[gmx-users] oligoglycines

Justin A. Lemkul jalemkul at vt.edu
Mon Mar 28 18:11:30 CEST 2011

nishap.patel at utoronto.ca wrote:
> Hello,
>    I want to simulate n-glycines (diglycine, triglycine..etc) I tried to 
> get the structure from PRODRG, but the program adds H's on the 
> N-terminal instead of on C- terminal. Is there another program I could 
> use, or a site where I could get the structure of oligoglycines? For 
> example, diglycine (NH2-CH2-CO-NH-CH2-COOH), but PRODRG gives me 
> ((NH3-CH2-CO-NH-CH2-COO)

Protonation state is easy to change with pdb2gmx when writing your topology. 
Use -ignh and/or -ter to set the proper state.  You can also tune this with 
PRODRG (see the FAQs regarding ADDHYD and DELHYD commands), but since you can do 
it all with Gromacs anyway, it shouldn't be necessary.


> Thanks!
> Nisha P


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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