<br><br><div class="gmail_quote">On Mon, May 30, 2011 at 10:10 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>
mohsen ramezanpour wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Dear Dr.Justin<br>
<br>
There is not any answer?<br>
<br>
</blockquote>
<br></div>
Please have a bit of patience. I'm not your personal answer service. You just happened to catch me at a good time this morning and I was able to respond quickly. I have my own work to do, you know.</blockquote><div>
<br>Thanks for your reply<br>No Dr.Justin,I didn't mean this by my question.It was your favour replying to my questions.<br>I just thought my question is not logical OR it is answer is not difficult And I must review articles in this field.just this. <br>
</div><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>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<br>
On Mon, May 30, 2011 at 7:58 PM, mohsen ramezanpour <<a href="mailto:ramezanpour.mohsen@gmail.com" target="_blank">ramezanpour.mohsen@gmail.com</a> <mailto:<a href="mailto:ramezanpour.mohsen@gmail.com" target="_blank">ramezanpour.mohsen@gmail.com</a>>> wrote:<br>
<br>
Yes,you are right<br>
I need to do more sampling.But the second attached file was just to<br>
transfer my mean :)<br>
</blockquote>
<br></div>
Always provide complete information. I can't get in your head to know everything you're thinking. If you want free help, make it easy to help you. Hack job files wind up causing confusion and delaying an answer rather than providing you with one.</blockquote>
<div><br>Yes,You are right <br></div><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>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
My final PMF curve is the first attached file.<br>
<br>
Sorry for asking more questions..<br>
<br>
Regarding my notes about windowses in last email and looking at<br>
FIRST attached file:<br>
Which one is my starting point?<br>
0.18 (with negative value ) OR 0.03 (with about zero value) OR the<br>
average in that region?<br>
<br>
</blockquote>
<br></div>
I have no idea. Watch your trajectories and see what your ligand is doing at these points. Presumably you have a window in which the ligand is bound in the protein's active/receptor site, and perhaps after some simulation the position moves to arrive at its energy minimum. In general, from a PMF curve, the highest point (as long as it's stable) minus the lowest point is your DeltaG.</blockquote>
<div><br>aha! <br></div><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>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Because there is a difference about 0.5 kcal/mol .<br>
</blockquote>
<br></div>
So there are some energetic differences in these windows. Watch the trajectories to figure out why.<div><div></div><div class="h5"></div></div></blockquote><div> </div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div><div class="h5">Sure <br>
<br>
-Justin<br>
<br>
-- <br>
========================================<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> | (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>
<br>
========================================<br>
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