[gmx-users] How to obtain a proper structure for glycine?

[Mark Abraham]

Hi,

Prodrg is not gromacs software, so there is probably a better place to ask
this question. I'd also look at their docs to find out how to suggest a
carboxylic acid.

Mark

On Sun, 6 Aug 2017 18:09 ZHANG Cheng <272699575 at qq.com> wrote:

> Dear Gromacs,
> I would like to perform simulations for a protein with glycines.
>
>
> I think I should use "insert-molecules" as shown on
>
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/biphasic/01_genconf.html
>
>
> So I went to PRODRG2 Server to obtain the glycine structure by "text
> drawing":
>
>
>     O
>     "
> N-C-C-O
>
>
> But I got a suggested structure of NH3-CH2-COO, instead of NH2-CH2-COOH.
> Can I ask why is that?
>
>
> Thank you.
>
>
> Yours sincerely
> Cheng
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