Thanks jason for the reply and the thanks for the great tool xparmed.py and
parmed.py.
The print dihedrals can be used to print the dihedrals that are defined
between atoms. Is that right ?
I have 53 atoms in the simulation. I am used the command in xparmed.py like
.1-53. But what
I would like to get isthe list of all the unique dihedraltypes that are
defined. For example I want an output like this.
X -NB-CU-X 1 0.000 180.000 3.000
X -CU-SH-X 1 0.000 180.000 3.000
X -CU-S -X 1 0.000 180.000 3.000
X -CT-SH-X 3 1.000 0.000 3.000
I am not sure how to to do this with parmed.py. Can you please help ?.
Should I use readparm or any other command ?
The reason I am asking this is I am creating a bond between two atoms.
I need to know the new bond type, angle types and the dihedral types
dhedral types that are to be defined.
Thanks
Arun
On Sun, Sep 14, 2014 at 3:34 PM, Jason Swails <jason.swails.gmail.com>
wrote:
>
>
> > On Sep 14, 2014, at 2:47 PM, Arun Srikanth <askforarun.gmail.com> wrote:
> >
> > Does any one how to get the dihedral types from the amber topology file.
>
> The printDihedrals command in ParmEd will do it.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
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Received on Sun Sep 14 2014 - 14:30:02 PDT
