[gmx-users] Regarding naming dipeptide in charmm36 Forcefield

[Justin Lemkul]

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

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Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

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