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 <[email protected]> > > > On 14/03/11, *Yulian Gavrilov * <[email protected]> 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 > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- Sincerely, Yulian Gavrilov
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