I suggest looking at the cpptraj rst command. It makes the disang input for
you.
An example of a Com disang is this :
iat=-1,-1,
igr1=12781,12786,12792,12797,13056,13061,13065,13069,13072,13080,13438,13444,13451,13455,13459,
igr2=3742,3743,3748,3749,3754,3755,3759,3760,3765,3766,3770,3771,3776,3777,3782,3783,
ifvari=1, nstep1=0, nstep2=40000000,
r1=0.0,r2=87.50,r3=87.50,r4=150.0,rk2=7.0,rk3=7.0,
r1a=0.0,r2a=62.5,r3a=62.5,r4a=150.0,rk2a=7.0,rk3a=7.0,
&end
On Sat, Sep 20, 2025, 1:49 AM Gourav Das via AMBER <amber.ambermd.org>
wrote:
> Greetings everyone!
>
>
>
> I want to perform steered molecular dynamics (SMD) simulation using AMBER20
> and need to define the center of mass (COM) of two domains of a protein in
> the DISANG file.
>
>
>
> Could anyone kindly share a sample DISANG file or example input that
> demonstrates how to define COM of two domains in order to change
> the distance between them?
>
>
>
> For reference, I’ve included a standard DISANG file format for a distance
> restraint between two atoms:
>
>
>
> # Change distance between atoms 485 and 134 from 15 A to 20.0 A
> &rst iat=485,134, r2=15., rk2 = 5000., r2a=20.0, /
>
>
>
> Any guidance, suggestions, or example files would be greatly appreciated.
>
>
>
> Thanks and regards,
>
>
> Gourav Das
>
> Research Scholar
>
> IIT Kharagpur
> India
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Received on Sat Sep 20 2025 - 06:30:02 PDT
