[gmx-users] new block lactitol

[cesteban at unsl.edu.ar]

Hi Justin
Thanks for your answer.
I had check the relevant sugar, but I still have the problem of
parameterization of the open GLC ring that forms the lactitol molecule.
If you know of a similar example please let me know.
Thanks very much
Carmen
>
> cesteban at unsl.edu.ar wrote:
>> Hi All
>> I am trying to analize the dynamics of polysaccharid which include
>> lactitol grups (b-D-Galp-(1-4)-D-Glc-ol), using ffG53a6 force field.
>> I need to make a new building block in .rtp file, but I don´t know about
>> the proper parameters.
>
> Most of the fundamental building blocks you need are already present in
> the
> force field.  Check out the relevant .rtp file and you'll find the sugars,
> as
> well as phosphate within a few entities.
>
> Validation will be another story, unless you think "chemical intuition"
> will be
> enough.  But real parameter development is laborious.  See here:
>
> http://wiki.gromacs.org/index.php/Parameterization
>
> -Justin
>
>> Someone has made a lactitol´s block  or can help me with the proper
>> parameters?
>> Any help would be appreciated.
>> Carmen
>>
>>
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>
> --
> ========================================
>
> Justin A. Lemkul
> Graduate Research Assistant
> ICTAS Doctoral Scholar
> 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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