setenv AMBERHOME /usr/local/amber/amber9 /usr/local/amber/amber9/exe/tleap -I: Adding /usr/local/amber/amber9/dat/leap/prep to search path. -I: Adding /usr/local/amber/amber9/dat/leap/lib to search path. -I: Adding /usr/local/amber/amber9/dat/leap/parm to search path. -I: Adding /usr/local/amber/amber9/dat/leap/cmd to search path. Welcome to LEaP! (no leaprc in search path) > source leaprc.ff99 ----- Source: /usr/local/amber/amber9/dat/leap/cmd/leaprc.ff99 ----- Source of /usr/local/amber/amber9/dat/leap/cmd/leaprc.ff99 done Log file: ./leap.log Loading parameters: /usr/local/amber/amber9/dat/leap/parm/parm99.dat Reading title: PARM99 for DNA,RNA,AA, organic molecules, TIP3P wat. Polariz.& LP incl.02/04/99 Loading library: /usr/local/amber/amber9/dat/leap/lib/all_nucleic94.lib Loading library: /usr/local/amber/amber9/dat/leap/lib/all_amino94.lib Loading library: /usr/local/amber/amber9/dat/leap/lib/all_aminoct94.lib Loading library: /usr/local/amber/amber9/dat/leap/lib/all_aminont94.lib Loading library: /usr/local/amber/amber9/dat/leap/lib/ions94.lib Loading library: /usr/local/amber/amber9/dat/leap/lib/solvents.lib > source leaprc.gaff ----- Source: /usr/local/amber/amber9/dat/leap/cmd/leaprc.gaff ----- Source of /usr/local/amber/amber9/dat/leap/cmd/leaprc.gaff done Log file: ./leap.log Loading parameters: /usr/local/amber/amber9/dat/leap/parm/gaff.dat Reading title: AMBER General Force Field for organic mol., add. info. at the end (June, 2003) > mol = loadpdb RET.pdb Loading PDB file: ./RET.pdb Unknown residue: RET number: 0 type: Terminal/last ..relaxing end constraints to try for a dbase match -no luck Creating new UNIT for residue: RET sequence: 132 Created a new atom named: N within residue: .R Created a new atom named: CA within residue: .R Created a new atom named: CB within residue: .R Created a new atom named: CG within residue: .R Created a new atom named: CD within residue: .R Created a new atom named: CE within residue: .R Created a new atom named: NZ within residue: .R Created a new atom named: C within residue: .R Created a new atom named: O within residue: .R Created a new atom named: C1 within residue: .R Created a new atom named: C2 within residue: .R Created a new atom named: C3 within residue: .R Created a new atom named: C4 within residue: .R Created a new atom named: C5 within residue: .R Created a new atom named: C6 within residue: .R Created a new atom named: C7 within residue: .R Created a new atom named: C8 within residue: .R Created a new atom named: C9 within residue: .R Created a new atom named: C10 within residue: .R Created a new atom named: C11 within residue: .R Created a new atom named: C12 within residue: .R Created a new atom named: C13 within residue: .R Created a new atom named: C14 within residue: .R Created a new atom named: C15 within residue: .R Created a new atom named: C16 within residue: .R Created a new atom named: C17 within residue: .R Created a new atom named: C18 within residue: .R Created a new atom named: C19 within residue: .R Created a new atom named: C20 within residue: .R total atoms in file: 29 The file contained 29 atoms not in residue templates > n = createAtom N N -0.55074 > h = createAtom H H 0.33150 > c21 = createAtom CA CT 0.00425 > h31 = createAtom HA H1 0.11095 > c22 = createAtom CB CT -0.10677 > h32 = createAtom 2HB HC 0.04233 > h33 = createAtom 3HB HC 0.04233 > c23 = createAtom CG CT 0.08603 > h34 = createAtom 2HG HC 0.01293 > h35 = createAtom 3HG HC 0.01293 > c24 = createAtom CD CT -0.16515 > h36 = createAtom 2HD HC 0.06985 > h37 = createAtom 3HD HC 0.06985 > c25 = createAtom CE CT -0.05106 > h38 = createAtom 2HE HC 0.12176 > h39 = createAtom 3HE HC 0.12176 > n2 = createAtom NZ NZ -0.32463 > h40 = createAtom HZ HZ 0.32114 > c = createAtom C C 0.64435 > o = createAtom O O -0.55681 > c1 = createAtom C1 ce 0.24079 > h1 = createAtom H1 h4 0.14988 > c2 = createAtom C2 ce -0.44295 > h2 = createAtom H2 ha 0.17678 > c3 = createAtom C3 cf 0.45084 > c4 = createAtom C4 c3p -0.39309 > h3 = createAtom H3 hc 0.13067 > h4 = createAtom H4 hc 0.13067 > h5 = createAtom H5 hc 0.13067 > c5 = createAtom C5 cf -0.52321 > h6 = createAtom H6 ha 0.22833 > c6 = createAtom C6 ce 0.22024 > h7 = createAtom H7 ha 0.13608 > c7 = createAtom C7 ce -0.47298 > h8 = createAtom H8 ha 0.19104 > c8 = createAtom C8 cf 0.38069 > c9 = createAtom C9 c3p -0.35674 > h9 = createAtom H9 hc 0.10947 > h10 = createAtom H10 hc 0.10947 > h11 = createAtom H11 hc 0.10947 > c10 = createAtom C10 cf -0.43043 > h12 = createAtom H12 ha 0.19549 > c11 = createAtom C11 ce 0.17028 > h13 = createAtom H13 ha 0.10451 > c12 = createAtom C12 ce -0.48956 > c13 = createAtom C13 c3p 0.62671 > c14 = createAtom C14 c3p -0.48990 > h14 = createAtom H14 hc 0.11031 > h15 = createAtom H15 hc 0.11031 > h16 = createAtom H16 hc 0.11031 > c15 = createAtom C15 c3p -0.48990 > h17 = createAtom H17 hc 0.11031 > h18 = createAtom H18 hc 0.11031 > h19 = createAtom H19 hc 0.11031 > c16 = createAtom C16 c3p -0.17958 > h20 = createAtom H20 hc 0.04312 > h21 = createAtom H21 hc 0.04312 > c17 = createAtom C17 c3p 0.03859 > h22 = createAtom H22 hc 0.01755 > h23 = createAtom H23 hc 0.01755 > c18 = createAtom C18 c3p -0.23465 > h24 = createAtom H24 hc 0.08201 > h25 = createAtom H25 hc 0.08201 > c19 = createAtom C19 c2p 0.34235 > c20 = createAtom C20 c3p -0.50885 > h26 = createAtom H26 hc 0.14006 > h27 = createAtom H27 hc 0.14006 > h28 = createAtom H28 hc 0.14006 > set n element N > set h element H > set c21 element C > set h31 element H > set c22 element C > set h32 element H > set h33 element H > set c23 element C > set h34 element H > set h35 element H > set c24 element C > set h36 element H > set h37 element H > set c25 element C > set h38 element H > set h39 element H > set n2 element N > set h40 element H > set c element C > set o element O > set c1 element C > set h1 element H > set c2 element C > set h2 element H > set c3 element C > set c4 element C > set h3 element H > set h4 element H > set h5 element H > set c5 element C > set h6 element H > set c6 element C > set h7 element H > set c7 element C > set h8 element H > set c8 element C > set c9 element C > set h9 element H > set h10 element H > set h11 element H > set c10 element C > set h12 element H > set c11 element C > set h13 element H > set c12 element C > set c13 element C > set c14 element C > set h14 element H > set h15 element H > set h16 element H > set c15 element C > set h17 element H > set h18 element H > set h19 element H > set c16 element C > set h20 element H > set h21 element H > set c17 element C > set h22 element H > set h23 element H > set c18 element C > set h24 element H > set h25 element H > set c19 element C > set c20 element C > set h26 element H > set h27 element H > set h28 element H > ret = createResidue RET > add ret n > add ret h > add ret c21 > add ret h31 > add ret c22 > add ret h32 > add ret h33 > add ret c23 > add ret h34 > add ret h35 > add ret c24 > add ret h36 > add ret h37 > add ret c25 > add ret h38 > add ret h39 > add ret n2 > add ret h40 > add ret c > add ret o > add ret c1 > add ret h1 > add ret c2 > add ret h2 > add ret c3 > add ret c4 > add ret h3 > add ret h4 > add ret h5 > add ret c5 > add ret h6 > add ret c6 > add ret h7 > add ret c7 > add ret h8 > add ret c8 > add ret c9 > add ret h9 > add ret h10 > add ret h11 > add ret c10 > add ret h12 > add ret c11 > add ret h13 > add ret c12 > add ret c13 > add ret c14 > add ret h14 > add ret h15 > add ret h16 > add ret c15 > add ret h17 > add ret h18 > add ret h19 > add ret c16 > add ret h20 > add ret h21 > add ret c17 > add ret h22 > add ret h23 > add ret c18 > add ret h24 > add ret h25 > add ret c19 > add ret c20 > add ret h26 > add ret h27 > add ret h28 > bond n h > bond c21 n > bond c21 h31 > bond c22 c21 > bond c22 h32 > bond c22 h33 > bond c23 c22 > bond c23 h34 > bond c23 h35 > bond c24 c23 > bond c24 h36 > bond c24 h37 > bond c25 c24 > bond c25 h38 > bond c25 h39 > bond n2 c25 > bond n2 h40 > bond c21 c > bond o c D > bond n2 c1 D > bond h1 c1 > bond c2 c1 > bond h2 c2 > bond c3 c2 D > bond c4 c3 > bond h3 c4 > bond h4 c4 > bond h5 c4 > bond c5 c3 > bond h6 c5 > bond c6 c5 D > bond h7 c6 > bond c7 c6 > bond h8 c7 > bond c8 c7 D > bond c9 c8 > bond h9 c9 > bond h10 c9 > bond h11 c9 > bond c10 c8 > bond h12 c10 > bond c11 c10 D > bond h13 c11 > bond c12 c11 > bond c13 c12 > bond c14 c13 > bond h14 c14 > bond h15 c14 > bond h16 c14 > bond c15 c13 > bond h17 c15 > bond h18 c15 > bond h19 c15 > bond c16 c13 > bond h20 c16 > bond h21 c16 > bond c17 c16 > bond h22 c17 > bond h23 c17 > bond c18 c17 > bond h24 c18 > bond h25 c18 > bond c19 c18 > bond c19 c12 D > bond c20 c19 > bond h26 c20 > bond h27 c20 > bond h28 c20 > RET = createUnit RET > > add RET ret > set RET.1 restype undefined > > zMatrix RET { > { N H 1.010 } > { CA N H 1.444 118.271 } > { HA CA N H 1.089 108.273 175.797 } > { CB CA N H 1.507 113.478 -63.472 } > {2HB CB CA N 1.091 108.295 60.178 } > {3HB CB CA N 1.090 108.283 178.720 } > { CG CB CA N 1.511 111.845 -60.519 } > {2HG CG CB CA 1.090 109.182 -150.852 } > {3HG CG CB CA 1.090 109.135 -31.264 } > { CD CG CB CA 1.549 110.198 88.956 } > {2HD CD CG CB 1.090 106.075 -98.696 } > {3HD CD CG CB 1.090 106.026 17.554 } > { CE CD CG CB 1.532 116.237 139.443 } > {2HE CE CD CG 1.089 109.050 49.747 } > {3HE CE CD CG 1.090 109.047 169.214 } > { NZ CE CD CG 1.446 110.312 -70.571 } > { HZ NZ CE CD 0.999 115.715 -10.294 } > { C CA N H 1.494 105.755 58.005 } > { O C CA N 1.202 124.430 -37.457 } > { C1 NZ C25 C24 1.323 128.557 169.608 } > { H1 C1 NZ C25 1.069 117.330 179.067 } > { C2 C1 NZ C25 1.447 125.385 -0.850 } > { H2 C2 C1 NZ 1.070 119.061 9.565 } > { C3 C2 C1 NZ 1.349 121.910 -170.365 } > { C4 C3 C2 C1 1.487 121.206 -3.311 } > { H3 C4 C3 C2 1.069 109.446 -110.389 } > { H4 C4 C3 C2 1.070 109.446 129.645 } > { H5 C4 C3 C2 1.070 109.448 9.667 } > { C5 C3 C2 C1 1.438 118.883 -179.111 } > { H6 C5 C3 C2 1.069 118.499 5.159 } > { C6 C5 C3 C2 1.346 122.980 -174.893 } > { H7 C6 C5 C3 1.071 120.762 0.246 } > { C7 C6 C5 C3 1.447 118.559 -179.780 } > { H8 C7 C6 C5 1.071 117.880 6.231 } > { C8 C7 C6 C5 1.321 124.252 -173.800 } > { C9 C8 C7 C6 1.495 120.788 -3.996 } > { H9 C9 C8 C7 1.071 109.431 -101.227 } > {H10 C9 C8 C7 1.070 109.487 138.756 } > {H11 C9 C8 C7 1.070 109.489 18.764 } > {C10 C8 C7 C6 1.447 117.636 -178.786 } > {H12 C10 C8 C7 1.070 119.330 -5.029 } > {C11 C10 C8 C7 1.289 121.421 174.974 } > {H13 C11 C10 C8 1.069 115.913 -0.740 } > {C12 C11 C10 C8 1.460 128.109 179.157 } > {C13 C12 C11 C10 1.481 113.815 -153.387 } > {C14 C13 C12 C11 1.526 112.582 -36.843 } > {H14 C14 C13 C12 1.070 109.456 -72.714 } > {H15 C14 C13 C12 1.071 109.522 167.233 } > {H16 C14 C13 C12 1.070 109.448 47.210 } > {C15 C13 C12 C11 1.512 108.196 76.900 } > {H17 C15 C13 C12 1.070 109.455 -31.855 } > {H18 C15 C13 C12 1.070 109.519 -151.779 } > {H19 C15 C13 C12 1.069 109.502 88.119 } > {C16 C13 C12 C11 1.527 112.752 -158.195 } > {H20 C16 C13 C12 1.071 109.249 74.522 } > {H21 C16 C13 C12 1.070 109.330 -166.019 } > {C17 C16 C13 C12 1.520 110.453 -45.705 } > {H22 C17 C16 C13 1.070 109.340 -178.811 } > {H23 C17 C16 C13 1.071 109.316 -59.181 } > {C18 C17 C16 C13 1.498 110.259 60.982 } > {H24 C18 C17 C16 1.071 108.424 75.699 } > {H25 C18 C17 C16 1.069 108.442 -166.742 } > {C19 C18 C17 c16 1.500 114.518 -45.470 } > {C20 C19 C18 C17 1.499 114.299 -170.405 } > {H26 C20 C19 C18 1.070 109.506 59.067 } > {H27 C20 C19 C18 1.070 109.494 179.134 } > {H28 C20 C19 C18 1.070 109.435 -60.983 } > } zMatrix: Argument #3 is type ?? Unknown type ?? must be of type: [atom] zMatrix: Illegal object in zMatrix entry. Entry was ignored zMatrix: Argument #4 is type ?? Unknown type ?? must be of type: [atom] zMatrix: Illegal object in zMatrix entry. Entry was ignored zMatrix: Argument #4 is type ?? Unknown type ?? must be of type: [atom] zMatrix: Illegal object in zMatrix entry. Entry was ignored >