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
>>
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Received on Mon May 13 2019 - 07:30:03 PDT
