The OPLS-AA force field is used for glucose and trehalose in conjunction with other force fields in the article by Sukit Leekumjorn and Amadeu K. Sum:<br><br>"Molecular Dynamics Study on the Stabilization of Dehydrated Lipid Bilayers with Glucose and Trehalose". J. Phys. Chem. B, 2008, 112 (34), pp 10732–10740<br>
<br>Are you suggesting that the authors used incorrect parameters?<br><br><br><div class="gmail_quote">On Mon, Aug 10, 2009 at 6:05 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div class="im"><br>
<br>
Nancy wrote:<br>
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Hello,<br>
<br>
I have successfully minimised and equilibrated two systems, one consisting of a single molecule of ethylene glycol (1,2-ethanediol) in a water box, and the other is one molecule of glycerol, also in a water box. I am planning to proceed to simulate other sugar alcohols (e.g. erythritol, arabitol, mannitol, etc). I used topolbuild 1.2 to generate topologies for ethanediol and glycerol, and for the various atoms in these molecules, I used charge values from methanol (the methanol tutorial included with GROMACS), i.e. +0.398 for hydroxyl hydrogens, -0.574 for oxygens, and +0.176 for the carbons.<br>
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</blockquote>
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As I told you before, the origin of these charges, in the absence of some published validation of the parameters, is questionable at best.<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Should I use these charge values for an arbitrary sugar alcohol, or should I use the charge values specified in the article:<br>
<br>
"OPLS All-Atom Force Field for Carbohydrates". Damm, W., A. Frontera, J. Tirado-Rives, and W. L. Jorgensen. 1997. J. Comput. Chem. 18:1955–1970.<br>
<br>
</blockquote>
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If you are using OPLS, probably yes. But as I recall, you were running simulations with GROMOS96. If this is the case, then using OPLS charges or other parameters is wholly inappropriate. The simple fact is, you must use charges from the parameter set you intend to simulate, otherwise go through the laborious process of deriving them yourself.<div class="im">
<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Also, are there programs that will automatically generate charge values and other parameters for an arbitrary molecule?<br>
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</blockquote>
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There are several options, like the R.E.D. server or antechamber (available from the Amber folks), but be advised that you should always follow the methodology for whatever force field you're using. If it's GROMOS (like you've been using before), neither of these approaches is necessary, and they may not give you correct parameters. Read the primary literature and base your decisions on what you find.<br>
<br>
-Justin<br>
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<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Thank you.<br>
<br>
Nancy<br>
<br>
<br>
<br>
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-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
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