\-/ -/- PTRAJ: a utility for processing trajectory files /-\ \-/ Version: "AMBER 10.0 integrated" (2/15/2008) -/- Executable is: "/root/Documents/amber10/exe/ptraj" /-\ \-/ Residue labels: LYS GLY LYS LEU PRO PRO GLY PRO THR PRO LEU PRO PHE ILE GLY ASN TYR LEU GLN LEU ASN THR GLU GLN MET TYR ASN SER LEU MET LYS ILE SER GLU ARG TYR GLY PRO VAL PHE THR ILE HIE LEU GLY PRO ARG ARG VAL VAL VAL LEU CYS GLY HIE ASP ALA VAL ARG GLU ALA LEU VAL ASP GLN ALA GLU GLU PHE SER GLY ARG GLY GLU GLN ALA THR PHE ASP TRP VAL PHE LYS GLY TYR GLY VAL VAL PHE SER ASN GLY GLU ARG ALA LYS GLN LEU ARG ARG PHE SER ILE ALA THR LEU ARG ASP PHE GLY VAL GLY LYS ARG GLY ILE GLU GLU ARG ILE GLN GLU GLU ALA GLY PHE LEU ILE ASP ALA LEU ARG GLY THR GLY GLY ALA ASN ILE ASP PRO THR PHE PHE LEU SER ARG THR VAL SER ASN VAL ILE SER SER ILE VAL PHE GLY ASP ARG PHE ASP TYR LYS ASP LYS GLU PHE LEU SER LEU LEU ARG MET MET LEU GLY ILE PHE GLN PHE THR SER THR SER THR GLY GLN LEU TYR GLU MET PHE SER SER VAL MET LYS HIP LEU PRO GLY PRO GLN GLN GLN ALA PHE GLN LEU LEU GLN GLY LEU GLU ASP PHE ILE ALA LYS LYS VAL GLU HIE ASN GLN ARG THR LEU ASP PRO ASN SER PRO ARG ASP PHE ILE ASP SER PHE LEU ILE ARG MET GLN GLU GLU GLU LYS ASN PRO ASN THR GLU PHE TYR LEU LYS ASN LEU VAL MET THR THR LEU ASN LEU PHE ILE GLY GLY THR GLU THR VAL SER THR THR LEU ARG TYR GLY PHE LEU LEU LEU MET LYS HIE PRO GLU VAL GLU ALA LYS VAL HID GLU GLU ILE ASP ARG VAL ILE GLY LYS ASN ARG GLN PRO LYS PHE GLU ASP ARG ALA LYS MET PRO TYR MET GLU ALA VAL ILE HIE GLU ILE GLN ARG PHE GLY ASP VAL ILE PRO MET SER LEU ALA ARG ARG VAL LYS LYS ASP THR LYS PHE ARG ASP PHE PHE LEU PRO LYS GLY THR GLU VAL TYR PRO MET LEU GLY SER VAL LEU ARG ASP PRO SER PHE PHE SER ASN PRO GLN ASP PHE ASN PRO GLN HIE PHE LEU ASN GLU LYS GLY GLN PHE LYS LYS SER ASP ALA PHE VAL PRO PHE SER ILE GLY LYS ARG ASN CYH PHE GLY GLU GLY LEU ALA ARG MET GLU LEU PHE LEU PHE PHE THR THR VAL MET GLN ASN PHE ARG LEU LYS SER SER GLN SER PRO LYS ASP ILE ASP VAL SER PRO LYS HIP VAL GLY PHE ALA THR ILE PRO ARG ASN TYR THR MET SER PHE LEU PRO ARG Cl- Cl- Cl- Cl- Cl- Cl- Cl- WAT WAT WAT WAT WAT WAT 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 2a6_md2_nowat.mdcrd Checking coordinates: 2a6_md2_nowat.mdcrd PTRAJ: donor mask :GLN@OE1 Mask [:GLN@OE1] represents 22 atoms PTRAJ: donor mask :GLN@NE2 Mask [:GLN@NE2] represents 22 atoms PTRAJ: donor mask :ASN@OD1 Mask [:ASN@OD1] represents 19 atoms PTRAJ: donor mask :ASN@ND2 Mask [:ASN@ND2] represents 19 atoms PTRAJ: donor mask :TYR@OH Mask [:TYR@OH] represents 11 atoms PTRAJ: donor mask :ASP@OD1 Mask [:ASP@OD1] represents 23 atoms PTRAJ: donor mask :ASP@OD2 Mask [:ASP@OD2] represents 23 atoms PTRAJ: donor mask :GLU@OE1 Mask [:GLU@OE1] represents 31 atoms PTRAJ: donor mask :GLU@OE2 Mask [:GLU@OE2] represents 31 atoms PTRAJ: donor mask :SER@OG Mask [:SER@OG] represents 28 atoms PTRAJ: donor mask :THR@OG1 Mask [:THR@OG1] represents 25 atoms PTRAJ: donor mask :HIS@ND1 Mask [:HIS@ND1] represents 0 atoms !!!NO ATOMS DETECTED!!! WARNING in ptraj, donor: No atoms selected (:HIS@ND1), ignoring... PTRAJ: donor mask :HIE@ND1 Mask [:HIE@ND1] represents 6 atoms PTRAJ: donor mask :HID@NE2 Mask [:HID@NE2] represents 1 atoms PTRAJ: acceptor mask :ASN@ND2 :ASN@HD21 Mask [:ASN@ND2] represents 19 atoms Mask [:ASN@HD21] represents 19 atoms PTRAJ: acceptor mask :ASN@ND2 :ASN@HD22 Mask [:ASN@ND2] represents 19 atoms Mask [:ASN@HD22] represents 19 atoms PTRAJ: acceptor mask :TYR@OH :TYR@HH Mask [:TYR@OH] represents 11 atoms Mask [:TYR@HH] represents 11 atoms PTRAJ: acceptor mask :GLN@NE2 :GLN@HE21 Mask [:GLN@NE2] represents 22 atoms Mask [:GLN@HE21] represents 22 atoms PTRAJ: acceptor mask :GLN@NE2 :GLN@HE22 Mask [:GLN@NE2] represents 22 atoms Mask [:GLN@HE22] represents 22 atoms PTRAJ: acceptor mask :TRP@NE1 :TRP@HE1 Mask [:TRP@NE1] represents 1 atoms Mask [:TRP@HE1] represents 1 atoms PTRAJ: acceptor mask :LYS@NZ :LYS@HZ1 Mask [:LYS@NZ] represents 29 atoms Mask [:LYS@HZ1] represents 29 atoms PTRAJ: acceptor mask :LYS@NZ :LYS@HZ2 Mask [:LYS@NZ] represents 29 atoms Mask [:LYS@HZ2] represents 29 atoms PTRAJ: acceptor mask :LYS@NZ :LYS@HZ3 Mask [:LYS@NZ] represents 29 atoms Mask [:LYS@HZ3] represents 29 atoms PTRAJ: acceptor mask :SER@OG :SER@HG Mask [:SER@OG] represents 28 atoms Mask [:SER@HG] represents 28 atoms PTRAJ: acceptor mask :THR@OG1 :THR@HG1 Mask [:THR@OG1] represents 25 atoms Mask [:THR@HG1] represents 25 atoms PTRAJ: acceptor mask :ARG@NH2 :ARG@HH21 Mask [:ARG@NH2] represents 32 atoms Mask [:ARG@HH21] represents 32 atoms PTRAJ: acceptor mask :ARG@NH2 :ARG@HH22 Mask [:ARG@NH2] represents 32 atoms Mask [:ARG@HH22] represents 32 atoms PTRAJ: acceptor mask :ARG@NH1 :ARG@HH11 Mask [:ARG@NH1] represents 32 atoms Mask [:ARG@HH11] represents 32 atoms PTRAJ: acceptor mask :ARG@NH1 :ARG@HH12 Mask [:ARG@NH1] represents 32 atoms Mask [:ARG@HH12] represents 32 atoms PTRAJ: acceptor mask :ARG@NE :ARG@HE Mask [:ARG@NE] represents 32 atoms Mask [:ARG@HE] represents 32 atoms PTRAJ: acceptor mask :HIS@NE2 :HIS@HE2 Mask [:HIS@NE2] represents 0 atoms !!!NO ATOMS DETECTED!!! Mask [:HIS@HE2] represents 0 atoms !!!NO ATOMS DETECTED!!! WARNING in ptraj, acceptor: No heavy atom was selected (:HIS@NE2), ignoring... WARNING in ptraj, acceptor: No hydrogen atom was selected (:HIS@HE2), ignoring... PTRAJ: acceptor mask :HIE@NE2 :HIE@HE2 Mask [:HIE@NE2] represents 6 atoms Mask [:HIE@HE2] represents 6 atoms PTRAJ: acceptor mask :HID@ND1 :HID@HD1 Mask [:HID@ND1] represents 1 atoms Mask [:HID@HD1] represents 1 atoms PTRAJ: acceptor mask :HIP@ND1,NE2 :HIP@HE2,HD1 Mask [:HIP@ND1,NE2] represents 4 atoms Mask [:HIP@HE2,HD1] represents 4 atoms PTRAJ: donor mask @O Mask [@O] represents 15851 atoms PTRAJ: acceptor mask :2-4,7,9,11,13-37,39-45,47-140,142-201,203,205-231,233-234,236-252,254-291,293-311,313-320,322-337,339-356,358-363,365-372,374-378,380-383,385-401,403-438,440-445,447-454,456-463,465@N :2-465@H Mask [:2-4,7,9,11,13-37,39-45,47-140,142-201,203,205-231,233-234,236-252,254-291,293-311,313-320,322-337,339-356,358-363,365-372,374-378,380-383,385-401,403-438,440-445,447-454,456-463,465@N] represents 437 atoms Mask [:2-465@H] represents 437 atoms PTRAJ: donor mask @OXT Mask [@OXT] represents 1 atoms PTRAJ: acceptor mask :1@N :1@H1 Mask [:1@N] represents 1 atoms Mask [:1@H1] represents 1 atoms PTRAJ: acceptor mask :1@N :1@H2 Mask [:1@N] represents 1 atoms Mask [:1@H2] represents 1 atoms PTRAJ: acceptor mask :1@N :1@H3 Mask [:1@N] represents 1 atoms Mask [:1@H3] represents 1 atoms PTRAJ: hbond print .25 series hbt [No output trajectory specified (trajout)] PTRAJ: Successfully read the input file. Coordinate processing will occur on 349 frames. Summary of I/O and actions follows: INPUT COORDINATE FILES File (2a6_md2_nowat.mdcrd) is an AMBER trajectory with 349 sets NO OUTPUT COORDINATE FILE WAS SPECIFIED ACTIONS 1> HBOND saved to series hbt, inter-solvent hbonds will not be included, data will be sorted, intra-residue interactions will NOT be included, Distance cutoff is 3.00 angstroms, angle cutoff is 120.00 degrees Hydrogen bond information will be dumped for occupancies > 0.25 Estimated memory usage for this hbond call: 53.41 GB donors: 16113 acceptors: 845 frames: 349 Processing AMBER trajectory file 2a6_md2_nowat.mdcrd Set 1 .................................