Without knowing the details of the system, it is difficult to suggest ways to avoid the local deformation. Hopefully additional restraints will help.
An alternative approach you could try is a series of runs where the restrained distance(s) is slowly changed. For each value of the distance, perform a minimization followed by MD run.
Pratul K. Agarwal, Ph.D.
(Editorial Board Member: PLoS ONE, Microbial Cell Factories)
Web: http://www.agarwal-lab.org/
On 5/14/2019 6:03 AM, Akshay Prabhakant wrote:
Hi Pratul!
Thank you for the helpful reply. I tried varying the rk2, rk3 constants to
lower values, (and I'm even reduced the timestep of the computation to 1fs
instead of 2fs) but the helices still can't make a rotation without
deforming/stretching out in weird confrmations.
I am now trying to add restaraints between every pair of alpha carbon atoms
in the helix. There are about 10 atoms in there, so this will result in 50
new distance constraints. This to me seems like the best way to treat the
helix as a somewhat rigid body. Whle this will increase the computational
time, will it have any other unintended side effects?
Thanks!
On Mon, May 13, 2019 at 7:54 PM Pratul Agarwal <pratul.agarwal-lab.org><mailto:pratul.agarwal-lab.org>
wrote:
Short answer: Try lower values of rk2 and rk3, with longer simulations.
Long answer: Many things have to be considered when applying such
restraints. Does the protein topology have enough room and flexibility
to accommodate the change you are trying to induce? What about
time-scales? If you are effectively applying a large force in a short
time-frame, local rearrangement of atoms would likely be the result
(distorting the local interactions) instead of a larger conformational
change. Try lower values of force constants. Try several values -- I
would recommend lower force constants over longer time-scales.
Pratul K. Agarwal, Ph.D.
(Editorial Board Member: PLoS ONE, Microbial Cell Factories)
Web: http://www.agarwal-lab.org/
On 5/13/2019 10:01 AM, Akshay Prabhakant wrote:
Here's the restrain file contents (disang.30)
Restraints for bonds
! hold the bottom ends of the helices fixed
&rst
iat=-1,-1,
iresid=0,
r1=-99.0,r2=30.0,r3=30.0,r4=99.0,
rk2=2.5,rk3=2.5,
igr1=2858, 2882, 2897, 2911, 2927, 2934, 2958,
igr2=6204, 6228, 6243, 6257, 6273, 6280, 6304,
/
! vary the distance between the top ends of the helices, to simulate a
rotation
&rst
iat = -1,-1,
iresid=0,
r1=-170.0,r2=30.0,r3=30.0,r4=230.0,
rk2=2.5,rk3=2.5,
igr1=2977, 2996, 3018, 3035, 3054, 3069,
igr2=6323, 6342, 6364, 6381, 6400, 6415,
/
! distance between COM of top half and bottom half of helix 1 should be
constant
&rst
iat = -1,-1,
iresid=0,
r1=-12.0,r2=9.535,r3=9.535,r4=12.0,
rk2=2.5,rk3=2.5,
igr1=2858, 2882, 2897, 2911, 2927, 2934, 2958,
igr2=2977, 2996, 3018, 3035, 3054, 3069,
/
! distance between COM of top half and bottom half of helix 2 should be
constant
&rst
iat = -1,-1,
iresid=0,
r1=-12.0,r2=9.413,r3=9.413,r4=12.0,
rk2=2.5,rk3=2.5,
igr1=6204, 6228, 6243, 6257, 6273, 6280, 6304,
igr2=6323, 6342, 6364, 6381, 6400, 6415,
/
EOF
On Mon, May 13, 2019 at 7:23 PM Akshay Prabhakant <
akshayresearch16.gmail.com<mailto:akshayresearch16.gmail.com>> wrote:
Hello everyone,
I am trying to vary the distance between 2 alpha helices, and have set
up
my distance restraints to study that. However, for certain distances,
the
helices get really stretched out and lose most of their helicity. I then
set up additional distance restraints to constrain the length of the
helices to their initial value, but that resulted in similar weird
stretching out/bending of the helix.
Using COM distance based restraints, how do I keep my alpha helices from
losing their shape? I would like to treat both helices as rigid bodies
during the course of my simulation.
Thank you,
Akshay
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Received on Tue May 14 2019 - 07:00:02 PDT
