\-/ -/- PTRAJ: a utility for processing trajectory files /-\ \-/ Version: "AMBER 11.0 integrated" (4/2010) -/- Executable is: "ptraj" /-\ Running on 1 processor(s) \-/ Residue labels: MET GLU ILE LYS ARG PHE GLY ARG ILE ARG GLU VAL ILE PRO LEU PRO PRO LEU THR GLU ILE GLN VAL GLU SER TYR ARG ARG ALA LEU GLN ALA ASP VAL PRO PRO GLU LYS ARG GLU ASN VAL GLY ILE GLN ALA ALA PHE ARG GLU THR PHE PRO ILE GLU GLU GLU ASP LYS GLY LYS GLY GLY LEU VAL LEU ASP PHE LEU GLU TYR ARG LEU GLY GLU PRO PRO PHE PRO GLN ASP GLU CYS ARG GLU LYS ASP LEU THR TYR GLN ALA PRO LEU TYR ALA ARG LEU GLN LEU ILE HIE LYS ASP THR GLY LEU ILE LYS GLU ASP GLU VAL PHE LEU GLY HIE ILE PRO LEU MET THR GLU ASP GLY SER PHE ILE ILE ASN GLY ALA ASP ARG VAL ILE VAL SER GLN ILE HIE ARG SER PRO GLY VAL TYR PHE THR PRO ASP PRO ALA ARG PRO GLY ARG TYR ILE ALA SER ILE ILE PRO LEU PRO LYS ARG GLY PRO TRP ILE ASP LEU GLU VAL GLU PRO ASN GLY VAL VAL SER MET LYS VAL ASN LYS ARG LYS PHE PRO LEU VAL LEU LEU LEU ARG VAL LEU GLY TYR ASP GLN GLU THR LEU ALA ARG GLU LEU GLY ALA TYR GLY GLU LEU VAL GLN GLY LEU MET ASP GLU SER VAL PHE ALA MET ARG PRO GLU GLU ALA LEU ILE ARG LEU PHE THR LEU LEU ARG PRO GLY ASP PRO PRO LYS ARG ASP LYS ALA VAL ALA TYR VAL TYR GLY LEU ILE ALA ASP PRO ARG ARG TYR ASP LEU GLY GLU ALA GLY ARG TYR LYS ALA GLU GLU LYS LEU GLY ILE ARG LEU SER GLY ARG THR LEU ALA ARG PHE GLU ASP GLY GLU PHE LYS ASP GLU VAL PHE LEU PRO THR LEU ARG TYR LEU PHE ALA LEU THR ALA GLY VAL PRO GLY HIE GLU VAL ASP ASP ILE ASP HIE LEU GLY ASN ARG ARG ILE ARG THR VAL GLY GLU LEU MET THR ASP GLN PHE ARG VAL GLY LEU ALA ARG LEU ALA ARG GLY VAL ARG GLU ARG MET LEU MET GLY SER GLU ASP SER LEU THR PRO ALA LYS LEU VAL ASN SER ARG PRO LEU GLU ALA ALA ILE ARG GLU PHE PHE SER ARG SER GLN LEU SER GLN PHE LYS ASP GLU THR ASN PRO LEU SER SER LEU ARG HIE LYS ARG ARG ILE SER ALA LEU GLY PRO GLY GLY LEU THR ARG GLU ARG ALA GLY PHE ASP VAL ARG ASP VAL HIE ARG THR HIE TYR GLY ARG ILE CYS PRO VAL GLU THR PRO GLU GLY ALA ASN ILE GLY LEU ILE THR SER LEU ALA ALA TYR ALA ARG VAL ASP GLU LEU GLY PHE ILE ARG THR PRO TYR ARG ARG VAL VAL GLY GLY VAL VAL THR ASP GLU VAL VAL TYR MET THR ALA THR GLU GLU ASP ARG TYR THR ILE ALA GLN ALA ASN THR PRO LEU GLU GLY ASN ARG ILE ALA ALA GLU ARG VAL VAL ALA ARG ARG LYS GLY GLU PRO VAL ILE VAL SER PRO GLU GLU VAL GLU PHE MET ASP VAL SER PRO LYS GLN VAL PHE SER VAL ASN THR ASN LEU ILE PRO PHE LEU GLU HIE ASP ASP ALA ASN ARG ALA LEU MET GLY SER ASN MET GLN THR GLN ALA VAL PRO LEU ILE ARG ALA GLN ALA PRO VAL VAL MET THR GLY LEU GLU GLU ARG VAL VAL ARG ASP SER LEU ALA ALA LEU TYR ALA GLU GLU ASP GLY GLU VAL ALA LYS VAL ASP GLY ASN ARG ILE VAL VAL ARG TYR GLU ASP GLY ARG LEU VAL GLU TYR PRO LEU ARG ARG PHE TYR ARG SER ASN GLN GLY THR ALA LEU ASP GLN ARG PRO ARG VAL VAL VAL GLY GLN ARG VAL ARG LYS GLY ASP LEU LEU ALA ASP GLY PRO ALA SER GLU ASN GLY PHE LEU ALA LEU GLY GLN ASN VAL LEU VAL ALA ILE MET PRO PHE ASP GLY TYR ASN PHE GLU ASP ALA ILE VAL ILE SER GLU GLU LEU LEU LYS ARG ASP PHE TYR THR SER ILE HIE ILE GLU ARG TYR GLU ILE GLU ALA ARG ASP THR LYS LEU GLY PRO GLU ARG ILE THR ARG ASP ILE PRO HIE LEU SER GLU ALA ALA LEU ARG ASP LEU ASP GLU GLU GLY VAL VAL ARG ILE GLY ALA GLU VAL LYS PRO GLY ASP ILE LEU VAL GLY ARG THR SER PHE LYS GLY GLU SER GLU PRO THR PRO GLU GLU ARG LEU LEU ARG SER ILE PHE GLY GLU LYS ALA ARG ASP VAL LYS ASP THR SER LEU ARG VAL PRO PRO GLY GLU GLY GLY ILE VAL VAL ARG THR VAL ARG LEU ARG ARG GLY ASP PRO GLY VAL GLU LEU LYS PRO GLY VAL ARG GLU VAL VAL ARG VAL TYR VAL ALA GLN LYS ARG LYS LEU GLN VAL GLY ASP LYS LEU ALA ASN ARG HIE GLY ASN LYS GLY VAL VAL ALA LYS ILE LEU PRO VAL GLU ASP MET PRO HIE LEU PRO ASP GLY THR PRO VAL ASP VAL ILE LEU ASN PRO LEU GLY VAL PRO SER ARG MET ASN LEU GLY GLN ILE LEU GLU THR HIE LEU GLY LEU ALA GLY TYR PHE LEU GLY GLN ARG TYR ILE SER PRO ILE PHE ASP GLY ALA LYS GLU PRO GLU ILE LYS GLU LEU LEU ALA GLN ALA PHE GLU VAL TYR PHE GLY LYS ARG LYS GLY GLU GLY PHE GLY VAL ASP LYS ARG GLU VAL GLU VAL LEU ARG ARG ALA GLU LYS LEU GLY LEU VAL THR PRO GLY LYS THR PRO GLU GLU GLN LEU LYS GLU LEU PHE LEU GLN GLY LYS VAL VAL LEU TYR ASP GLY ARG THR GLY GLU PRO ILE GLU GLY PRO ILE VAL VAL GLY GLN MET PHE ILE MET LYS LEU TYR HIE MET VAL GLU ASP LYS MET HIE ALA ARG SER THR GLY PRO TYR SER LEU ILE THR GLN GLN PRO LEU GLY GLY LYS ALA GLN PHE GLY GLY GLN ARG PHE GLY GLU MET GLU VAL TRP ALA LEU GLU ALA TYR GLY ALA ALA HIE THR LEU GLN GLU MET LEU THR LEU LYS SER ASP ASP ILE GLU GLY ARG ASN ALA ALA TYR GLU ALA ILE ILE LYS GLY GLU ASP VAL PRO GLU PRO SER VAL PRO GLU SER PHE ARG VAL LEU VAL LYS GLU LEU GLN ALA LEU ALA LEU ASP VAL GLN THR LEU ASP GLU LYS ASP ASN PRO VAL ASP ILE PHE GLU GLY LEU ALA SER LYS ARG LYS LYS GLU VAL ARG LYS VAL ARG ILE ALA LEU ALA SER PRO GLU LYS ILE ARG SER TRP SER TYR GLY GLU VAL GLU LYS PRO GLU THR ILE ASN TYR ARG THR LEU LYS PRO GLU ARG ASP GLY LEU PHE ASP GLU ARG ILE PHE GLY PRO ILE LYS ASP TYR GLU CYS ALA CYS GLY LYS TYR LYS ARG GLN ARG PHE GLU GLY LYS VAL CYS GLU ARG CYS GLY VAL GLU VAL THR LYS SER ILE VAL ARG ARG TYR ARG MET GLY HIE ILE GLU LEU ALA THR PRO ALA ALA HIE ILE TRP PHE VAL LYS ASP VAL PRO SER LYS ILE GLY THR LEU LEU ASP LEU SER ALA THR GLU LEU GLU GLN VAL LEU TYR PHE SER LYS TYR ILE VAL LEU ASP PRO LYS GLY ALA ILE LEU ASN GLY VAL PRO VAL GLU LYS ARG GLN LEU LEU THR ASP GLU GLU TYR ARG GLU LEU ARG TYR GLY LYS GLN GLU THR TYR PRO LEU PRO PRO GLY VAL ASP ALA LEU VAL LYS ASP GLY GLU GLU VAL VAL LYS GLY GLN GLU LEU ALA PRO GLY VAL VAL SER ARG LEU ASP GLY VAL ALA LEU TYR ARG PHE ALA SER ILE LEU VAL VAL LYS ALA ARG VAL TYR PRO PHE GLU ASP ASP VAL GLU VAL SER THR GLY ASP ARG VAL ALA PRO GLY ASP VAL LEU ALA ASP GLY GLY LYS VAL LYS SER ASP VAL TYR GLY ARG VAL GLU VAL ASP LEU VAL ARG ASN VAL VAL ARG VAL VAL GLU SER TYR ASP ILE ASP ALA ARG MET GLY ALA GLU ALA ILE GLN GLN LEU LEU LYS GLU LEU ASP LEU GLU ALA LEU GLU LYS GLU LEU LEU GLU GLU MET LYS HIE PRO SER ARG ALA ARG ARG ALA LYS ALA ARG LYS ARG LEU GLU VAL VAL ARG ALA PHE LEU ASP SER GLY ASN ARG PRO GLU TRP MET ILE LEU GLU ALA VAL PRO VAL LEU PRO PRO ASP LEU ARG PRO MET VAL GLN VAL ASP GLY GLY ARG PHE ALA THR SER ASP LEU ASN ASP LEU TYR ARG ARG LEU ILE ASN ARG ASN ASN ARG LEU LYS LYS LEU LEU ALA GLN GLY ALA PRO GLU ILE ILE ILE ARG ASN GLU LYS ARG MET LEU GLN GLU ALA VAL ASP ALA LEU LEU ASP ASN GLY ARG ARG GLY ALA PRO VAL THR ASN PRO GLY SER ASP ARG PRO LEU ARG SER LEU THR ASP ILE LEU SER GLY LYS GLN GLY ARG PHE ARG GLN ASN LEU LEU GLY LYS ARG VAL ASP TYR SER GLY ARG SER VAL ILE VAL VAL GLY PRO GLN LEU LYS LEU HIE GLN CYS GLY LEU PRO LYS ARG MET ALA LEU GLU LEU PHE LYS PRO PHE LEU LEU LYS LYS MET GLU GLU LYS GLY ILE ALA PRO ASN VAL LYS ALA ALA ARG ARG MET LEU GLU ARG GLN ARG ASP ILE LYS ASP GLU VAL TRP ASP ALA LEU GLU GLU VAL ILE HIE GLY LYS VAL VAL LEU LEU ASN ARG ALA PRO THR LEU HIE ARG LEU GLY ILE GLN ALA PHE GLN PRO VAL LEU VAL GLU GLY GLN SER ILE GLN LEU HIE PRO LEU VAL CYS GLU ALA PHE ASN ALA ASP PHE ASP GLY ASP GLN MET ALA VAL HIE VAL PRO LEU SER SER PHE ALA GLN ALA GLU ALA ARG ILE GLN MET LEU SER ALA HIE ASN LEU LEU SER PRO ALA SER GLY GLU PRO LEU ALA LYS PRO SER ARG ASP ILE ILE LEU GLY LEU TYR TYR ILE THR GLN VAL ARG LYS GLU LYS LYS GLY ALA GLY LEU GLU PHE ALA THR PRO GLU GLU ALA LEU ALA ALA HIE GLU ARG GLY GLU VAL ALA LEU ASN ALA PRO ILE LYS VAL ALA GLY ARG GLU THR SER VAL GLY ARG LEU LYS TYR VAL PHE ALA ASN PRO ASP GLU ALA LEU LEU ALA VAL ALA HIE GLY ILE VAL ASP LEU GLN ASP VAL VAL THR VAL ARG TYR MET GLY LYS ARG LEU GLU THR SER PRO GLY ARG ILE LEU PHE ALA ARG ILE VAL ALA GLU ALA VAL GLU ASP GLU LYS VAL ALA TRP GLU LEU ILE GLN LEU ASP VAL PRO GLN GLU LYS ASN SER LEU LYS ASP LEU VAL TYR GLN ALA PHE LEU ARG LEU GLY MET GLU LYS THR ALA ARG LEU LEU ASP ALA LEU LYS TYR TYR GLY PHE THR PHE SER THR THR SER GLY ILE THR ILE GLY ILE ASP ASP ALA VAL ILE PRO GLU GLU LYS LYS GLN TYR LEU GLU GLU ALA ASP ARG LYS LEU LEU GLN ILE GLU GLN ALA TYR GLU MET GLY PHE LEU THR ASP ARG GLU ARG TYR ASP GLN ILE LEU GLN LEU TRP THR GLU THR THR GLU LYS VAL THR GLN ALA VAL PHE LYS ASN PHE GLU GLU ASN TYR PRO PHE ASN PRO LEU TYR VAL MET ALA GLN SER GLY ALA ARG GLY ASN PRO GLN GLN ILE ARG GLN LEU CYS GLY LEU ARG GLY LEU MET GLN LYS PRO SER GLY GLU THR PHE GLU VAL PRO VAL ARG SER SER PHE ARG GLU GLY LEU THR VAL LEU GLU TYR PHE ILE SER SER HIE GLY ALA ARG LYS GLY GLY ALA ASP THR ALA LEU ARG THR ALA ASP SER GLY TYR LEU THR ARG LYS LEU VAL ASP VAL THR HIE GLU ILE VAL VAL ARG GLU ALA ASP CYS GLY THR THR ASN TYR ILE SER VAL PRO LEU PHE GLN PRO ASP GLU VAL THR ARG SER LEU ARG LEU ARG LYS ARG ALA ASP ILE GLU ALA GLY LEU TYR GLY ARG VAL LEU ALA ARG GLU VAL GLU VAL LEU GLY VAL ARG LEU GLU GLU GLY ARG TYR LEU SER MET ASP ASP VAL HIE LEU LEU ILE LYS ALA ALA GLU ALA GLY GLU ILE GLN GLU VAL PRO VAL ARG SER PRO LEU THR CYS GLN THR ARG TYR GLY VAL CYS GLN LYS CYS TYR GLY TYR ASP LEU SER MET ALA ARG PRO VAL SER ILE GLY GLU ALA VAL GLY ILE VAL ALA ALA GLN SER ILE GLY GLU PRO GLY THR GLN LEU THR MET ARG THR PHE HIE THR GLY GLY VAL ALA GLY ALA ALA ASP ILE THR GLN GLY LEU PRO ARG VAL ILE GLU LEU PHE GLU ALA ARG ARG PRO LYS ALA LYS ALA VAL ILE SER GLU ILE ASP GLY VAL VAL ARG ILE GLU GLU THR GLU GLU LYS LEU SER VAL PHE VAL GLU SER GLU GLY PHE SER LYS GLU TYR LYS LEU PRO LYS GLU ALA ARG LEU LEU VAL LYS ASP GLY ASP TYR VAL GLU ALA GLY GLN PRO LEU THR ARG GLY ALA ILE ASP PRO HIE GLN LEU LEU GLU ALA LYS GLY PRO GLU ALA VAL GLU ARG TYR LEU VAL GLU GLU ILE GLN LYS VAL TYR ARG ALA GLN GLY VAL LYS LEU HIE ASP LYS HIE ILE GLU ILE VAL VAL ARG GLN MET MET LYS TYR VAL GLU VAL THR ASP PRO GLY ASP SER ARG LEU LEU GLU GLY GLN VAL LEU GLU LYS TRP ASP VAL GLU ALA LEU ASN GLU ARG LEU ILE ALA GLU GLY LYS THR PRO VAL ALA TRP LYS PRO LEU LEU MET GLY VAL THR LYS SER ALA LEU SER THR LYS SER TRP LEU SER ALA ALA SER PHE GLN ASN THR THR HIE VAL LEU THR GLU ALA ALA ILE ALA GLY LYS LYS ASP GLU LEU ILE GLY LEU LYS GLU ASN VAL ILE LEU GLY ARG LEU ILE PRO ALA GLY THR GLY SER ASP PHE VAL ARG PHE THR GLN VAL VAL ASP GLN LYS THR LEU LYS ALA ILE GLU GLU ALA ARG LYS GLU ALA VAL GLU ALA DC5 DC DC DT DG DT DC DT DG DG DC DG DT DT DC DG DC DG DC DG DC DC DG3 RG5 RA RG RU RC RU RG RC RG RG RC RG RC RG RC RG3 DA5 DC DG DC DC DA DG DA DC DA DG DG DG3 MG2 MG2 atp Na+ Na+ Na+ Na+ Na+ Na+ 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 WAT PRMTOP does not contain %FLAG RADIUS_SET Setting box to be an exact truncated octahedron, angle is 109.471221 PTRAJ: Processing input from "STDIN" ... PTRAJ: trajin 11RNAP_openMD37.mdcrd Checking coordinates: 11RNAP_openMD37.mdcrd Rank: 0 Atoms: 230188 FrameSize: 5593594 TitleSize: 30 NumBox: 3 Seekable 1 PTRAJ: center :1-2495 mass origin Mask [:1-2495] represents 40514 atoms PTRAJ: image origin center familiar Mask [*] represents 230188 atoms PTRAJ: distance first time 10 :2014@NZ :429@OD1 out 2014NZ_429OD1.txt Mask [:2014@NZ] represents 1 atoms Mask [:429@OD1] represents 1 atoms PTRAJ: go [No output trajectory specified (trajout)] PTRAJ: Successfully read the input file. Coordinate processing will occur on 38 frames. Summary of I/O and actions follows: INPUT COORDINATE FILES File (11RNAP_openMD37.mdcrd) is an AMBER trajectory (with box info) with 38 sets NO OUTPUT COORDINATE FILE WAS SPECIFIED ACTIONS 1> CENTER to origin via center of mass, atom selection follows :1-2495 2> IMAGE familiar by molecule to origin using the center of mass, atom selection * (All atoms are selected) IMAGE familiar, center is at origin 3> DISTANCE: between the atoms selections center of mass will be saved to array named first Processing AMBER trajectory file 11RNAP_openMD37.mdcrd ............... 75% ... 100% ./ptraj: line 1: 4573 Segmentation fault ptraj RNAP_open.prmtop