[gmx-users] Regarding naming dipeptide in charmm36 Forcefield
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.
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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