Thank you for your further explanation. I also measured the improper
dihedral angle (C, HA, N, CT). In the min.pdb file, two have values of
-155.4 and 159.4. This values are more like sp2 N than sp3 N (amines),
which have typical values of 120 degrees (-126.55, 125,7, -118.8, 118.3,
-123.5, 119.8, 119.1 for a set of amines).
If you want to reduce the loss of sp2 characteristics, you can make the
force constant of improper dihedral angles (c-c3-n-hn and c-ce-n-hn from
1.1 to 10.5). The attached min2.pdb was the minimized geometry using new
improper dihedral constant.
All the best
Junmei
On Fri, May 1, 2020 at 6:55 AM Arnaud Bondon <arnaud.bondon.univ-rennes1.fr>
wrote:
> Hi,
>
> Many thanks again for your careful analysis, nevertheless I still have
> comments
>
> i) Our peptide has also two extra carbons in the macrocycle (one peptide
> bond comes from the amino group of one hydroxyDAB; in the case of PMB it is
> similar with a DAB)
>
> ii) If both C and N are not pyramidal the O=C-N-H and CT-N-C-CT angles are
> correlated it is true even in cR9 where we observed for example 140 and
> 139.8; -87.6 and -91.5
>
> When looking at your min.pdb that you previously sent we observed for
> N1 177.7 and 150
> N13 178.9 and 148
> N14 179.1 and 166
> All the peptidic bonds are closed to 180, the difference in the CT-N-C-CT
> angles is only associated with the pyramidal character of the nitrogen
>
> I can understand distorsion of the angles due to the steric constraints of
> the cycle but the lost of sp2 character of the nitrogen remains surprising
> for me.
>
> sincerely
>
> arnaud
> Le 01/05/2020 à 05:15, Junmei Wang a écrit :
>
> I have carefully examined all the five structures, the following is my
> summary:
> BAL2 (7aa): contains an additional sp3 carbon in mainchain. The measured
> CT-N-C-CT angles are: -170.8, 175.0, -177.6, -176.1, 177.0, 178.8, -172.8
> cR9 (9aa): the only peptide has natural AAs, it has two structures
> (I): 177.8, 176.7, -179.1, -173.5, -157.6, -91.5, 139.9, -177.0,
> 161.8
> (II): -172.7 164.3, 176.5, 175.8, 178.7, -172.2, -164.2, 88.2,
> 143.0
> PMB (7aa): contains an additional sp3 carbon in mainchain. -3.1, 178.5,
> -177.6, 178.3, -178.0, -179.0, -179.2
> Tat2 (15aa): -179.5, 178.5, 179.5, 179.6, 179.7, 179.4, -179.4, 179.6,
> 179.5, 179.8, -180.0, -179.4, 178.9, -179.3, 178.9
> PMB2 (7aa): contains an additional sp3 carbon in mainchain. 179.9, 179.9,
> 179.5, 179.9, 179.9, 179.9, 179.9
>
> Clearly, Tat2 is a special case, as it has 15 AA residues and the
> ring-formation pressure is low. For others small ring peptides, introducing
> one additional sp3 carbon (other than CA) in the main chain can lower the
> ring-formation pressure (such as BAL2, PMB, PMB2). If all natural aa are
> used, such as cR9, some torsional angles are not close to 180 anymore due
> to the ring-formation pressure. My conclusion is that some torsional angles
> deviate from 180 degree because of ring-formation pressure.
>
> Best
>
> Junmei
>
>
>
> On Thu, Apr 30, 2020 at 4:27 AM Arnaud Bondon <arnaud.bondon.univ-rennes1.fr> <arnaud.bondon.univ-rennes1.fr>
> wrote:
>
>
> Hi,
>
> Please find attached five pdb, the more relevant are PMB and PMB2 or
> polymixin B closely related to our peptide.
>
> Some pdb are from large complexes with protein partners and accessible
> on the pdb. For clarity I kept only the peptides
>
> Thanks again
>
> arnuad
>
> Le 30/04/2020 à 06:45, Junmei Wang a écrit :
>
> 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
> Campus de villejean
> Université de Rennes 1
> 35043 RENNES Cedex France
> tel: (0)2 23 23 65 61arnaud.bondon.univ-rennes1.frhttp://iscr.univ-rennes1.fr
>
> _______________________________________________
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>
>
>
> _______________________________________________
> AMBER mailing listAMBER.ambermd.orghttp://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 61arnaud.bondon.univ-rennes1.frhttp://iscr.univ-rennes1.fr
>
> _______________________________________________
> AMBER mailing listAMBER.ambermd.orghttp://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
> AMBER mailing listAMBER.ambermd.orghttp://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 61arnaud.bondon.univ-rennes1.frhttp://iscr.univ-rennes1.fr
>
> _______________________________________________
> AMBER mailing listAMBER.ambermd.orghttp://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
> AMBER mailing listAMBER.ambermd.orghttp://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 61arnaud.bondon.univ-rennes1.frhttp://iscr.univ-rennes1.fr
>
> _______________________________________________
> AMBER mailing listAMBER.ambermd.orghttp://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
> AMBER mailing listAMBER.ambermd.orghttp://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 61arnaud.bondon.univ-rennes1.frhttp://iscr.univ-rennes1.fr
>
>
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Received on Fri May 01 2020 - 13:00:02 PDT
