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>
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> 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
> >>
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue May 14 2019 - 03:30:02 PDT
