Justin A. Lemkul
jalemkul at vt.edu
Thu Jan 13 21:52:13 CET 2011
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.
> -Nisha P
> Quoting "Justin A. Lemkul" <jalemkul at vt.edu>:
>> nishap.patel at utoronto.ca wrote:
>>> 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:
>>> -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
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Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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