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 | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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