ceste...@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
ceste...@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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--
========================================
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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