The N1 and N13 are almost planar (torsional angles of O=C-N-H are 177 and
179 degrees). I don't think they are like pyramidal nitrogen in amines. I
think the slightly deviation from the ideal geometry is because your
molecule is cyclic peptide.
Best
Junmei
On Wed, Apr 29, 2020 at 10:52 AM Arnaud Bondon <
arnaud.bondon.univ-rennes1.fr> wrote:
> Hi,
>
> I looked at your min.pdb and for me the N13 displays a pyramidal
> character and also the N1 a little
>
> May be less pronounced that my previous pdb but not really planar
>
> I start the same command, I'll tell you
>
> thanks
>
> arnaud
>
>
>
> Le 29/04/2020 à 16:12, Junmei Wang a écrit :
> > I have tested your molecule using your prepin and frcmod files. I also
> did
> > igb=1 minimization for 10,000 steps. I did not observe weird behavior of
> > amide groups. Please check if you can reproduce my result.
> >
> > All the best
> >
> > Junmei
> >
> > On Wed, Apr 29, 2020 at 4:44 AM Arnaud Bondon <
> arnaud.bondon.univ-rennes1.fr>
> > wrote:
> >
> >> Hi,
> >>
> >> Thanks for the two responses.
> >>
> >> About solvent I only used igb=1 when performing simulated annealing
> >> under NMR restraints (sa.in)
> >>
> >> The prep directory is attached.
> >>
> >> Many thanks for your help
> >>
> >> sincerely
> >>
> >> arnaud
> >>
> >> Le 28/04/2020 à 23:02, Junmei Wang a écrit :
> >>> Gaff adopted the good parameters from amber biomolecular force field.
> So
> >>> the peptide-like parameters should be similar. For you minimization,
> did
> >>> you consider solvent effect? If you send me your prep file, I will
> check
> >> if
> >>> it is a force field issue or not.
> >>>
> >>> Best
> >>>
> >>> Junmei
> >>>
> >>> On Fri, Apr 24, 2020 at 11:02 AM David A Case <david.case.rutgers.edu>
> >>> wrote:
> >>>
> >>>> On Fri, Apr 24, 2020, Arnaud Bondon wrote:
> >>>>
> >>>>> ). Clearly the N10 amide nitrogen
> >>>>> has an pyramidal character. And the omega dihedral angles are not
> good
> >>>>>
> >>>>> The molecule was prepared as a mol2 file Nitrogen are N.am
> >>>> The input atoms types don't matter: you should look at the output
> types
> >>>> in the prep file. If this is a peptide-like molecule, it may be that
> >>>> the gaff types don't do as well as the tuned Amber atom types.
> >>>> You might want to see what happens if you request Amber atom types.
> >>>>
> >>>> I'm not sure whether GAFF has types that are specifically tuned for
> >>>> peptide bonds or not...cc-ing Junmei here.
> >>>>
> >>>> ...good luck...dac
> >>>>
> >>>>
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> >>>>
> >>> _______________________________________________
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> >> --
> >> POUR UNE RECONNAISSANCE DE LA PALESTINE DANS LES FRONTIERES DE 1967
> >> OU UN ETAT COMMUN
> >>
> >> Arnaud BONDON
> >> Equipe CORINT, UMR CNRS 6226
> >> PRISM
> >> CS 34317
> >> Campus de villejean
> >> Université de Rennes 1
> >> 35043 RENNES Cedex France
> >> tel: (0)2 23 23 65 61
> >> arnaud.bondon.univ-rennes1.fr
> >> http://iscr.univ-rennes1.fr
> >>
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> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >>
> >>
> >> _______________________________________________
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> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
>
> --
> POUR UNE RECONNAISSANCE DE LA PALESTINE DANS LES FRONTIERES DE 1967
> OU UN ETAT COMMUN
>
> Arnaud BONDON
> Equipe CORINT, UMR CNRS 6226
> PRISM
> CS 34317
> Campus de villejean
> Université de Rennes 1
> 35043 RENNES Cedex France
> tel: (0)2 23 23 65 61
> arnaud.bondon.univ-rennes1.fr
> http://iscr.univ-rennes1.fr
>
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Wed Apr 29 2020 - 08:30:01 PDT
