AMBER Archive (2009)

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

From: Marek Malý (maly_at_sci.ujep.cz)
Date: Thu Apr 16 2009 - 16:25:12 CDT

Dear Carl,

thank you very much for your additional information !

Best,

   Marek

Dne Wed, 15 Apr 2009 09:07:00 +0200 Karl Kirschner
<kkirsch_at_scai.fraunhofer.de> napsal/-a:

> Hi,
>
> I would recommend using the Glycam force field when sugars are involved
> in
> the simulation (but I am a bit biased :) ). In the development of Glycam
> and
> my personal use of it I have not seen "dramatic" differences when using
> the
> scaling factors. If I recall correctly, using the default scaling factor
> seems to effect the rotational barriers by reducing them (or raising the
> minima, depending on your perspective). You also get slightly different
> conformational populations (~1-10%) when using scaling factors versus no
> scaling factor, so it has some effects on the relative minima as well.
> However, I haven't seen a significant effect yet... One observable I
> would
> monitor if you use Glycam with scaling factors is the carbohydrate
> puckering.
> If your simulation alters the puckering, which is normally 4C1 for many
> sugars, then I would question if that is due to the use of scaling
> factors.
>
> Glycam has been extensively tested on it ability to reproduce
> experimental
> observables of carbohydrates. I can not comment on the ability of GAFF to
> model carbohydrates.
>
> Cheers,
> Karl
> 

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