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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Received on Sat Sep 17 2011 - 23:30:03 PDT
