AMBER Archive (2009)

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

From: Karl Kirschner (kkirsch_at_scai.fraunhofer.de)
Date: Wed Apr 15 2009 - 02:07:00 CDT

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 

-- 
------------------------------------ 
Karl N. Kirschner, Ph.D.
Fraunhofer-Institute for Algorithms
    and Scientific Computing - SCAI
Department of Simulation Engineering
Schloss Birlinghoven
53754 Sankt Augustin, Germany
Tel: +49 (0) 2241-14-2052
Fax: +49 (0) 2241-14-1328
------------------------------------ 

On Wednesday 15 April 2009 01:27, Ross Walker wrote:
> Hi Marek,
>
> > thank you very much for your complex and valuable answer !
> >
> > Just for the curiosity, is this discussed combination:
> >
> >   GLYCAM_06 + ff99SB + GAFF
> >
> > remarkably better solution than only:
> >
> > ff99SB + GAFF
> >
> >        ?
>
> I would be VERY surprised if GAFF gets the subtleties of conformation in
> sugars correct. To the point that I think the error would be larger than
> the 1-4 scaling not necessarily being optimal. This is only a hunch though,
> I have not tried it. Your best option would probably be to try a single
> maltose and let Antechamber parameterise it and then compare certain
> properties (dihedral barriers etc) with the Glycam 06 ones. This will give
> you an idea of the differences.
>
> Rob Woods can probably comment some more on this.
>
> All the best
> Ross
>
>
> /\
> \/
>
> |\oss Walker
> |
> | Assistant Research Professor |
> | San Diego Supercomputer Center |
> | Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
> | http://www.rosswalker.co.uk | PGP Key available on request |
>
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