[gmx-users] oligoglycines

Tsjerk Wassenaar tsjerkw at gmail.com
Tue Mar 29 06:16:18 CEST 2011

Hi Nisha,

For building you can also use pymol if you have it installed. On the
command line you can issue:

pymol -qcd 'editor.build_peptide("GGG");cmd.save("triglycine.pdb","not hydro")'

Hope it helps,


On Mon, Mar 28, 2011 at 6:05 PM,  <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)
> Thanks!
> Nisha P
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Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands

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