[gmx-users] galactose

[Justin A. Lemkul]

nishap.patel at utoronto.ca wrote:
> 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.
> 

You have to add the terminal atoms to the .rtp entries, that's all.

-Justin

> -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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> 
> 
> 

-- 
========================================

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

========================================