Hello Gustaf,
The way that I know is to use a restraint file to specify the dihedral
angle and constraint forces. In the following example (using a filename of
02.rest), I have constrained atoms 1-5-8-11 to an angle of 30.0 degrees
using a force of 30000.0 :
&rst iat = 1, 5, 8, 11,
r1 = 29.0, r2 = 30.0, r3 = 30.0, r4 = 31.0,
rk2 = 30000.0, rk3 = 30000.0,
&end
Then within the min.in file you need to refer to this file:
Gas-Phase Constraint Minimization
&cntrl
imin=1, dielc=1,ntb=0,
maxcyc=20000,ntxo=1
drms=0.01,nmropt=1,
cut=40.0,
&end
&wt type='END' &end
LISTOUT=POUT
DISANG=02.rest
Of course if you using a good input structure (by specifying it in leap to
create the coordinate file for running the minimization) for each angle
that you are wanting to model, you will ensure better results. The example
that I give is for a gas-phase, so you will need to consider if and how to
include solvation effects.
Best regards,
Karl
Karl. N. Kirschner, Ph.D.
Research Associate
Department of Computer Science
University of Applied Sciences Bonn-Rhein-Sieg
Grantham-Allee 20, 54757 Sankt Augustin, Germany
Twitter: .k_n_kirschner <https://twitter.com/k_n_kirschner>
On Thu, Sep 26, 2019 at 8:30 AM Gustaf Olsson <gustaf.olsson.lnu.se> wrote:
> I was curious if anyone has experience with calculating rotational/torsion
> energy over a single bond using amber? I am looking for a smooth way to get
> an indication of potential energy barriers and an estimate of the size.
>
> If anyone knows of any tutorials or online resources describing the
> process I’d greatly appreciate some tips.
>
> Best regards
> // Gustaf
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Sep 26 2019 - 01:00:02 PDT
