[gmx-users] new block lactitol

[Justin A. Lemkul]

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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-- 
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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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