[gmx-users] Regarding naming dipeptide in charmm36 Forcefield

[Dilip H N]

Thank you sir.,
1] If so thn, is there any other possible way such that i can get a peptide
(two aminoacids linked) and thn simulate it in CHARMM FF.. ?? (or) in
alanine dipeptide case which is the residue name in the .rtp file..?? and
how can i remove the n-methyl and  acetyl groups in order to get only
alanine dipeptide...
2] Or should i modify modify any aminoacid (eg., glycine into diglycine)
into a peptide to run the simulation, and if so thn how can i take care of
charges in the peptide (since thee will be removal of H2O molecule between
them and diglycine case there will be some net charge resulting )..
I am running out of ideas....So any suggestions are welcome....

Thank you...



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On Thu, Aug 17, 2017 at 5:41 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 8/17/17 12:01 AM, Dilip H N wrote:
>
>> Thank you Justin Sir for replying...
>> Yes, the term "dipeptide" is ambiguous....
>> But is there any other smallest  molecule with an amide linkage (two
>> aminoacids linked through peptide bond) or any other small peptide
>> molecule
>> that can be found in CHARMM36 FF..  with the corresponding residue naming
>> in charmm...
>>
>
> As I said, no, there's not.  You have the smallest possible polypeptide,
> two amino acids linked in the normal way.  So that means you have a
> sequence of GLY GLY, and the tool to produce that topology is pdb2gmx.
>
> -Justin
>
> Thank you...
>>
>>
>>
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>>
>>
>> On Wed, Aug 16, 2017 at 9:26 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>
>>
>>> On 8/16/17 11:41 AM, Dilip H N wrote:
>>>
>>> Hello,
>>>> I want to simulate a small dipeptide with mixture of solvents in
>>>> charmm36
>>>> forcefield, (the solvents are already in charmm36 forcefield), but i am
>>>> unable to find any small dipeptide molecule in charmm36 FF, since i have
>>>> solvent molecules in charmm36 FF, but not the dipeptide, which would
>>>> also
>>>> be easy in getting the topology file by gmx pdb2gmx command...
>>>> So can anybody help me how to find the dipeptide molecules (eg.,
>>>> diglycine)
>>>> in charmm36 FF...??
>>>>
>>>> There is no such special residue.  For diglycine, you have two GLY. It's
>>> like any peptide sequence.  The only dipeptide that CHARMM has is alanine
>>> dipeptide, but it's not ALA-ALA, it's ALA capped with acetyl and N-methyl
>>> groups, so there are two peptide bonds, but not two residues (hence why
>>> the
>>> term "dipeptide" is ambiguous).
>>>
>>> -Justin
>>>
>>> --
>>> ==================================================
>>>
>>> Justin A. Lemkul, Ph.D.
>>> Assistant Professor
>>> Virginia Tech Department of Biochemistry
>>>
>>> 303 Engel Hall
>>> 340 West Campus Dr.
>>> Blacksburg, VA 24061
>>>
>>> jalemkul at vt.edu | (540) 231-3129
>>> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>>>
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>>
>>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
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-- 
With Best Regards,

DILIP.H.N
Ph.D Student