AMBER Archive (2007)

Subject: Re: AMBER: using glycam04 parameters

From: kkirschn_at_hamilton.edu
Date: Wed Apr 25 2007 - 15:02:49 CDT

Hi Ross and Amber community,

        Let me add my thoughts on this, given below.

On 19.04.2007, at 15:00, Ross Walker wrote:
>> from another force field. This has to be done with caution. The
>> recent versions of Glycam (04-06) was developed using unity scaling
>> factors (ie. SCEE=SCNB=1). This is in contrast to how the other
>> Amber force fields are developed. Mixing parameters from different
>> force fields is likely to introduce artifacts into the calculations,
>
> Is this true? I thought that the Glycam 04 force field - in
> contrast to the
> earlier Glycam versions - specifically used SCEE = 1.2 and SCNB =
> 2.0 so
> that one could mix sugar and amino acid simulations which earlier
> could not
> be done?

Yes, this is true, SCEE=SCNB=1.0 for the most recent Glycam versions.
These recent versions (Glycam 04-06) were developed to avoid the use
of 1-4 electrostatic or non-bonded scaling factors. Carbohydrates
provide and interesting case for these scaling factors because of the
omega-angle rotation (O5-C5-C6-O6). The O6 oxygen may interact with
either O4 oxygen (a 1-5 relationship) or O5 (a 1-4 relationship) at
equivalent non-bonded distances. The use of 1-4 scaling unbalances
these interactions leading to an inability to correctly predict
rotamer populations (PNAS 2001, 98(19), 10541 eludes to this idea).

> Or perhaps I am confusing things here with 10-12 vs 6-12 VDW terms...

> Perhaps Rob Woods could comment some more on how one mixes AMBER
> amino acid
> force fields with the Glycam force fields in a single simulation...
> If the
> different value of SCEE in the two force fields is indeed still an
> issue
> then perhaps we should look to implement this "mixture" in the
> code... -
> Perhaps by just hardwiring the prmtop and do away with scee and
> scnb as
> namelist variables all together??

Now when mixing with Amber amino acid (AA) force fields, we suggest
using the scaling factors that were used in the development of AA
force fields (ie. SCEE = 1.2 and SCNB = 2.0). This will cause the
loss of accurate populations for the omega-angle rotation, but
"should not" change the carbohydrate structure or stability. (This
is stated in the Amber manuel under the Glycam force field.) We
performed some test on pure monosaccharides using the Amber default
scaling factors, and did not see any unusually conformational changes
in the sugars. [I believe that the use of scaling factors reduces the
rotational barriers for 1-4 interactions (or if you prefer,
destabilizes the minima some).] One should always check their
simulation results when mixing the carbohydrate and the AA
parameters, to make sure that the sugars do not undergo some strange
dynamics or ring flipping. Of course, your solution of doing a
"mixture" code would be best :) .

Hope this helps clarify some. We have a manuscript that has been
submitted to J. Comp. Chem., which discusses the development of
Glycam06 force field in detail.

Cheers,
Karl
____________________________________
Karl N. Kirschner, Ph.D.
Center for Molecular Design, Co-Director
Department of Chemistry
Hamilton College, Clinton NY 13323
____________________________________

> All the best
> Ross
>
> /\
> \/
> |\oss Walker
>
> | HPC Consultant and Staff Scientist |
> | 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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