[gmx-users] galactose

[nishap.patel at utoronto.ca]

Thanks. I am going to look over it. But I was wondering is it possible  
to just simulate one molecule of sucrose (glucose+fructose) in water  
using any of the force fields by Gromacs? I realize I would have to  
add the parameters to the .rtp files, but as you mentioned that the  
force fields recognizes them as part of the larger polymer and so it  
doesn't take into account the missing atoms.

-Nisha P


Quoting "Justin A. Lemkul" <jalemkul at vt.edu>:

>
>
> 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
>>
>
> -- 
> ========================================
>
> 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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