AMBER Archive (2009)
Subject: Re: [AMBER] Possibility to use ff99 + GAFF + GLYCAM_06 in one time for complex system ?
From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Wed Apr 15 2009 - 08:33:00 CDT
and please do NOT use ff99! use ff99SB. my opinion is that work using
ff99 should no longer be publishable- previously published work may be
just fine, but now that we have known for years that there is
something much better at no extra cost, there is just no reason to use
the less accurate model.
On Wed, Apr 15, 2009 at 3:07 AM, Karl Kirschner
> 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.
> 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
>> |\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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