[gmx-users] isopeptide bond

[Yulian Gavrilov]

Dear Mark,
Thank you for your help! Now it works! I made MD without errors.
I  changed N3 to N, add one additional [angletype] to .itp (HP  CT  N) and
removed one of HZ1 from Lys that participate in isopeptide bond; made
appropriate changes in .atp, .hdp, .rtp and specbond.dat.

2011/3/14 Mark Abraham <mark.abraham at anu.edu.au>

>
>
> On 14/03/11, *Yulian Gavrilov * <zzeppelin87 at gmail.com> wrote:
>
> 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.
>
>
> N3 is used in a quaternary amine. N is used in an amide. Atom types are
> related to the chemical functional group they are *now* in, not what they
> were before a notional peptide condensation. You have an amide, and the
> nitrogen in it cannot be protonated. I said that in an email a fortnight
> ago. Use normal peptide parameters.
>
>
> *[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
>
>
> Atom 766 is bound to two carbon atoms and two hydrogen atoms. There is no
> such thing as a quaternary amide nitrogen, and certainly AMBER does not have
> parameters for it.
>
>
>  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
>
>
> OK, you have the N-C bond for the peptide link.
>
>
>  769 770 1
>
> 769 771 1
>
>
>
>  2440 2441 1
>
> 2440 2442 1
>
> 2442 2443 1
>
> 2442 2444 1
>
> 2442 2445 1
>
> 2445 2446 1
>
>
> Does 2445 make any other bonds? If not, how did you handle the chain
> termination?
>
> Mark
> --
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-- 

Sincerely,

Yulian Gavrilov
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