[gmx-users] Regarding naming dipeptide in charmm36 Forcefield

Justin Lemkul jalemkul at vt.edu
Fri Aug 18 19:02:44 CEST 2017

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 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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