[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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