[gmx-users] oligoglycines

[nishap.patel at utoronto.ca]

Thanks Tsjerk! Looks like it is working!


Quoting Tsjerk Wassenaar <tsjerkw at gmail.com>:

> 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,
>
> Tsjerk
>
> 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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