Hi Urzula,
I'll give you an example. These are "restraints" and not "constraints".You
have to have a separate restraint file that looks like below.
&rst iat=15360,15377, r1=0.0, r2=13.8, r3=13.8, r4=100.0, rk2 = 10.0, rk3
= 10.0, /
The above restraint file says
1) The distance restraints will be applied to the distance between atom
15360 and atom 15377
2) The shape of the potential has been changed from a "U"shape to a
harmonic shape by making r2 equal to r2.
3) The minimum of the harmonic potential is at r2=r3=13.8 Angstrom
4) The force constant is 20 kcalmol-1A-2 (because Amber regards 0.5K as the
constant)
5) The potential will be harmonic from distance = 0A to distance=100A,
beyond that it would increase linearly.
In you amber input file you have to have
DISANG=name of the above restraint file
DUMPAVE=name of the distance output file (the values of the distance will
be written to this file as the MD simulation continues)
Hope this helps
Sajeewa
On Wed, Apr 2, 2014 at 9:33 AM, Urszula Uciechowska <
urszula.uciechowska.biotech.ug.edu.pl> wrote:
> Dear Amber users,
>
> I am trying to apply distance constraints between the residue of my
> portein and nuc.acid of my DNA molecule. Can someone suggest me how should
> I start.
> I went through the Tutorial 4 but do not know how to relate it to my case.
> Sould I prepare 7colum file?
> Could anyone suggest me something?
>
> Thank you
>
> best regards
> Urszula
>
>
> -----------------------------------------
> Ta wiadomość została wysłana z serwera Uniwersytetu Gdańskiego
> http://www.ug.edu.pl/
>
>
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Received on Wed Apr 02 2014 - 07:00:09 PDT
