[gmx-users] new block lactitol

[Justin A. Lemkul]

cesteban at unsl.edu.ar wrote:
> 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.

Hence why parameterization is difficult :)  But I maintain that all of the 
relevant functional groups (which in your case are primarily alcohols) are 
present within the force field to get you started.  There are slight differences 
between sugar alcohol groups (i.e., GLC/GAL) and alcohols on amino acids 
(SER/TYR), especially in terms of charge.  You will have to decide what is best 
for your molecule.  Thorough validation of the accuracy of these parameters is 
necessary in all cases of new parameters.

Sorry, there is no easy answer when developing new parameters.  It is a very 
difficult part of running simulations :)

-Justin

> 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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> 
> 
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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

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