[gmx-users] isopeptide bond

Tue Mar 15 09:19:14 CET 2011

Thanks! I understand it, but I had several errors about it. Without adding
of (HP  CT  N) [angletype] it does not work. How to force it to take its
type from its current environment, not its historical one?

2011/3/15 Mark Abraham <mark.abraham at anu.edu.au>

>
>
> 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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>
>
>
> --
>
> Sincerely,
>
> Yulian Gavrilov
>
>
> --
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-- 

Sincerely,

Yulian Gavrilov
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