Dear, Mark You asking about this (?):
According to ffamber99.atp: amber99_34 14.01000 ; N sp2 nitrogen in amide groups amber99_39 14.01000 ; N3 sp3 N for charged amino groups (Lys, etc) If I don't mix, “N” is used in peptide bond in amber99 and “N3” is used in Lys side chain. That is why I didn't use backbone peptide. *[atoms] and [bonds] section for LYQ and GLQ in topol.top * [ atoms ] ; nr type resnr residue atom cgnr charge mass typeB chargeB massB 750 amber99_34 48 LYQ N 748 -0.4157 14.01 ; qtot -5.416 751 amber99_17 48 LYQ H 749 0.2719 1.008 ; qtot -5.144 752 amber99_11 48 LYQ CA 750 -0.07206 12.01 ; qtot -5.216 753 amber99_19 48 LYQ HA 751 0.0994 1.008 ; qtot -5.116 754 amber99_11 48 LYQ CB 752 -0.04845 12.01 ; qtot -5.165 755 amber99_18 48 LYQ HB1 753 0.034 1.008 ; qtot -5.131 756 amber99_18 48 LYQ HB2 754 0.034 1.008 ; qtot -5.097 757 amber99_11 48 LYQ CG 755 0.06612 12.01 ; qtot -5.031 758 amber99_18 48 LYQ HG1 756 0.01041 1.008 ; qtot -5.02 759 amber99_18 48 LYQ HG2 757 0.01041 1.008 ; qtot -5.01 760 amber99_11 48 LYQ CD 758 -0.03768 12.01 ; qtot -5.048 761 amber99_18 48 LYQ HD1 759 0.01155 1.008 ; qtot -5.036 762 amber99_18 48 LYQ HD2 760 0.01155 1.008 ; qtot -5.025 763 amber99_11 48 LYQ CE 761 0.32604 12.01 ; qtot -4.699 764 amber99_28 48 LYQ HE1 762 -0.03358 1.008 ; qtot -4.732 765 amber99_28 48 LYQ HE2 763 -0.03358 1.008 ; qtot -4.766 766 amber99_39 48 LYQ NZ 764 -1.03581 14.01 ; qtot -5.801 767 amber99_17 48 LYQ HZ1 765 0.38604 1.008 ; qtot -5.415 768 amber99_17 48 LYQ HZ2 766 0.38604 1.008 ; qtot -5.029 769 amber99_2 48 LYQ C 767 0.5973 12.01 ; qtot -4.432 770 amber99_41 48 LYQ O 768 -0.5679 16 ; qtot -5 2440 amber99_34 152 GLQ N 2438 -0.4157 14.01 ; qtot -12.42 2441 amber99_17 152 GLQ H 2439 0.2719 1.008 ; qtot -12.14 2442 amber99_11 152 GLQ CA 2440 -0.0252 12.01 ; qtot -12.17 2443 amber99_19 152 GLQ HA1 2441 0.0698 1.008 ; qtot -12.1 2444 amber99_19 152 GLQ HA2 2442 0.0698 1.008 ; qtot -12.03 2445 amber99_2 152 GLQ C 2443 0.5973 12.01 ; qtot -11.43 2446 amber99_41 152 GLQ O 2444 -0.5679 16 ; qtot -12 [ bonds ] ; ai aj funct c0 c1 c2 c3 750 751 1 750 752 1 752 753 1 752 754 1 752 769 1 754 755 1 754 756 1 754 757 1 757 758 1 757 759 1 757 760 1 760 761 1 760 762 1 760 763 1 763 764 1 763 765 1 763 766 1 766 767 1 766 768 1 766 2445 1 769 770 1 769 771 1 2440 2441 1 2440 2442 1 2442 2443 1 2442 2444 1 2442 2445 1 2445 2446 1 -- Sincerely, Yulian Gavrilov
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