Hi,
thanks for your proposal it seems to be great. However, I am afraid that
I still need your help, if possible, because I do not know how to
implement these improper dihedral constants in a general way. I am also
interested for other pseudopeptides.
You mean improper dihedral angle (C, HN, N, CT)?
Thanks again I feel that you are closed to the completion
arnaud
Le 01/05/2020 à 21:50, Junmei Wang a écrit :
> 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 <mailto: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>
>> <mailto: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
>>>> <mailto: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
>>>>>>>> <mailto: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
>>>>>>>>> <mailto: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 <http://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 <mailto: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
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>> AMBER mailing list
>>>>>>>>>>>>> AMBER.ambermd.org <mailto:AMBER.ambermd.org>
>>>>>>>>>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>>>>>>>>>>
>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>> AMBER mailing list
>>>>>>>>>>>> AMBER.ambermd.org <mailto: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
>>>>>>>>>>> <mailto:arnaud.bondon.univ-rennes1.fr>
>>>>>>>>>>> http://iscr.univ-rennes1.fr
>>>>>>>>>>>
>>>>>>>>>>> _______________________________________________
>>>>>>>>>>> AMBER mailing list
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>>>>>>>>>>>
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>>>>>>>>>>> AMBER mailing list
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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
>>>>>>>>> <mailto:arnaud.bondon.univ-rennes1.fr>
>>>>>>>>> http://iscr.univ-rennes1.fr
>>>>>>>>>
>>>>>>>>> _______________________________________________
>>>>>>>>> AMBER mailing list
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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
>>>>> <mailto:arnaud.bondon.univ-rennes1.fr>
>>>>> http://iscr.univ-rennes1.fr
>>>>>
>>>>> _______________________________________________
>>>>> AMBER mailing list
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>>>>>
>>>> _______________________________________________
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>>>> 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 <mailto:arnaud.bondon.univ-rennes1.fr>
>>> http://iscr.univ-rennes1.fr
>>>
>>> _______________________________________________
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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 <mailto:arnaud.bondon.univ-rennes1.fr>
> http://iscr.univ-rennes1.fr
>
--
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 Sat May 02 2020 - 06:00:02 PDT
