[gmx-users] Imitation of the protein part

Justin A. Lemkul jalemkul at vt.edu
Mon Mar 5 17:01:34 CET 2012

Specifying "none" for the termini, in conjunction with suitable capping groups 
to create uncharged peptide bonds at the termini (which have to be built on with 
external software), is the best approach to modeling such a system, in my opinion.


Steven Neumann wrote:
> Hi Gmx Users,
> I am simulationg parts of the big protein so in this case imitating non 
> charged terminals. For this purpose I use option:
> pdb2gmx -f Protein.pdb -ter
> Which option would be suitable and safe to imitate it:
> a) NH2 and COOH
> b) None
> Thank you!
> Steven


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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