[gmx-users] Aspartate at high pH

[Tsjerk Wassenaar]

Hi Valentina,

Use pdb2gmx -ter

Cheers,

Tsjerk

On Wed, Feb 13, 2013 at 1:22 PM, Valentina Erastova
<valentina.erastova at durham.ac.uk> wrote:
> Hello!
>
> I am simulating Aspartate at pH > 10, so it needs to be fully deprotonated (COO-, COO- and NH2).
>
> pdb2gmx allows to easily set side chains to be deprotanted, but is there a straightforward way to make NH2, not NH3+?
>
> Thank you very much!
>
>
> Kind regards,
> Valentina
>
> __________________________
> Dr Valentina Erastova
>
> Postdoctoral Research Assistant
> Department of Earth Sciences
> Durham University
>
> Editor-in-Chief,
> Kaleidoscope
>
> +44 786 131 6686
>
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-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Biocomputing Group
Department of Biological Sciences
2500 University Drive NW
Calgary, AB T2N 1N4
Canada