Oh, thanks!<br><br><div class="gmail_quote">On Thu, Oct 6, 2011 at 7:59 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="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<br>
<br>
Sai Janani Ganesan wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Hi,<br>
<br><div class="im">
Thanks for the reply!<br>
<br>
I tried the rates, and only the terminal with positive rate gets pulled.<br>
<br>
The first and the last amino acids are spatially oriented one behind the other. I think defining a vector might work better, but I am not sure why nothing happens when I define a pull_vec1 and pull_vec2. Am I missing anything?<br>
<br>
</div></blockquote>
<br>
When setting "distance" as the pull_geometry, only pull_dim is used; pull_vec is ignored. If you want to define vectors, use the "direction" pull_geometry.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Thanks,<br>
Sai<div><div></div><div class="h5"><br>
<br>
<br>
<br>
On Thu, Oct 6, 2011 at 9:14 AM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>> wrote:<br>
<br>
<br>
<br>
Sai Janani Ganesan wrote:<br>
<br>
Hi,<br>
<br>
I am trying to pull the first from the last amino acid of a<br>
protein to completely unfold the protein in the X direction. I<br>
chose the middle amino acid as the reference, and the groups get<br>
pulled in the same direction or opposite direction (which is<br>
what I want) depending on the trial. I am trying to find a<br>
definite method to completely unfold it.<br>
I define a different vector (pull_vec1 and pull_vec2) with +x<br>
and -x values and that does not even pull the protein<br>
I tried using only pull_group1 and pull_group2, without a<br>
reference, and neither groups get pulled.<br>
I chose different references, I do have some success but I don't<br>
think it is the best way to do it.<br>
<br>
How do I pull the N and C terminal apart, by simultaneously<br>
pulling them in opposite directions?Why is my vector definition<br>
wrong?<br>
<br>
This is my pull code:<br>
<br>
pull = umbrella<br>
pull_geometry = distance<br>
pull_dim = Y N N<br>
pull_start = yes pull_ngroups = 2<br>
pull_group0 = Chain-C<br>
pull_group1 = Chain-B<br>
pull_group2 = Chain-A<br>
<br>
%pull_vec1 = -31 0 0<br>
%pull_vec2 = 31 0 0<br>
<br>
<br>
I suspect the % signs will mess things up, but probably will give a<br>
fatal error, if nothing else.<br>
<br>
<br>
pull_rate1 = 0.002 pull_k1 = 1000 pull_rate2<br>
= 0.002 pull_k2 = 1000 <br>
<br>
Here's the problem. You're telling the two pulled groups to move in<br>
the same direction. With "distance" geometry, the selections are a<br>
bit more simplistic. If you set pull_rate1 to -0.002 and pull_rate2<br>
to 0.002, the groups will be pulled in opposite directions.<br>
Otherwise, you're just towing your protein along in the box.<br>
<br>
-Justin<br>
<br></div></div>
-- ==============================<u></u>__==========<div class="im"><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></div>
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</blockquote><div><div></div><div class="h5">
<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" value="+15402319080" target="_blank">(540) 231-9080</a><br>
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