Re: [AMBER] Deprotonated serine residue.

From: Dd H <ddhecnu.gmail.com>
Date: Thu, 27 Oct 2016 20:06:40 +0800

Thank you very much, I'll have a try.

On 26 October 2016 at 16:27, FyD <fyd.q4md-forcefieldtools.org> wrote:

> Dear Dading Huang,
>
> > I want to simulate a protein that contains a deprotonated serine residue.
>
> you could create your own force field - residue...
>
> See http://q4md-forcefieldtools.org/Tutorial/Tutorial-4.php
> http://q4md-forcefieldtools.org/Tutorial/Tutorial-4.php#16
> http://q4md-forcefieldtools.org/Tutorial/Tutorial-4.php#25
> http://q4md-forcefieldtools.org/Tutorial/Tutorial-4.php#26
>
> and use http://q4md-forcefieldtools.org/REDServer-Development/
>
> You will likely have to create a new atom type for that O(-) oxygen.
>
> See http://q4md-forcefieldtools.org/Tutorial/Mini-HowTo-InputFiles.pdf
> then once you got the QM data re-run PyRED using the Re_Fit job to
> generate/update the FF.
> see http://upjv.q4md-forcefieldtools.org/Tutorial/Tutorial-4-demo1.pdf
>
> regards, Francois
>
>
> F.-Y. Dupradeau
> ---
> http://q4md-forcefieldtools.org/FyD/
>
>
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Received on Thu Oct 27 2016 - 05:30:04 PDT