Thank you!<br><br>
<div class="gmail_quote">On Wed, Feb 22, 2012 at 4:08 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br>
<blockquote style="BORDER-LEFT:#ccc 1px solid;MARGIN:0px 0px 0px 0.8ex;PADDING-LEFT:1ex" class="gmail_quote">
<div class="im"><br><br>Steven Neumann wrote:<br>
<blockquote style="BORDER-LEFT:#ccc 1px solid;MARGIN:0px 0px 0px 0.8ex;PADDING-LEFT:1ex" class="gmail_quote">Dear Gmx Users, Dear Justin,<br> I run pulling of my ligand away from my protein. Then I used Justin perl script to extract distances for umbrella sampling windows between my ligand and crucial residue of my protein (Isoleucine). The number of hydrogen bonds between ligand and protein during the pulling is app. 3 at the begining, then 4 in some frames and then obviously zero (when ligand dissociated).<br>
Would you use the 1st frame as a starting window when number of hbonds is 3 or further window when this is number is 4?<br></blockquote><br></div>Assuming the first frame represents a fully-bound configuration, you should start there. I'm guessing you're trying to determine the DeltaG of binding for your ligand. If you define an arbitrary reaction coordinate, you get an arbitrary answer. Starting and ending points dictate the value of DeltaG (since it is a state function).
<div class="im"><br><br>
<blockquote style="BORDER-LEFT:#ccc 1px solid;MARGIN:0px 0px 0px 0.8ex;PADDING-LEFT:1ex" class="gmail_quote">Is spacing of 0.2 nm (pulling of app 6 nm) sufficent for the system where interactions are via hydrogen bonds and hydrophobic interactions only?<br>
<br></blockquote><br></div>Most systems interact via hydrogen bonds and hydrophobic interactions. Generally, 0.2 nm is a decent starting point, but should by no means be viewed as any sort of universal standard. It worked for me in my tutorial, it may not work for others. Consult the literature for similar systems and proceed. If you find under-sampled regions along the reaction coordinate, it is trivial to add a new window.<br>
<br>-Justin<br><br>-- <br>==============================<u></u>==========<br><br>Justin A. Lemkul<br>Ph.D. Candidate<br>ICTAS Doctoral Scholar<br>MILES-IGERT Trainee<br>Department of Biochemistry<br>Virginia Tech<br>Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu/" target="_blank">vt.edu</a> | <a href="tel:%28540%29%20231-9080" target="_blank" value="+15402319080">(540) 231-9080</a><br><a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.<u></u>vt.edu/Pages/Personal/justin</a><br>
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