You should definitely use the different scaling factors. To do that,
you need to generate the input files using tleap from AmberTools 1.5,
fully patched. If you do that, then the appropriate scaling factors
will be applied. To verify this, inspect the first page or two of the
output file (sander or pmemd). Somewhere near the top, it should tell
you that it is reading the scaling factors from the topology file.
The scaling factors affect structure. They will not directly affect
non-bonded interactions. They only affect them indirectly in that
they ensure a better representation of the molecular structure. To
get the best representation of the carbohydrate's structure, you
should use the scaling factors appropriate to the carbohydrate, and,
likewise for the protein. Remember that the scaling factors only
affect interactions between atoms that are three bonds removed from
each other. That is, A and D in the bonded sequence A-B-C-D.
:-) Lachele
On Sat, Sep 17, 2011 at 6:43 PM, Yun Shi <yunshi09.gmail.com> wrote:
> 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
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>
--
:-) Lachele
Lachele Foley
CCRC/UGA
Athens, GA USA
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Received on Sat Sep 17 2011 - 19:30:02 PDT
