AMBER Archive (2009)

Subject: Re: [AMBER] Possibility to use ff99 + GAFF + GLYCAM_06 in one time for complex system ? - Last detail

From: FyD (fyd_at_q4md-forcefieldtools.org)
Date: Mon Apr 20 2009 - 09:50:12 CDT

Hi Marek

> As I reported sooner I would like to simulate dendrimers
> "decorated" with maltose.
>
> Unfortunately binding of maltose to terminal dendrimer amines
> requires opening of one glucose ring and creating bond between
> C1' and dendrimer terminal amine ( please see the attached picture ).
>
> In this case I assume that GLYCAM_06 forcefield could be
> used only for parametrisation of the second ( unbroken ) glucose
> ring and the broken one should be parametrised using GAFF ff.

Using GLYCAM, you could follow a similar idea to what is described @
http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#26

This is exactly the same idea: you need to split your
dendrimer-(pseudo-maltose)n in different "well chosen" building blocks.

regards, Francois

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