[gmx-users] sugar force fields

[Oliver Grant]

This is review of all the carbohydrate force fields. It's only missing the
latest CHARM one which I think is available in the latest release of
gromacs.

E. Fadda and R.J. Woods, “*Molecular* *Simulations* of *Carbohydrates* and *
Protein-Carbohydrate* *Interactions*: *Motivation*, *Issues*, and *Prospects
*”, *Drug* Discov.*Today*., *2010*
**
*Oliver*
**
**


On 7 April 2011 07:47, <nishap.patel at utoronto.ca> wrote:

> Here are few papers you can refer to:
>
>   Gromos forcefield for hexopyronase-based carbohydrates - Roberto D.Lins
>   and Philippe H. Hunenberger 2005
>
> (In gromos forcefield there are parameters for galactose)
>
>   An improved OPLS?AA force field for carbohydrates- D Kony 2002
>
> Hope it helps!
>
> Nisha P
>
>
>
>
>
>
> Quoting Michael Brunsteiner <mbx0009 at yahoo.com>:
>
>
>> Dear all,
>>
>> I understand that most major force fields (charmm, opls, amber,
>> gromos?...)
>> come with parameters for sugars. I wonder:
>>
>> 1)  if any work has been done/published comparing
>> the accuracy of these different sugar force fields
>>
>> 2) Of the force fields that come with gromacs is there one
>> for which making sugar topologies is as straight forward as making
>> topologies for amino acids, or if there is no such thing for which FF is
>> making a sugar topology the least tedious?
>>
>> BTW: I want to model simple sugar molecules, monomers,
>> dimers (no polymers)
>>
>> thanks!
>>
>> Michael
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>
>
>
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