[gmx-users] Regarding naming dipeptide in charmm36 Forcefield
Dilip H N
cy16f01.dilip at nitk.edu.in
Thu Aug 17 06:01:52 CEST 2017
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
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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:
>> 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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With Best Regards,
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