------------------------------------------------------------------------------- Amber2accent version 0.3 14:32, 17.08.2007 ------------------------------------------------------------------------------- Parameters: Using prmtop file prmtop Using trajectory file mdcrd Ptraj used to calculate BAT values Solute residues: 1 Root atoms will be selected automatically ------------------------------------------------------------------------------- Reading amber prmtop file 901 residue pointers read Atom map generated Connectivity table build Atoms 2, 1, 4 selected as Root atoms Bond, Angle, Torsional Tree for residue selection: 1 2 -1 -1 n 2 -1 -1 -1 n 3 1 2 4 i 4 1 2 -1 n 5 4 1 2 p 6 5 4 1 p 7 9 11 13 p 8 7 9 11 p 9 11 13 4 p 10 9 11 13 p 11 13 4 1 p 12 11 13 4 p 13 4 1 2 p 14 13 4 1 p 15 1 2 4 i ------------------------------------------------------------------------------- PTRAJ output: \-/ -/- PTRAJ: a utility for processing trajectory files /-\ \-/ Version: "AMBER 9.0 integrated" (April 2006) -/- Executable is: "ptraj" /-\ \-/ Residue labels: Checking coordinates: mdcrd MOL WAT WAT WAT WAT WAT WAT WAT WAT WAT WAT WAT WAT WAT WAT WAT WAT WAT WAT WAT ... WAT PTRAJ: Processing input from file ptraj1.in PTRAJ: trajin mdcrd PTRAJ: distance bond0001 @1 @2 out bond0001 Mask [@1] represents 1 atoms Mask [@2] represents 1 atoms PTRAJ: distance bond0003 @3 @1 out bond0003 Mask [@3] represents 1 atoms Mask [@1] represents 1 atoms PTRAJ: angle angle0003 @3 @1 @2 out angle0003 Mask [@3] represents 1 atoms Mask [@1] represents 1 atoms Mask [@2] represents 1 atoms PTRAJ: dihedral torsion0003 @3 @1 @2 @4 out torsion0003 Mask [@3] represents 1 atoms Mask [@1] represents 1 atoms Mask [@2] represents 1 atoms Mask [@4] represents 1 atoms PTRAJ: distance bond0004 @4 @1 out bond0004 Mask [@4] represents 1 atoms Mask [@1] represents 1 atoms PTRAJ: angle angle0004 @4 @1 @2 out angle0004 Mask [@4] represents 1 atoms Mask [@1] represents 1 atoms Mask [@2] represents 1 atoms PTRAJ: distance bond0005 @5 @4 out bond0005 Mask [@5] represents 1 atoms Mask [@4] represents 1 atoms PTRAJ: angle angle0005 @5 @4 @1 out angle0005 Mask [@5] represents 1 atoms Mask [@4] represents 1 atoms Mask [@1] represents 1 atoms PTRAJ: dihedral torsion0005 @5 @4 @1 @2 out torsion0005 Mask [@5] represents 1 atoms Mask [@4] represents 1 atoms Mask [@1] represents 1 atoms Mask [@2] represents 1 atoms PTRAJ: distance bond0006 @6 @5 out bond0006 Mask [@6] represents 1 atoms Mask [@5] represents 1 atoms PTRAJ: angle angle0006 @6 @5 @4 out angle0006 Mask [@6] represents 1 atoms Mask [@5] represents 1 atoms Mask [@4] represents 1 atoms PTRAJ: dihedral torsion0006 @6 @5 @4 @1 out torsion0006 Mask [@6] represents 1 atoms Mask [@5] represents 1 atoms Mask [@4] represents 1 atoms Mask [@1] represents 1 atoms PTRAJ: distance bond0007 @7 @9 out bond0007 Mask [@7] represents 1 atoms Mask [@9] represents 1 atoms PTRAJ: angle angle0007 @7 @9 @11 out angle0007 Mask [@7] represents 1 atoms Mask [@9] represents 1 atoms Mask [@11] represents 1 atoms PTRAJ: dihedral torsion0007 @7 @9 @11 @13 out torsion0007 Mask [@7] represents 1 atoms Mask [@9] represents 1 atoms Mask [@11] represents 1 atoms Mask [@13] represents 1 atoms PTRAJ: distance bond0008 @8 @7 out bond0008 Mask [@8] represents 1 atoms Mask [@7] represents 1 atoms PTRAJ: angle angle0008 @8 @7 @9 out angle0008 Mask [@8] represents 1 atoms Mask [@7] represents 1 atoms Mask [@9] represents 1 atoms PTRAJ: dihedral torsion0008 @8 @7 @9 @11 out torsion0008 Mask [@8] represents 1 atoms Mask [@7] represents 1 atoms Mask [@9] represents 1 atoms Mask [@11] represents 1 atoms PTRAJ: distance bond0009 @9 @11 out bond0009 Mask [@9] represents 1 atoms Mask [@11] represents 1 atoms PTRAJ: angle angle0009 @9 @11 @13 out angle0009 Mask [@9] represents 1 atoms Mask [@11] represents 1 atoms Mask [@13] represents 1 atoms PTRAJ: dihedral torsion0009 @9 @11 @13 @4 out torsion0009 Mask [@9] represents 1 atoms Mask [@11] represents 1 atoms Mask [@13] represents 1 atoms Mask [@4] represents 1 atoms PTRAJ: distance bond0010 @10 @9 out bond0010 Mask [@10] represents 1 atoms Mask [@9] represents 1 atoms PTRAJ: angle angle0010 @10 @9 @11 out angle0010 Mask [@10] represents 1 atoms Mask [@9] represents 1 atoms Mask [@11] represents 1 atoms PTRAJ: dihedral torsion0010 @10 @9 @11 @13 out torsion0010 Mask [@10] represents 1 atoms Mask [@9] represents 1 atoms Mask [@11] represents 1 atoms Mask [@13] represents 1 atoms PTRAJ: distance bond0011 @11 @13 out bond0011 Mask [@11] represents 1 atoms Mask [@13] represents 1 atoms PTRAJ: angle angle0011 @11 @13 @4 out angle0011 Mask [@11] represents 1 atoms Mask [@13] represents 1 atoms Mask [@4] represents 1 atoms PTRAJ: dihedral torsion0011 @11 @13 @4 @1 out torsion0011 Mask [@11] represents 1 atoms Mask [@13] represents 1 atoms Mask [@4] represents 1 atoms Mask [@1] represents 1 atoms PTRAJ: distance bond0012 @12 @11 out bond0012 Mask [@12] represents 1 atoms Mask [@11] represents 1 atoms PTRAJ: angle angle0012 @12 @11 @13 out angle0012 Mask [@12] represents 1 atoms Mask [@11] represents 1 atoms Mask [@13] represents 1 atoms PTRAJ: dihedral torsion0012 @12 @11 @13 @4 out torsion0012 Mask [@12] represents 1 atoms Mask [@11] represents 1 atoms Mask [@13] represents 1 atoms Mask [@4] represents 1 atoms PTRAJ: distance bond0013 @13 @4 out bond0013 Mask [@13] represents 1 atoms Mask [@4] represents 1 atoms PTRAJ: angle angle0013 @13 @4 @1 out angle0013 Mask [@13] represents 1 atoms Mask [@4] represents 1 atoms Mask [@1] represents 1 atoms PTRAJ: dihedral torsion0013 @13 @4 @1 @2 out torsion0013 Mask [@13] represents 1 atoms Mask [@4] represents 1 atoms Mask [@1] represents 1 atoms Mask [@2] represents 1 atoms PTRAJ: distance bond0014 @14 @13 out bond0014 Mask [@14] represents 1 atoms Mask [@13] represents 1 atoms PTRAJ: angle angle0014 @14 @13 @4 out angle0014 Mask [@14] represents 1 atoms Mask [@13] represents 1 atoms Mask [@4] represents 1 atoms PTRAJ: dihedral torsion0014 @14 @13 @4 @1 out torsion0014 Mask [@14] represents 1 atoms Mask [@13] represents 1 atoms Mask [@4] represents 1 atoms Mask [@1] represents 1 atoms PTRAJ: distance bond0015 @15 @1 out bond0015 Mask [@15] represents 1 atoms Mask [@1] represents 1 atoms PTRAJ: angle angle0015 @15 @1 @2 out angle0015 Mask [@15] represents 1 atoms Mask [@1] represents 1 atoms Mask [@2] represents 1 atoms PTRAJ: dihedral torsion0015 @15 @1 @2 @4 out torsion0015 Mask [@15] represents 1 atoms Mask [@1] represents 1 atoms Mask [@2] represents 1 atoms Mask [@4] represents 1 atoms [No output trajectory specified (trajout)] PTRAJ: Successfully read the input file. Coordinate processing will occur on 10 frames. Summary of I/O and actions follows: INPUT COORDINATE FILES File (mdcrd) is an AMBER trajectory (with box info) with 10 sets NO OUTPUT COORDINATE FILE WAS SPECIFIED ACTIONS 1> DISTANCE: between the atoms selections center of mass will be saved to array named bond0001 Atom selection 1 is :1@CB Atom selection 2 is :1@HB2 Data will be dumped to a file named bond0001 7> DISTANCE: between the atoms selections center of mass will be saved to array named bond0003 Atom selection 1 is :1@HB3 Atom selection 2 is :1@CB Data will be dumped to a file named bond0003 7> ANGLE: saved to array named angle0003 Atom selection 1 is :1@HB3 Atom selection 2 is :1@CB Atom selection 3 is :1@HB2 Data will be dumped to a file named angle0003 7> DIHEDRAL: saved to array named torsion0003 Atom selection 1 is :1@HB3 Atom selection 2 is :1@CB Atom selection 3 is :1@HB2 Atom selection 4 is :1@CG Data will be dumped to a file named torsion0003 7> DISTANCE: between the atoms selections center of mass will be saved to array named bond0004 Atom selection 1 is :1@CG Atom selection 2 is :1@CB Data will be dumped to a file named bond0004 7> ANGLE: saved to array named angle0004 Atom selection 1 is :1@CG Atom selection 2 is :1@CB Atom selection 3 is :1@HB2 Data will be dumped to a file named angle0004 7> DISTANCE: between the atoms selections center of mass will be saved to array named bond0005 Atom selection 1 is :1@CD1 Atom selection 2 is :1@CG Data will be dumped to a file named bond0005 7> ANGLE: saved to array named angle0005 Atom selection 1 is :1@CD1 Atom selection 2 is :1@CG Atom selection 3 is :1@CB Data will be dumped to a file named angle0005 7> DIHEDRAL: saved to array named torsion0005 Atom selection 1 is :1@CD1 Atom selection 2 is :1@CG Atom selection 3 is :1@CB Atom selection 4 is :1@HB2 Data will be dumped to a file named torsion0005 7> DISTANCE: between the atoms selections center of mass will be saved to array named bond0006 Atom selection 1 is :1@HD1 Atom selection 2 is :1@CD1 Data will be dumped to a file named bond0006 7> ANGLE: saved to array named angle0006 Atom selection 1 is :1@HD1 Atom selection 2 is :1@CD1 Atom selection 3 is :1@CG Data will be dumped to a file named angle0006 7> DIHEDRAL: saved to array named torsion0006 Atom selection 1 is :1@HD1 Atom selection 2 is :1@CD1 Atom selection 3 is :1@CG Atom selection 4 is :1@CB Data will be dumped to a file named torsion0006 7> DISTANCE: between the atoms selections center of mass will be saved to array named bond0007 Atom selection 1 is :1@CE1 Atom selection 2 is :1@CZ Data will be dumped to a file named bond0007 7> ANGLE: saved to array named angle0007 Atom selection 1 is :1@CE1 Atom selection 2 is :1@CZ Atom selection 3 is :1@CE2 Data will be dumped to a file named angle0007 7> DIHEDRAL: saved to array named torsion0007 Atom selection 1 is :1@CE1 Atom selection 2 is :1@CZ Atom selection 3 is :1@CE2 Atom selection 4 is :1@CD2 Data will be dumped to a file named torsion0007 7> DISTANCE: between the atoms selections center of mass will be saved to array named bond0008 Atom selection 1 is :1@HE1 Atom selection 2 is :1@CE1 Data will be dumped to a file named bond0008 7> ANGLE: saved to array named angle0008 Atom selection 1 is :1@HE1 Atom selection 2 is :1@CE1 Atom selection 3 is :1@CZ Data will be dumped to a file named angle0008 7> DIHEDRAL: saved to array named torsion0008 Atom selection 1 is :1@HE1 Atom selection 2 is :1@CE1 Atom selection 3 is :1@CZ Atom selection 4 is :1@CE2 Data will be dumped to a file named torsion0008 7> DISTANCE: between the atoms selections center of mass will be saved to array named bond0009 Atom selection 1 is :1@CZ Atom selection 2 is :1@CE2 Data will be dumped to a file named bond0009 7> ANGLE: saved to array named angle0009 Atom selection 1 is :1@CZ Atom selection 2 is :1@CE2 Atom selection 3 is :1@CD2 Data will be dumped to a file named angle0009 7> DIHEDRAL: saved to array named torsion0009 Atom selection 1 is :1@CZ Atom selection 2 is :1@CE2 Atom selection 3 is :1@CD2 Atom selection 4 is :1@CG Data will be dumped to a file named torsion0009 7> DISTANCE: between the atoms selections center of mass will be saved to array named bond0010 Atom selection 1 is :1@HZ Atom selection 2 is :1@CZ Data will be dumped to a file named bond0010 7> ANGLE: saved to array named angle0010 Atom selection 1 is :1@HZ Atom selection 2 is :1@CZ Atom selection 3 is :1@CE2 Data will be dumped to a file named angle0010 7> DIHEDRAL: saved to array named torsion0010 Atom selection 1 is :1@HZ Atom selection 2 is :1@CZ Atom selection 3 is :1@CE2 Atom selection 4 is :1@CD2 Data will be dumped to a file named torsion0010 7> DISTANCE: between the atoms selections center of mass will be saved to array named bond0011 Atom selection 1 is :1@CE2 Atom selection 2 is :1@CD2 Data will be dumped to a file named bond0011 7> ANGLE: saved to array named angle0011 Atom selection 1 is :1@CE2 Atom selection 2 is :1@CD2 Atom selection 3 is :1@CG Data will be dumped to a file named angle0011 7> DIHEDRAL: saved to array named torsion0011 Atom selection 1 is :1@CE2 Atom selection 2 is :1@CD2 Atom selection 3 is :1@CG Atom selection 4 is :1@CB Data will be dumped to a file named torsion0011 7> DISTANCE: between the atoms selections center of mass will be saved to array named bond0012 Atom selection 1 is :1@HE2 Atom selection 2 is :1@CE2 Data will be dumped to a file named bond0012 7> ANGLE: saved to array named angle0012 Atom selection 1 is :1@HE2 Atom selection 2 is :1@CE2 Atom selection 3 is :1@CD2 Data will be dumped to a file named angle0012 7> DIHEDRAL: saved to array named torsion0012 Atom selection 1 is :1@HE2 Atom selection 2 is :1@CE2 Atom selection 3 is :1@CD2 Atom selection 4 is :1@CG Data will be dumped to a file named torsion0012 7> DISTANCE: between the atoms selections center of mass will be saved to array named bond0013 Atom selection 1 is :1@CD2 Atom selection 2 is :1@CG Data will be dumped to a file named bond0013 7> ANGLE: saved to array named angle0013 Atom selection 1 is :1@CD2 Atom selection 2 is :1@CG Atom selection 3 is :1@CB Data will be dumped to a file named angle0013 7> DIHEDRAL: saved to array named torsion0013 Atom selection 1 is :1@CD2 Atom selection 2 is :1@CG Atom selection 3 is :1@CB Atom selection 4 is :1@HB2 Data will be dumped to a file named torsion0013 7> DISTANCE: between the atoms selections center of mass will be saved to array named bond0014 Atom selection 1 is :1@HD2 Atom selection 2 is :1@CD2 Data will be dumped to a file named bond0014 7> ANGLE: saved to array named angle0014 Atom selection 1 is :1@HD2 Atom selection 2 is :1@CD2 Atom selection 3 is :1@CG Data will be dumped to a file named angle0014 7> DIHEDRAL: saved to array named torsion0014 Atom selection 1 is :1@HD2 Atom selection 2 is :1@CD2 Atom selection 3 is :1@CG Atom selection 4 is :1@CB Data will be dumped to a file named torsion0014 7> DISTANCE: between the atoms selections center of mass will be saved to array named bond0015 Atom selection 1 is :1@H21 Atom selection 2 is :1@CB Data will be dumped to a file named bond0015 7> ANGLE: saved to array named angle0015 Atom selection 1 is :1@H21 Atom selection 2 is :1@CB Atom selection 3 is :1@HB2 Data will be dumped to a file named angle0015 7> DIHEDRAL: saved to array named torsion0015 Atom selection 1 is :1@H21 Atom selection 2 is :1@CB Atom selection 3 is :1@HB2 Atom selection 4 is :1@CG Data will be dumped to a file named torsion0015 Processing AMBER trajectory file mdcrd Set 1 .......... PTRAJ: Successfully read in 10 sets and processed 10 sets. Dumping accumulated results (if any) PTRAJ DISTANCE dumping distance bond0001 PTRAJ DISTANCE dumping distance bond0003 PTRAJ ANGLE dumping named values angle0003 PTRAJ DIHEDRAL dumping named values torsion0003 PTRAJ DISTANCE dumping distance bond0004 PTRAJ ANGLE dumping named values angle0004 PTRAJ DISTANCE dumping distance bond0005 PTRAJ ANGLE dumping named values angle0005 PTRAJ DIHEDRAL dumping named values torsion0005 PTRAJ DISTANCE dumping distance bond0006 PTRAJ ANGLE dumping named values angle0006 PTRAJ DIHEDRAL dumping named values torsion0006 PTRAJ DISTANCE dumping distance bond0007 PTRAJ ANGLE dumping named values angle0007 PTRAJ DIHEDRAL dumping named values torsion0007 PTRAJ DISTANCE dumping distance bond0008 PTRAJ ANGLE dumping named values angle0008 PTRAJ DIHEDRAL dumping named values torsion0008 PTRAJ DISTANCE dumping distance bond0009 PTRAJ ANGLE dumping named values angle0009 PTRAJ DIHEDRAL dumping named values torsion0009 PTRAJ DISTANCE dumping distance bond0010 PTRAJ ANGLE dumping named values angle0010 PTRAJ DIHEDRAL dumping named values torsion0010 PTRAJ DISTANCE dumping distance bond0011 PTRAJ ANGLE dumping named values angle0011 PTRAJ DIHEDRAL dumping named values torsion0011 PTRAJ DISTANCE dumping distance bond0012 PTRAJ ANGLE dumping named values angle0012 PTRAJ DIHEDRAL dumping named values torsion0012 PTRAJ DISTANCE dumping distance bond0013 PTRAJ ANGLE dumping named values angle0013 PTRAJ DIHEDRAL dumping named values torsion0013 PTRAJ DISTANCE dumping distance bond0014 PTRAJ ANGLE dumping named values angle0014 PTRAJ DIHEDRAL dumping named values torsion0014 PTRAJ DISTANCE dumping distance bond0015 PTRAJ ANGLE dumping named values angle0015 PTRAJ DIHEDRAL dumping named values torsion0015 ------------------------------------------------------------------------------- Outputting list of bond distances Outputting list of angles Outputting list of torsion values ------------------------------------------------------------------------------- Execution of amber2accent finished -------------------------------------------------------------------------------