[gmx-users] Regarding naming dipeptide in charmm36 Forcefield

[Justin Lemkul]

On 8/18/17 1:13 AM, Dilip H N wrote:
> 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...

This doesn't make any sense to me.  The capping groups are what make 
alanine dipeptide (ALAD) what it is, not removing them.

If you need to *generate* coordinates, then that's another matter. 
Plenty of software can do that (see links on gromacs.org).

> 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....

Have you run pdb2gmx to process a simple protein or polypeptide? This is 
done for you.  Each amino acid is defined.  If you supply a coordinate 
file with a GLY-GLY peptide, pdb2gmx does everything you need.

-Justin

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

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