On Thu, May 15, 2014 at 10:05 AM, Rossen Apostolov <rossen.kth.se> wrote:
> Hi,
>
> The NALA terminal charges are the same in both Amber03 and Amber99
> although the corresponding ALA residue charges are different in those
> forcefields. Here is the report by a Gromacs user who noticed it:
> http://redmine.gromacs.org/issues/1466
>
> Is that correct or the charges need to be fixed?
>
I will also try to clarify something in the post you linked here. The
quote:
"""
The main-chain torsion parameters were obtained by fitting to the energy
profiles of Ace-Ala-Nme and Ace-Gly-Nme di-peptides
calculated using MP2/cc-pVTZ//HF/6-31G** quantum mechanical methods. All
other parameters were taken from the existing AMBER data base.
"""
Here, "all other parameters" probably should have been reworded into
"all other torsion parameters". The design strategy of ff03 as I
understand it was to design a new charge model which necessitated
refitting torsion parameters (bond and angle parameters are fairly
reliable and transferable).
I'll certainly agree with Chris Neale that the above quote is misleading
and that the interpretation that the terminal charges are unchanged is
reasonable, but I would not have drawn the same conclusion. For one
thing, the paper also explicitly states that a new charge scheme was
used and the charge philosophy is inherently different from that used by
ff99/ff94. Given the context and the intent of the entire article, I
think the conclusion that the terminal charges are _not_ the same as
ff99 is more plausible.
All the best,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Thu May 15 2014 - 09:30:03 PDT
