[gmx-users] galactose

[Justin A. Lemkul]

nishap.patel at utoronto.ca wrote:
> Hello,
> 
>    I am trying to simulate galactose in water using Gromos FFG53A6 force 
> field. The molecular formula for galactose is C6H12O6, however in the 
> FFG53A6.rtp file, the molecular formula is C6H10O5 for galactose-A and 
> B. Why is it different? I would really appreciate some help!
> 

The Gromos96 sugar parameters assume the residues are part of a larger polymer, 
thus condensation of sugars eliminates the "missing" H2O.

There is a newer version of these parameters that was recently published, which 
may have some relevant details:

dx.doi.org/10.1002/jcc.21675

-Justin

> Thanks
> 
> -Nisha P
> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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