\-/ -/- PTRAJ: a utility for processing trajectory files /-\ \-/ Version: "AMBER 11.0 integrated" (4/2010) -/- Executable is: "/net/bccs/cbu/linux64/amber11/bin/ptraj" /-\ Running on 1 processor(s) \-/ Residue labels: ALA ALA LYS ASP VAL LYS PHE GLY ASN ASP ALA ARG VAL LYS MET LEU ARG GLY VAL ASN VAL LEU ALA ASP ALA VAL LYS VAL THR LEU GLY PRO LYS GLY ARG ASN VAL VAL LEU ASP LYS SER PHE GLY ALA PRO THR ILE THR LYS ASP GLY VAL SER VAL ALA ARG GLU ILE GLU LEU GLU ASP LYS PHE GLU ASN MET GLY ALA GLN MET VAL LYS GLU VAL ALA SER LYS ALA ASN ASP ALA ALA GLY ASP GLY THR THR THR ALA THR VAL LEU ALA GLN ALA ILE ILE THR GLU GLY LEU LYS ALA VAL ALA ALA GLY MET ASN PRO MET ASP LEU LYS ARG GLY ILE ASP LYS ALA VAL THR ALA ALA VAL GLU GLU LEU LYS ALA LEU SER VAL PRO CYS SER ASP SER LYS ALA ILE ALA GLN VAL GLY THR ILE SER ALA ASN SER ASP GLU THR VAL GLY LYS LEU ILE ALA GLU ALA MET ASP LYS VAL GLY LYS GLU GLY VAL ILE THR VAL GLU ASP GLY THR GLY LEU GLN ASP GLU LEU ASP VAL VAL GLU GLY MET GLN PHE ASP ARG GLY TYR LEU SER PRO TYR PHE ILE ASN LYS PRO GLU THR GLY ALA VAL GLU LEU GLU SER PRO PHE ILE LEU LEU ALA ASP LYS LYS ILE SER ASN ILE ARG GLU MET LEU PRO VAL LEU GLU ALA VAL ALA LYS ALA GLY LYS PRO LEU LEU ILE ILE ALA GLU ASP VAL GLU GLY GLU ALA LEU ALA THR LEU VAL VAL ASN THR MET ARG GLY ILE VAL LYS VAL ALA ALA VAL LYS ALA PRO GLY PHE GLY ASP ARG ARG LYS ALA MET LEU GLN ASP ILE ALA THR LEU THR GLY GLY THR VAL ILE SER GLU GLU ILE GLY MET GLU LEU GLU LYS ALA THR LEU GLU ASP LEU GLY GLN ALA LYS ARG VAL VAL ILE ASN LYS ASP THR THR THR ILE ILE ASP GLY VAL GLY GLU GLU ALA ALA ILE GLN GLY ARG VAL ALA GLN ILE ARG GLN GLN ILE GLU GLU ALA THR SER ASP TYR ASP ARG GLU LYS LEU GLN GLU ARG VAL ALA LYS LEU ALA GLY GLY VAL ALA VAL ILE LYS VAL GLY ALA ALA THR GLU VAL GLU MET LYS GLU LYS LYS ALA ARG VAL GLU ASP ALA LEU HID ALA THR ARG ALA ALA VAL GLU GLU GLY VAL VAL ALA GLY GLY GLY VAL ALA LEU ILE ARG VAL ALA SER LYS LEU ALA ASP LEU ARG GLY GLN ASN GLU ASP GLN ASN VAL GLY ILE LYS VAL ALA LEU ARG ALA MET GLU ALA PRO LEU ARG GLN ILE VAL LEU ASN CYS GLY GLU GLU PRO SER VAL VAL ALA ASN THR VAL LYS GLY GLY ASP GLY ASN TYR GLY TYR ASN ALA ALA THR GLU GLU TYR GLY ASN MET ILE ASP MET GLY ILE LEU ASP PRO THR LYS VAL THR ARG SER ALA LEU GLN TYR ALA ALA SER VAL ALA GLY LEU MET ILE THR THR GLU CYS MET VAL THR ASP LEU PRO ADP MG2 WAT WAT WAT WAT WAT WAT WAT WAT WAT WAT WAT WAT WAT WAT ... WAT Setting box to be an exact truncated octahedron, angle is 109.471221 PTRAJ: Processing input from file _MMPBSA_cenptraj.in PTRAJ: trajin ../trajs/open_complex_300ns.nc 101 600 5 Checking coordinates: ../trajs/open_complex_300ns.nc NETCDF file: PTRAJ: strip :WAT Mask [:WAT] represents 120525 atoms PTRAJ: center :1-524 mass origin Mask [:1-524] represents 7835 atoms PTRAJ: image origin center Mask [*] represents 7875 atoms PTRAJ: center :1-526 mass origin Mask [:1-526] represents 7875 atoms PTRAJ: image origin center Mask [*] represents 7875 atoms PTRAJ: rms first mass :1-524 Mask [:1-524] represents 7835 atoms PTRAJ: average _MMPBSA_avgcomplex.pdb pdb Mask [*] represents 7875 atoms PTRAJ: trajout _MMPBSA_complex.mdcrd nobox PTRAJ: Successfully read the input file. Coordinate processing will occur on 100 frames. Summary of I/O and actions follows: INPUT COORDINATE FILES File (../trajs/open_complex_300ns.nc) is a NetCDF AMBER trajectory with box info with 600 sets (processing only 100) OUTPUT COORDINATE FILE File (_MMPBSA_complex.mdcrd) is an AMBER trajectory ACTIONS 1> STRIP: 120525 atoms will be removed from trajectory: :527-40701 2> CENTER to origin via center of mass, atom selection follows :1-524 3> IMAGE by molecule to origin using the center of mass, atom selection * (All atoms are selected) 4> CENTER to origin via center of mass, atom selection follows * (All atoms are selected) 5> IMAGE by molecule to origin using the center of mass, atom selection * (All atoms are selected) 6> RMS to first frame using mass weighting Atom selection follows :1-524 7> AVERAGE: dumping the average of the coordinates to file _MMPBSA_avgcomplex.pdb start: 1 Stop [at final frame] Offset: 1 Atom selection * (All atoms are selected) Output file information: File (_MMPBSA_avgcomplex.pdb) is a PDB file ..... 25% ............ 50% ............ 75% ............ 100% PTRAJ: Successfully read in 100 sets and processed 100 sets. Dumping accumulated results (if any)