[gmx-users] Regarding naming dipeptide in charmm36 Forcefield
jalemkul at vt.edu
Thu Aug 17 14:11:38 CEST 2017
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.
> Thank you...
> <https://mailtrack.io/> Sent with Mailtrack
> 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:
>>> 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.,
>>> 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 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
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Justin A. Lemkul, Ph.D.
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalemkul at vt.edu | (540) 231-3129
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