Sai Janani Ganesan wrote:
Hi,
Thanks for the reply!
I tried the rates, and only the terminal with positive rate gets pulled.
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?
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.
-Justin
Thanks,
Sai
On Thu, Oct 6, 2011 at 9:14 AM, Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu>> wrote:
Sai Janani Ganesan wrote:
Hi,
I am trying to pull the first from the last amino acid of a
protein to completely unfold the protein in the X direction. I
chose the middle amino acid as the reference, and the groups get
pulled in the same direction or opposite direction (which is
what I want) depending on the trial. I am trying to find a
definite method to completely unfold it.
I define a different vector (pull_vec1 and pull_vec2) with +x
and -x values and that does not even pull the protein
I tried using only pull_group1 and pull_group2, without a
reference, and neither groups get pulled.
I chose different references, I do have some success but I don't
think it is the best way to do it.
How do I pull the N and C terminal apart, by simultaneously
pulling them in opposite directions?Why is my vector definition
wrong?
This is my pull code:
pull = umbrella
pull_geometry = distance
pull_dim = Y N N
pull_start = yes pull_ngroups = 2
pull_group0 = Chain-C
pull_group1 = Chain-B
pull_group2 = Chain-A
%pull_vec1 = -31 0 0
%pull_vec2 = 31 0 0
I suspect the % signs will mess things up, but probably will give a
fatal error, if nothing else.
pull_rate1 = 0.002 pull_k1 = 1000 pull_rate2
= 0.002 pull_k2 = 1000
Here's the problem. You're telling the two pulled groups to move in
the same direction. With "distance" geometry, the selections are a
bit more simplistic. If you set pull_rate1 to -0.002 and pull_rate2
to 0.002, the groups will be pulled in opposite directions.
Otherwise, you're just towing your protein along in the box.
-Justin
--
==============================__==========
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
<tel:%28540%29%20231-9080>
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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
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========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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