Re: [AMBER] How to restrain minimum distance between proteins?

From: Gustavo Seabra via AMBER <amber.ambermd.org>
Date: Wed, 26 Oct 2022 14:39:23 -0400

Hi Matthew,

Have you tried to set a restraint on the distance between COMs of the two
proteins? I suppose you can have something like:

&rst
    iat=-1,-1,
    igr1= (list CAs fr the first protein),
    igr2= (list CAs for the second protein),
    r1=(minimal distance - some tolerance), r2=(minimal distance),
r3=(minimal distance), r4=(minimal distance + tolerance),
    rk2=(some force constant), rk3=0.0
 /

As long as the "minimal distance" is larger than the sum of the protein
radii, that should avoid them to get in contact.

Al the best,

--
Gustavo Seabra.
On Tue, Oct 25, 2022 at 12:11 AM Matthew Guberman-Pfeffer via AMBER <
amber.ambermd.org> wrote:
> Dear AMBER community,
>
> I’m running simulations where there are two proteins in the simulation box
> and I need to prevent them from getting close enough to interact. Is there
> a way to restrain the minimum distance between any pair of atoms for the
> two proteins?
>
> I’ve tried all sorts of restraints (e.g., fixing the X-, Y-, and
> Z-components of the centers of mass), but somehow the minimum distance
> always gets smaller.
>
> Best,
> Matthew
>
>
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Received on Wed Oct 26 2022 - 12:00:02 PDT