[gmx-users] isopeptide bond
Mark Abraham
mark.abraham at anu.edu.au
Tue Mar 15 08:52:17 CET 2011
On 15/03/11, Yulian Gavrilov <zzeppelin87 at gmail.com> wrote:
> 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.
>
>
Good. Like I've said a few times, you have a normal peptide bond and those interaction types all exist already; you do not need to add more interaction types. Look up in the .rtp what the HP atom type is used for. The H atom on the N should take its type from its current environment, not its historical one. Until your peptide bond resembles a backbone peptide in *all* particulars, it is not a well-modeled peptide bond.
Mark
> 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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> >
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> >
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> >
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> >
>
>
>
>
> --
>
>
> Sincerely,
>
>
> Yulian Gavrilov
>
>
>
>
>
>
>
>
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