\-/ -/- PTRAJ: a utility for processing trajectory files /-\ \-/ Version: "AMBER 10.0 integrated" (2/15/2008) -/- Executable is: "ptraj" /-\ \-/ Residue labels: THR SER HIE GLU ALA GLY ILE VAL CYS ARG ILE THR LYS PRO ALA LEU LEU VAL LEU ASN HIE GLU THR ALA LYS VAL ILE GLN THR ALA PHE GLN ARG ALA SER TYR PRO ASP ILE THR GLY GLU LYS ALA MET MET LEU LEU GLY GLN VAL LYS TYR GLY LEU HIE ASN ILE GLN ILE SER HIE LEU SER ILE ALA SER SER GLN VAL GLU LEU VAL GLU ALA LYS SER ILE ASP VAL SER ILE GLN ASP VAL SER VAL VAL PHE LYS GLY THR LEU LYS TYR GLY TYR THR THR ALA TRP TRP LEU GLY ILE ASP GLN SER ILE ASP PHE GLU ILE ASP SER ALA ILE ASP LEU GLN ILE ASN THR GLN LEU THR ALA ASP SER GLY ARG VAL ARG THR ASP ALA PRO ASP CYX TYR LEU SER PHE HIE LYS LEU LEU LEU HIE LEU GLN GLY GLU ARG GLU PRO GLY TRP ILE LYS GLN LEU PHE THR ASN PHE ILE SER PHE THR LEU LYS LEU VAL LEU LYS GLY GLN ILE CYX LYS GLU ILE ASN VAL ILE SER ASN ILE MET ALA ASP PHE VAL GLN THR ARG ALA ALA SER ILE LEU SER ASP GLY ASP ILE GLY VAL ASP ILE SER LEU THR GLY ASP PRO VAL ILE THR ALA SER TYR LEU GLU SER HIE HIE LYS GLY HIE PHE ILE TYR LYS ASP VAL SER GLU ASP LEU PRO LEU PRO THR PHE SER PRO THR LEU LEU GLY ASP SER ARG MET LEU TYR PHE TRP PHE SER GLU ARG VAL PHE HIE SER LEU ALA LYS VAL ALA PHE GLN ASP GLY ARG LEU MET LEU SER LEU MET GLY ASP GLU PHE LYS ALA VAL LEU GLU THR TRP GLY PHE ASN THR ASN GLN GLU ILE PHE GLN GLU VAL VAL GLY GLY PHE PRO SER GLN ALA GLN VAL THR VAL HIE CYS LEU LYS MET PRO LYS ILE SER CYS GLN ASN LYS GLY VAL VAL VAL ASP SER SER VAL MET VAL LYS PHE LEU PHE PRO ARG PRO ASP GLN GLN HIE SER VAL ALA TYR THR PHE GLU GLU ASP ILE VAL THR THR VAL GLN ALA SER TYR SER LYS LYS LYS LEU PHE LEU SER LEU LEU ASP PHE GLN ILE THR PRO LYS THR VAL SER ASN LEU THR GLU SER SER SER GLU SER ILE GLN SER PHE LEU GLN SER MET ILE THR ALA VAL GLY ILE PRO GLU VAL MET SER ARG LEU GLU VAL VAL PHE THR ALA LEU MET ASN SER LYS GLY VAL SER LEU PHE ASP ILE ILE ASN PRO GLU ILE ILE THR ARG ASP GLY PHE LEU LEU LEU GLN MET ASP PHE GLY PHE PRO GLU HIE LEU LEU VAL ASP PHE LEU GLN SER LEU SER PCW PCW Q2O Q2O Na+ Na+ Na+ Na+ Na+ Na+ Na+ Na+ Na+ Na+ Na+ Na+ Na+ Na+ Na+ WAT WAT WAT WAT WAT 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 "STDIN" ... PTRAJ: trajin ../heat.mdcrd Checking coordinates: ../heat.mdcrd PTRAJ: trajin ../density.mdcrd Checking coordinates: ../density.mdcrd PTRAJ: trajin ../equil.mdcrd Checking coordinates: ../equil.mdcrd PTRAJ: trajin ../prod1.mdcrd Checking coordinates: ../prod1.mdcrd trajin ../prod1.mdcrd ignored; could not open file (../prod1.mdcrd) PTRAJ: trajin ../prod2.mdcrd Checking coordinates: ../prod2.mdcrd trajin ../prod2.mdcrd ignored; could not open file (../prod2.mdcrd) PTRAJ: trajin ../prod3.mdcrd Checking coordinates: ../prod3.mdcrd trajin ../prod3.mdcrd ignored; could not open file (../prod3.mdcrd) PTRAJ: center origin :1-476 Mask [:1-476] represents 7970 atoms PTRAJ: image origin center Mask [*] represents 167375 atoms PTRAJ: strip :WAT Mask [:WAT] represents 159390 atoms PTRAJ: strip :Na+ Mask [:Na+] represents 15 atoms PTRAJ: trajout MD.binpos binpos PTRAJ: rms reference out rec.mdcrd :1-472@CA,C,N WARNING in ptraj(), rms to reference: missing reference structure. Set this prior to this rms with the command "reference" Ignoring command... PTRAJ: rms reference out 473.mdcrd :473 WARNING in ptraj(), rms to reference: missing reference structure. Set this prior to this rms with the command "reference" Ignoring command... PTRAJ: rms reference out 474.mdcrd :474 WARNING in ptraj(), rms to reference: missing reference structure. Set this prior to this rms with the command "reference" Ignoring command... PTRAJ: rms reference out 475.mdcrd :475 WARNING in ptraj(), rms to reference: missing reference structure. Set this prior to this rms with the command "reference" Ignoring command... PTRAJ: rms reference out 476.mdcrd :476 WARNING in ptraj(), rms to reference: missing reference structure. Set this prior to this rms with the command "reference" Ignoring command... PTRAJ: Successfully read the input file. Coordinate processing will occur on 300 frames. Summary of I/O and actions follows: INPUT COORDINATE FILES File (../heat.mdcrd) is an AMBER trajectory (with box info) with 100 sets File (../density.mdcrd) is an AMBER trajectory (with box info) with 100 sets File (../equil.mdcrd) is an AMBER trajectory (with box info) with 100 sets OUTPUT COORDINATE FILE File (MD.binpos) is a BINPOS file ACTIONS 1> CENTER to origin via center of geometry, atom selection follows :1-476 2> IMAGE by molecule to origin using the center of mass, atom selection * (All atoms are selected) 3> STRIP: 159390 atoms will be removed from trajectory: :492-53621 4> STRIP: 15 atoms will be removed from trajectory: :477-491 Processing AMBER trajectory file ../heat.mdcrd Set 1 ................................................. Set 50 ................................................. Set 100 Processing AMBER trajectory file ../density.mdcrd Set 1 ................................................. Set 50 ................................................. Set 100 Processing AMBER trajectory file ../equil.mdcrd Set 1 ................................................. Set 50 ................................................. Set 100 PTRAJ: Successfully read in 300 sets and processed 300 sets. Dumping accumulated results (if any)