\-/ -/- PTRAJ: a utility for processing trajectory files /-\ \-/ Version: "AMBER 12.0 integrated" (4/2012) -/- Executable is: "ptraj" /-\ Running on 1 processor(s) \-/ Residue labels: GLY LEU THR GLU GLU GLN ARG MET MET ILE ARG GLU LEU MET ASP ALA GLN MET LYS THR PHE ASP THR THR PHE SER HIE PHE LYS ASN PHE ARG LEU PRO GLY VAL LEU SER SER GLY CYS GLU LEU PRO GLU SER LEU GLN ALA PRO SER ARG GLU GLU ALA ALA LYS TRP SER GLN VAL ARG LYS ASP LEU CYS SER LEU LYS VAL SER LEU GLN LEU ARG GLY GLU ASP GLY SER VAL TRP ASN TYR LYS PRO PRO ALA ASP SER GLY GLY LYS GLU ILE PHE SER LEU LEU PRO HIE MET ALA ASP MET SER THR TYR MET PHE LYS GLY ILE ILE SER PHE ALA LYS VAL ILE SER TYR PHE ARG ASP LEU PRO ILE GLU ASP GLN ILE SER LEU LEU LYS GLY ALA ALA PHE GLU LEU CYS GLN LEU ARG PHE ASN THR VAL PHE ASN ALA GLU THR GLY THR TRP GLU CYS GLY ARG LEU SER TYR CYS LEU GLU ASP THR ALA GLY GLY PHE GLN GLN LEU LEU LEU GLU PRO MET LEU LYS PHE HIE TYR MET LEU LYS LYS LEU GLN LEU HIE GLU GLU GLU TYR VAL LEU MET GLN ALA ILE SER LEU PHE SER PRO ASP ARG PRO GLY VAL LEU GLN HIE ARG VAL VAL ASP GLN LEU GLN GLU GLN PHE ALA ILE THR LEU LYS SER TYR ILE GLU CYS ASN ARG PRO GLN PRO ALA HIE ARG PHE LEU PHE LEU LYS ILE MET ALA MET LEU THR GLU LEU ARG SER ILE ASN ALA GLN HIE THR GLN ARG LEU LEU ARG ILE GLN ASP ILE HIE PRO PHE ALA THR PRO LEU MET GLN GLU LEU PHE GLY ILE THR GLY SER Na+ Na+ Na+ WAT WAT WAT WAT WAT WAT WAT WAT WAT WAT WAT WAT WAT WAT ... WAT WAT WAT PTRAJ: Processing input from "STDIN" ... PTRAJ: trajin ../5md.crd Checking coordinates: ../5md.crd Rank: 0 Atoms: 49482 FrameSize: 1202438 TitleSize: 81 NumBox: 3 Seekable 1 PTRAJ: vector v1 :160@N ired :160@H Mask [:160@N] represents 1 atoms Mask [:160@H] represents 1 atoms PTRAJ: vector v2 :200@N ired :200@H Mask [:200@N] represents 1 atoms Mask [:200@H] represents 1 atoms PTRAJ: vector v3 :140@N ired :140@H Mask [:140@N] represents 1 atoms Mask [:140@H] represents 1 atoms PTRAJ: vector v4 :198@N ired :198@H Mask [:198@N] represents 1 atoms Mask [:198@H] represents 1 atoms PTRAJ: vector v5 :25@N ired :25@H Mask [:25@N] represents 1 atoms Mask [:25@H] represents 1 atoms PTRAJ: matrix ired name matired order 2 PTRAJ: analyze matrix matired order vecs 5 out ired_NH.vec [No output trajectory specified (trajout)] ../5md.crd: 2500 frames. PTRAJ: Successfully read the input file. Coordinate processing will occur on 2500 frames. Summary of I/O and actions follows: INPUT COORDINATE FILES File (../5md.crd) is an AMBER trajectory (with box info) with 2500 sets NO OUTPUT COORDINATE FILE WAS SPECIFIED ACTIONS 1> VECTOR: storage to array named v1 Calculate the vector between the center of mass of the two atom selections which follow (with the origin at the center of mass of the first) Atom selection 1 is :160@N Atom selection 2 is :160@H 2> VECTOR: storage to array named v2 Calculate the vector between the center of mass of the two atom selections which follow (with the origin at the center of mass of the first) Atom selection 1 is :200@N Atom selection 2 is :200@H 3> VECTOR: storage to array named v3 Calculate the vector between the center of mass of the two atom selections which follow (with the origin at the center of mass of the first) Atom selection 1 is :140@N Atom selection 2 is :140@H 4> VECTOR: storage to array named v4 Calculate the vector between the center of mass of the two atom selections which follow (with the origin at the center of mass of the first) Atom selection 1 is :198@N Atom selection 2 is :198@H 5> VECTOR: storage to array named v5 Calculate the vector between the center of mass of the two atom selections which follow (with the origin at the center of mass of the first) Atom selection 1 is :25@N Atom selection 2 is :25@H 6> MATRIX: Calculating ired matrix by atom using no mass weighting Order of Legendre polynomials: 2 Storing matrix on internal stack with name: matired ANALYZE 1> ANALYZE MATRIX: Analyzing matrix matired and dumping results to ired_NH.vec Calculating 5 eigenvectors and no thermodynamic data Calculating 5 eigenvectors and order parameters Processing AMBER trajectory file ../5md.crd 1% ............ 25% ............ 50% ............ 75% ............ 100% PTRAJ: Successfully read in 2500 sets and processed 2500 sets. Dumping accumulated results (if any) PTRAJ: Analyzing accumulated data ************************************ - Calculated iRed order parameters - ************************************ vector S2 ---------------------- 0 1.00000 1 1.00000 2 1.00000 3 1.00000 4 1.00000