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.abra...@anu.edu.au> > > > On 15/03/11, *Yulian Gavrilov * <zzeppeli...@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.abra...@anu.edu.au> > >> >> >> On 14/03/11, *Yulian Gavrilov * <zzeppeli...@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 >> -- >> gmx-users mailing list gmx-users@gromacs.org >> 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 gmx-users-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > > > > -- > > Sincerely, > > Yulian Gavrilov > > > -- > gmx-users mailing list gmx-users@gromacs.org > 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 gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- Sincerely, Yulian Gavrilov
-- gmx-users mailing list gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
