[gmx-users] Regarding naming dipeptide in charmm36 Forcefield

[Justin Lemkul]

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

==================================================