For the residue topology file generated by you, testsirus.prepin, many
torsional angles of CT-C-N-CT have values around 150 to 160 or -160 to
-150. If you know NMR structures of cyclic peptides that have similar
number of residues, could you list the PDB ids?
Thanks
Junmei
On Wed, Apr 29, 2020 at 12:51 PM Arnaud Bondon <
arnaud.bondon.univ-rennes1.fr> wrote:
> Sorry again for the angles I wanted to write
> Calpha-1 - C - N - Calpha of 148 and 150° respectively.
> As you mentionned the standard O=C-N-H are pretty close to 180° and
> Calpha-1 - C - N - Calpha should also be 180°. The differences are only
> associated with the pyramidal character of the nitrogen atoms.
>
> I looked for many cyclic peptide structures solved by NMR or X-Ray and I
> did not find examples of such distorsions, so I am still in trouble.
>
>
> arnaud
> Le 29/04/2020 à 17:22, Arnaud Bondon a écrit :
> > Sorry the angles were
> >
> > *C**a**_- *_1 -C*_-1 -N-C**a***
> >
> >
> >
> > Le 29/04/2020 à 17:13, Arnaud Bondon a écrit :
> >> I reproduced your minimization and I have hopefully the same pdb, which
> >> correponds to the distorted N3 and N1 and dihedral omega angles of 148
> >> and 150° respectively.
> >>
> >> I believed these values were out of range even for cyclic peptide but if
> >> you say that it is consistent with reality I have to trust you.
> >> Many thanks again
> >>
> >> arnuad
> >>
> >> Le 29/04/2020 à 17:09, Junmei Wang a écrit :
> >>> 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
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> >>>>>> arnaud.bondon.univ-rennes1.fr
> >>>>>> http://iscr.univ-rennes1.fr
> >>>>>>
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> >>>> OU UN ETAT COMMUN
> >>>>
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> >>>> Equipe CORINT, UMR CNRS 6226
> >>>> PRISM
> >>>> CS 34317
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> >>>> 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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> --
> 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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Received on Wed Apr 29 2020 - 22:00:02 PDT
