[gmx-users] isopeptide bond

[Mark Abraham]

On 14/03/11, Yulian Gavrilov  <zzeppelin87 at gmail.com> wrote:
> Dear, Mark
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> You asking about this (?): 
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> According to ffamber99.atp:
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> amber99_34        14.01000	; N  sp2
> nitrogen in amide groups
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> amber99_39        14.01000	; N3  sp3 N
> for charged amino groups (Lys, etc)
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> 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.
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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.


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> [atoms] and [bonds] section for LYQ
> and GLQ in topol.top 
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> [ atoms ]
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> ;   nr       type  resnr residue  atom 
>  cgnr     charge       mass  typeB    chargeB      massB
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>    750 amber99_34     48    LYQ      N 
>   748    -0.4157      14.01   ; qtot -5.416
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>    751 amber99_17     48    LYQ      H 
>   749     0.2719      1.008   ; qtot -5.144
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>    752 amber99_11     48    LYQ     CA 
>   750   -0.07206      12.01   ; qtot -5.216
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>    753 amber99_19     48    LYQ     HA 
>   751     0.0994      1.008   ; qtot -5.116
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>    754 amber99_11     48    LYQ     CB 
>   752   -0.04845      12.01   ; qtot -5.165
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>    755 amber99_18     48    LYQ    HB1 
>   753      0.034      1.008   ; qtot -5.131
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>    756 amber99_18     48    LYQ    HB2 
>   754      0.034      1.008   ; qtot -5.097
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>    757 amber99_11     48    LYQ     CG 
>   755    0.06612      12.01   ; qtot -5.031
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>    758 amber99_18     48    LYQ    HG1 
>   756    0.01041      1.008   ; qtot -5.02
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>    759 amber99_18     48    LYQ    HG2 
>   757    0.01041      1.008   ; qtot -5.01
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>    760 amber99_11     48    LYQ     CD 
>   758   -0.03768      12.01   ; qtot -5.048
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>    761 amber99_18     48    LYQ    HD1 
>   759    0.01155      1.008   ; qtot -5.036
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>    762 amber99_18     48    LYQ    HD2 
>   760    0.01155      1.008   ; qtot -5.025
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>    763 amber99_11     48    LYQ     CE 
>   761    0.32604      12.01   ; qtot -4.699
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>    764 amber99_28     48    LYQ    HE1 
>   762   -0.03358      1.008   ; qtot -4.732
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>    765 amber99_28     48    LYQ    HE2 
>   763   -0.03358      1.008   ; qtot -4.766
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>    766 amber99_39     48    LYQ     NZ 
>   764   -1.03581      14.01   ; qtot -5.801
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>    767 amber99_17     48    LYQ    HZ1 
>   765    0.38604      1.008   ; qtot -5.415
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>    768 amber99_17     48    LYQ    HZ2 
>   766    0.38604      1.008   ; qtot -5.029
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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.


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>    769  amber99_2     48    LYQ      C 
>   767     0.5973      12.01   ; qtot -4.432
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>    770 amber99_41     48    LYQ      O 
>   768    -0.5679         16   ; qtot -5
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>   2440 amber99_34    152    GLQ      N 
>  2438    -0.4157      14.01   ; qtot -12.42
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>   2441 amber99_17    152    GLQ      H 
>  2439     0.2719      1.008   ; qtot -12.14
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>   2442 amber99_11    152    GLQ     CA 
>  2440    -0.0252      12.01   ; qtot -12.17
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>   2443 amber99_19    152    GLQ    HA1 
>  2441     0.0698      1.008   ; qtot -12.1
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>   2444 amber99_19    152    GLQ    HA2 
>  2442     0.0698      1.008   ; qtot -12.03
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>   2445  amber99_2    152    GLQ      C 
>  2443     0.5973      12.01   ; qtot -11.43
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>   2446 amber99_41    152    GLQ      O 
>  2444    -0.5679         16   ; qtot -12
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> [ bonds ]
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> ;  ai    aj funct            c0        
>    c1            c2            c3
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>   750   751     1 
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>   750   752     1 
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>   752   753     1 
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>   752   754     1 
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>   752   769     1 
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>   754   755     1 
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>   754   756     1 
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>   754   757     1 
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>   757   758     1 
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>   757   759     1 
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>   757   760     1 
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>   760   761     1 
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>   760   762     1 
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>   760   763     1 
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>   763   764     1 
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>   763   765     1 
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>   763   766     1 
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>   766   767     1 
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>   766   768     1 
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>   766  2445     1 
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OK, you have the N-C bond for the peptide link.


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>   769   770     1 
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>   769   771     1 
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>  2440  2441     1 
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>  2440  2442     1 
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>  2442  2443     1 
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>  2442  2444     1 
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>  2442  2445     1 
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>  2445  2446     1 
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Does 2445 make any other bonds? If not, how did you handle the chain termination?

Mark
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