Generating charges properly requires ensemble averaging. That is, you
can't just use one structure. You need to generate an ensemble of
reasonable structures and average those charges. I'm sure this has
been discussed previously on the list. The procedure is also given in
the Glycam06 paper. If you want to use Glycam properly, this is how
you should generate charges.
Did you do your QM in the gas phase? The presence of water definitely
has an effect. If you want to determine the quality of the
conformations you get from the simulation, it is probably best to find
a good experiment. For example, you might look for an NMR study of
NOE's or J-couplings for the system.
:-) Lachele
On Mon, Aug 1, 2011 at 9:46 AM, David A Case <case.biomaps.rutgers.edu> wrote:
> On Mon, Aug 01, 2011, Thomas Exner wrote:
>>
>> I am trying to simulate the interaction between a protein and mannose
>> and modifications of mannose. Since there are no parameters for these
>> modifications....
>
> Why not use GLYCAM? Sections 2.9 and 3.5 of the AmberTools Users' Manual
> gives details, including mannose, man-9, etc.
>
> ...dac
>
>
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>
--
:-) Lachele
Lachele Foley
CCRC/UGA
Athens, GA USA
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Received on Mon Aug 01 2011 - 08:30:04 PDT
