> Obvisouly, scaling factors for 1-4 non-bonding
> interactions + type of RESP charges + dihedral FF parameters have to
> be correctly used/mixed.
How is this different from what I said? If you plan to use glycam and
ff99sb, the most correct thing to do is to apply amber scaling to the
protein and glycam scaling to the carbohydrate.
Of course, you can deviate from the prescribed procedure. And, if you
get better results, we are interested to hear about it.
:-) Lachele
On Sun, Sep 18, 2011 at 2:14 AM, FyD <fyd.q4md-forcefieldtools.org> wrote:
> Dear Yun,
>
> I do not agree with Lachele'statement "You should definitely use the
> different scaling factors". You are free to do what you want.
>
> 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.
>
> 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.
>
> regards, Francois
>
>
> Quoting Yun Shi <yunshi09.gmail.com>:
>
>> Hi all,
>>
>> I want to study the interaction of a carbohydrate ligand with a protein
>> receptor, and they are of course NOT covalently linked.
>>
>> It seems people would use glycam for the sugar part and ff99sb for the
>> protein part while implementing the 'amber' scaling factors for the entire
>> system. But I wonder if it would be reasonable to apply different set of
>> scaling factors for the protein part and the sugar part, since amber11
>> already has this function?
>>
>> And it seems to me that different set of scaling factors will not affect
>> inter-molecular interactions.
>>
>> Thanks,
>> Yun
>
>
>
> F.-Y. Dupradeau
> ---
> http://q4md-forcefieldtools.org/FyD/
>
>
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>
--
:-) Lachele
Lachele Foley
CCRC/UGA
Athens, GA USA
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Received on Sun Sep 18 2011 - 15:30:02 PDT
