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
