Hi, I'm trying to construct diketopiperazine with gromacs. The problem that I have right now is forming the bond that unites the C and N termi to make the cyclic peptide. I tried using specbond.dat but so far I've been unsucessful. Here is my specbond.dat file and pdb file:
specbond.dat 8 CYS SG 1 CYS SG 1 0.2 CYS2 CYS2 CYS SG 1 HEME FE 2 0.25 CYS2 HEME CYS SG 1 HEME CAB 1 0.18 CYS2 HEME CYS SG 1 HEME CAC 1 0.18 CYS2 HEME HIS NE2 1 HEME FE 1 0.2 HIS1 HEME MET SD 1 HEME FE 1 0.24 MET HEME CYM SG 1 CYM SG 1 0.2 CYS2 CYS2 TRP N 1 HISH C 1 0.2 TRP HISH whdikp.pdb REMARK S 14 x 14 mn oif ATOM 1 N TRP 1 -0.813 0.594 1.164 ATOM 2 H TRP 1 -0.249 1.064 1.843 ATOM 3 CA TRP 1 -0.264 -0.210 0.004 ATOM 4 HA TRP 1 0.855 -0.244 0.066 ATOM 5 CB TRP 1 -0.633 0.484 -1.321 ATOM 6 HB1 TRP 1 -1.672 0.344 -1.531 ATOM 7 HB2 TRP 1 -0.408 1.528 -1.262 ATOM 8 CG TRP 1 0.205 -0.166 -2.397 ATOM 9 CD1 TRP 1 0.227 -1.464 -2.727 ATOM 10 HD1 TRP 1 -0.407 -2.173 -2.195 ATOM 11 CD2 TRP 1 1.119 0.455 -3.258 ATOM 12 NE1 TRP 1 1.166 -1.607 -3.796 ATOM 13 HE1 TRP 1 1.401 -2.473 -4.259 ATOM 14 CE2 TRP 1 1.673 -0.432 -4.078 ATOM 15 CE3 TRP 1 1.485 1.803 -3.344 ATOM 16 HE3 TRP 1 1.065 2.575 -2.699 ATOM 17 CZ2 TRP 1 2.626 -0.117 -5.054 ATOM 18 HZ2 TRP 1 3.035 -0.902 -5.690 ATOM 19 CZ3 TRP 1 2.444 2.145 -4.320 ATOM 20 HZ3 TRP 1 2.741 3.190 -4.402 ATOM 21 CH2 TRP 1 2.990 1.222 -5.140 ATOM 22 HH2 TRP 1 3.727 1.540 -5.878 ATOM 23 C TRP 1 -0.816 -1.621 0.004 ATOM 24 O TRP 1 -0.072 -2.712 0.004 ATOM 25 N HISH 2 -2.331 -1.621 0.004 ATOM 26 H HISH 2 -2.895 -2.093 -0.674 ATOM 27 CA HISH 2 -2.881 -0.816 1.162 ATOM 28 HA HISH 2 -4.000 -0.781 1.098 ATOM 29 CB HISH 2 -2.516 -1.510 2.488 ATOM 30 HB1 HISH 2 -1.564 -1.990 2.400 ATOM 31 HB2 HISH 2 -2.494 -0.794 3.283 ATOM 32 CG HISH 2 -3.591 -2.538 2.747 ATOM 33 ND1 HISH 2 -3.867 -3.560 1.846 ATOM 34 HD1 HISH 2 -3.399 -3.715 0.964 ATOM 35 CD2 HISH 2 -4.447 -2.700 3.792 ATOM 36 HD2 HISH 2 -4.608 -2.157 4.723 ATOM 37 CE1 HISH 2 -4.846 -4.291 2.344 ATOM 38 HE1 HISH 2 -5.219 -5.152 1.791 ATOM 39 NE2 HISH 2 -5.203 -3.793 3.502 ATOM 40 HE2 HISH 2 -5.932 -4.166 4.093 ATOM 41 C HISH 2 -2.329 0.595 1.164 ATOM 42 O HISH 2 -3.089 1.710 1.164 Thanks for any suggestions, Jose Tusell
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