[gmx-users] isopeptide bond

[Yulian Gavrilov]

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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