> I do not agree with Lachele'statement "You should definitely use the
> different scaling factors". You are free to do what you want.
This should of course come with the caveat (that Francois gives at the end
of his email but which I think should be in bold at the beginning) that
while you are free to do what you want you should be able to demonstrate
that your approach is MORE 'correct' than the approach suggested and be able
to vigorously defend this decision when it comes to publication.
I should add that the FF99SB parameters for amino acids and nucleic acids
were parameterized with 1-4 scaling factors of 1.2 for EEL and 2.0 for VDW.
Glycam on the other hand uses no scaling factor for the 1-4s (so 1.0 and
1.0). Hence using anything different than this is outside of the way in
which the parameters were generated and so would need to be explicitly
defended.
> The article presented . http://www.ncbi.nlm.nih.gov/pubmed/21792425 is
> an example where the Amber scaling factors for 1-4 non-bonding
> interactions are applied to all the glycopeptide. The approach
> followed is far more simple and is efficient even for heterogeneous
> CD-based glycopeptides. Obvisouly, scaling factors for 1-4 non-bonding
> interactions + type of RESP charges + dihedral FF parameters have to
> be correctly used/mixed.
But this approach, refitting all the charges etc, is no longer necessary. To
use Dave Case's terminology if you use tleap from a fully patched
AMBER11+AmberTools 1.5 AMBER just "Does the right thing"(tm). It will
automatically use no scaling for the glycam-glycam interactions and 1.2/2.0
for the FF99SB interactions and then 1.2/2.0 for Glycam-FF99SB interactions.
> Whatever approach you will decide to follow, you simply need to
> demonstrate that it works. Once again you should run MD & see how it
> goes to build your own experience.
My point being the same as Lachele's here. AMBER now does the correct thing
with respect to the Glycam and Amino Acid force fields when you mix them and
thus there is no need to add all the complexities of refitting resp charges,
adjusting dihedral parameters etc etc unless you are in the business of
making your own force fields.
All the best
Ross
/\
\/
|\oss Walker
---------------------------------------------------------
| Assistant Research Professor |
| San Diego Supercomputer Center |
| Adjunct Assistant Professor |
| Dept. of Chemistry and Biochemistry |
| University of California San Diego |
| NVIDIA Fellow |
|
http://www.rosswalker.co.uk |
http://www.wmd-lab.org/ |
| Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
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Received on Sun Sep 18 2011 - 18:30:03 PDT
