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Re: [sdpd] mol_tpcr
Hi
you need to create an instruction file like this one (example from fullprof).
You just have to transform the atomic coordinate in a good form (cartesian,
z-matrix....). For that, you can use Babel for example.
After running the executable mol_tpcr (you'll find him in the directory of
fullprof), you'll get the atomic coordinate in a good form for use the rigid
body option.
Good luck
Karim
------------------ start File: urea.cfl
-------------------------------------------
!
! Example of molecule given in a crystal
!
!
CELL 5.584001 5.584001 4.688990 90.0 90.0 90.0
!
MOLEX 8 Urea F
! Xc Yc Xc Phi theta Chi TypeAngles
TypeThermal
0.00000 0.50000 0.32811 0.0 0.0 0.0 P ISO
0 0 0 0 0 0 !Refinement
codes
!Atm Spe x y z N1 N2 N3 Biso Occ
Ur1 C 0.00000 0.50000 0.32811 0 0 0 0.50000 1.00000
Ur2 O 0.00000 0.50000 0.59574 0 0 0 0.50000 1.00000
Ur3 N 0.14466 0.64466 0.17816 0 0 0 0.50000 1.00000
Ur4 N -0.14466 0.35534 0.17816 0 0 0 0.50000 1.00000
Ur5 H 0.14261 0.64261 -0.03550 0 0 0 0.50000 1.00000
Ur6 H 0.25589 0.75589 0.28398 0 0 0 0.50000 1.00000
Ur7 H -0.14261 0.35739 -0.03550 0 0 0 0.50000 1.00000
Ur8 H -0.25589 0.24411 0.28398 0 0 0 0.50000 1.00000
! x(P1) y(P1) z(P1) x(P2) y(P2) z(P2)
x(P3) y(P3) z(P3)
XYZ_Frame 0.00000 0.50000 0.59574 1.00000 0.50000 0.32811
0.00000 0.50000 0.32811
!
------------------ End File: urea.mol
-------------------------------------------
The meaning of the keyword CELL and other parameters are obvious from
the given
names.
The keyword MOLEX must be followed by the number of atoms in the molecule, the
name
of the molecule and the kind of coordinates provided below (F: for fractional
coordinates
with respect the the given cell, C: cartesian, Z: for Z-matrix or S: for
spherical coordinates )
The parameters Xc, Yc, Zc are the fractional coordinates of the origin of the
internal
Cartesian system with respect to the given unit cell.
The angles Phi,Theta and Chi are Euler angles (two types, P: Phi and Theta are
the polar
spherical angles of the Z-axis of the Cartesian internal frame with respect to
the
Cartesian frame attached to the unit Cell, E: conventional Euler angles).
The keyword "XYZ_Frame" is followed by the fractional coordinates of three
points in the
unit cell. These three points will serve to position the molecule in
the crystal
and to calculate
the centre and Euler angles. The origin of the Cartesian internal
system will be
put in the
third given point. The z-axis is parallel to the vector P1-P3, the x-axis lies
within the plane
(P1-P3,P2-P3), and the y-axis completes the direct frame.
The numbers N1,N2,N3 are integers defining the connectivity of the molecule as
it is conventional
in the Z-matrix formulation. If all of them are put to zero, the program will
generate automatically
a connectivity table taking the first atom as the origin, the second along "x"
and the third in
the x-y plane. This internal Cartesian frame will be put
Quoting José Miguel Galiana <dimuoh...@yahoo.es>:
> Dear all
> anyone know how to use the mol_tpcr software in Fullprof?
> Thank you.
>
>
>
>
> [Non-text portions of this message have been removed]
>
>
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