On 15/03/11, Yulian Gavrilov <[email protected]> wrote: > 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? > >
Your .rtp and .hdp specify the atom types. Mark > > > > 2011/3/15 Mark Abraham <[email protected]> > > > > > > > > > On 15/03/11, Yulian Gavrilov <[email protected]> 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 <[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 > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > -- > > > > 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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