AMBER Archive (2009)

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

From: Karl Kirschner (kkirsch_at_scai.fraunhofer.de)
Date: Mon Apr 20 2009 - 07:27:45 CDT

Hello Marek,

        You should be able to model the "broken" glucose fine using Glycam_06.
Glycam_06 was parameterized using hydrocarbons, alcohols, and ethers (plus a
more limited number of nitrogen and RCO2- compounds; J. Comput Chem 29, 2008,
622). It was tested on a small molecule test suite and on carbohydrates.
Thus, Glycam_06 should work well for simulating the broken glucose.

        You may be missing parameters for where the glucose is linked to the
dendrimer. You could use parameters from either ff99 or gaff for the missing
parameters. Due to the flexibility and the number of highly rotatable bonds
of your system, it would be advantageous to test the resulting force field
against experiment or QM to validate your parameter choices.

Cheers,
Karl

On Monday 20 April 2009 13:52, Marek MalĂ½ wrote:
> Dear all, I have very last question to this topic.
>
> 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.
>
> Am I right ?
>
>
> Thanks in advance for answering of this my very last
> question.
>
> Marek

_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber