@H=] RMSD: (:972-1252&!@H*), reference is first frame (:972-1252&!@H*). Best-fit RMSD will be calculated, coords will be rotated and translated. [average crdset muOR-average] Setting active reference for distance-based masks: 'muOR-average' AVERAGE: Averaging over coordinates in mask [*] Start: 1 Stop: Final frame Saving averaged coords to set 'muOR-average' [createcrd muOR-trajectories] CREATECRD: Saving coordinates from Top 01_6DDE_BU72_nowater.prmtop to "muOR-trajectories" [run] ---------- RUN BEGIN ------------------------------------------------- PARAMETER FILES (2 total): 0: [BU72] 01_6DDE_BU72_nowater.prmtop, 19680 atoms, 1253 res, box: Orthogonal, 6 mol 1: [BU72_PAM] 02_6DDE_BU72_PAM_nowater.prmtop, 19712 atoms, 1254 res, box: Orthogonal, 7 mol INPUT TRAJECTORIES (2 total): 0: '01_6DDE_BU72_nowater.dcd' is a CHARMM DCD file Little Endian 32 bit, Parm 01_6DDE_BU72_nowater.prmtop (Orthogonal box) (reading 100000 of 176797) 1: '02_6DDE_BU72_PAM_nowater.dcd' is a CHARMM DCD file Little Endian 32 bit, Parm 02_6DDE_BU72_PAM_nowater.prmtop (Orthogonal box) (reading 100000 of 130483) Coordinate processing will occur on 200000 frames. REFERENCE FRAMES (1 total): 0: muOR-average Active reference frame for distance-based masks is 'muOR-average' BEGIN TRAJECTORY PROCESSING: ..................................................... ACTION SETUP FOR PARM '01_6DDE_BU72_nowater.prmtop' (3 actions): 0: [rms first :972-1252&!@H=] Target mask: [:972-1252&!@H*](2256) Reference mask: [:972-1252&!@H*](2256) 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 muOR-average] Mask [*] corresponds to 19680 atoms. Averaging over 19680 atoms. 2: [createcrd muOR-trajectories] Estimated memory usage (100000 frames): 23.618 GB ----- 01_6DDE_BU72_nowater.dcd (1-100000, 1) ----- 0% 10% 20% 30% 40% Error: # atoms in current topology (19712) != # atoms in coords set "muOR-trajectories" (19680) Error: Setup failed for [createcrd] ..................................................... ACTION SETUP FOR PARM '02_6DDE_BU72_PAM_nowater.prmtop' (3 actions): 0: [rms first :972-1252&!@H=] Target mask: [:972-1252&!@H*](2256) 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 muOR-average] Mask [*] corresponds to 19712 atoms. Warning: Topology '02_6DDE_BU72_PAM_nowater.prmtop' selected # atoms (19712) > original topology '01_6DDE_BU72_nowater.prmtop' (19680) 19712 atoms will be averaged for '02_6DDE_BU72_PAM_nowater.prmtop'. 2: [createcrd muOR-trajectories] Warning: Could not set up actions for 02_6DDE_BU72_PAM_nowater.prmtop: skipping. Read 100000 frames and processed 100000 frames. TIME: Avg. throughput= 2223.3887 frames / second. ACTION OUTPUT: AVERAGE: 100000 frames, COORDS set 'muOR-average' TIME: Analyses took 0.0000 seconds. DATASETS (2 total): RMSD_00002 "RMSD_00002" (double, rms), size is 100000 muOR-trajectories "muOR-trajectories" (coordinates), size is 100000 (23.618 GB) Box Coords, 19680 atoms RUN TIMING: TIME: Init : 0.0000 s ( 0.00%) TIME: Trajectory Process : 44.9764 s ( 99.99%) TIME: Action Post : 0.0034 s ( 0.01%) TIME: Analysis : 0.0000 s ( 0.00%) TIME: Data File Write : 0.0001 s ( 0.00%) TIME: Other : 0.0011 s ( 0.00%) TIME: Run Total 44.9810 s ---------- RUN END --------------------------------------------------- [crdaction muOR-trajectories rms ref muOR-average :972-1252&!@H=] Using set 'muOR-trajectories' ----- muOR-trajectories (1-100000, 1) ----- RMSD: (:972-1252&!@H*), reference is "muOR-average" (:972-1252&!@H*). Best-fit RMSD will be calculated, coords will be rotated and translated. Target mask: [:972-1252&!@H*](2256) Reference mask: [:972-1252&!@H*](2256) 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. 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. TIME: Total action execution time: 22.1714 seconds. [crdaction muOR-trajectories matrix covar name muOR-covar :972-1252&!@H=] Using set 'muOR-trajectories' ----- muOR-trajectories (1-100000, 1) ----- MATRIX: Calculating covariance matrix, output is by atom. Matrix data set is 'muOR-covar' Start: 1 Stop: Final frame Mask1 is ':972-1252&!@H*' Mask [:972-1252&!@H*] corresponds to 2256 atoms. 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. TIME: Total action execution time: 2371.7976 seconds. [runanalysis diagmatrix muOR-covar out muOR-evecs.dat vecs 3 name myEvecs nmwiz nmwizvecs 3 nmwizfile muOR.nmd nmwizmask :972-1252&!@H=] Mask [:972-1252&!@H*] corresponds to 2256 atoms. nmwiz topology 2256 atoms, 281 res, box: Orthogonal, 0 mol Changed DataFile 'muOR-evecs.dat' type to Evecs file for set myEvecs DIAGMATRIX: Diagonalizing matrix muOR-covar and writing modes to muOR-evecs.dat Calculating 3 eigenvectors. Writing 3 modes to NMWiz file muOR.nmd Storing modes with name: myEvecs Eigenmode calculation for 'muOR-covar' Calculating eigenvectors and eigenvalues. Calculating first 3 eigenmodes. TIME: Total analysis execution time: 2.2848 seconds. [crdaction muOR-trajectories projection bu72 modes myEvecs beg 1 end 3 :972-1252&!@H= crdframes 1,100000] Using set 'muOR-trajectories' ----- muOR-trajectories (1-100000, 1) ----- PROJECTION: Calculating projection using eigenvectors 1 to 3 of myEvecs Start: 1 Stop: Final frame Atom Mask: [:972-1252&!@H*] Mask [:972-1252&!@H*] corresponds to 2256 atoms. 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% Error: start 100001 > #Frames (100000), no frames will be processed. 1 errors encountered reading input. Error: Error(s) occurred during execution. 100% Complete. TIME: Total action execution time: 4.8287 seconds. [crdaction muOR-trajectories projection bu72_pam modes myEvecs beg 1 end 3 :972-1252&!@H= crdframes 100001,last] Using set 'muOR-trajectories' TIME: Total execution time: 2455.3913 seconds.