# Re: [AMBER] Rotational/torsion energy

From: Daniel Roe <daniel.r.roe.gmail.com>
Date: Thu, 3 Oct 2019 15:33:08 -0400

Hi,

I know I'm late to respond here, but you could use the
'permutedihedrals' command in cpptraj to generate a pseudo-trajectory
with a dihedral rotated at regular intervals, then use 'crdaction
<COORDS> energy' to get the energy. Something like:

parm <topology>
permutedihedrals crdset MyCrd resrange 7 interval 30 phi crdout Rotate
crdaction Rotate energy out Rotate.energy.dat
quit

This will create a pseudo-trajectory named Rotate by rotating around
residue 7 phi by 30 degrees, then calculate the energy of that pseudo
trajectory. See the manual for full details on the commands.

Hope this helps,

-Dan

On Thu, Sep 26, 2019 at 6:14 AM Gustaf Olsson <gustaf.olsson.lnu.se> wrote:
>
> Thank you very much Karl
>
> This is a very good start and I’ll look into it. At this point I’m just interested in qualitative results, "is there an apparent barrier or not". The actual numbers are of less importance right now and if needed I’ll probably turn to some QM calculations.
>
> Best regards
> // Gustaf
>
> > On 26 Sep 2019, at 09:48, Karl Kirschner <k.n.kirschner.gmail.com> wrote:
> >
> > 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
> >
> >
> > 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
> >>
> >>
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Received on Thu Oct 03 2019 - 13:00:02 PDT
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