hydroxyapatite

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1

Dear all

who knows how can I use Crystallographic Information Framework (CIF) information to build hydroxyapatite structure that is my big problem, i found some information in Amerivan Mineralogist Crystal Structure Database (AMCSD) but it’s not complete information of hydroxyapatite’s molecule that I know it consist of 88 atoms.here is the information that I found in AMCSD :

Sudarsanan K, Young R A

Acta Crystallographica B25 (1969) 1534-1543

Significant precision in crystal structural details: Holly Springs

hydroxyapatite

Locality: Holly Springs, Cherokee County, Georgia, USA

Sample: X-23-4

_database_code_amcsd 0009353

9.424 9.424 6.879 90 90 120 P6_3/m

atom x y z occ B(1,1) B(2,2) B(3,3) B(1,2) B(1,3) B(2,3)

CaI 1/3 2/3 .0015 .0031 .0031 .0018 .00155 0 0

CaII .2468 .9934 .25 .0021 .0023 .0028 .0010 0 0

P .3987 .3685 .25 .0019 .0017 .0025 .0010 0 0

OI .3284 .4848 .25 .0039 .0030 .0054 .0027 0 0

OII .5873 .4651 .25 .0020 .0026 .0096 .0009 0 0

OIII .3437 .2579 .0702 .0092 .0042 .0049 .0045 -.0041 -.0027

Oh 0 0 .1950 .5 .0025 .0025 .0102 .00125 0 0

H 0 0 .0608 .5 .0129 .0129 .0104 .00645 0 0

Alex

2

I don't know what all that means. But at the end of the
day, if it's a crystal lattice, it should come down to
a unit cell and some basis atoms. Figure that out
and you can use the lattice custom command in LAMMPS.

Steve

3

I don't know what all that means. But at the end of the
day, if it's a crystal lattice, it should come down to
a unit cell and some basis atoms. Figure that out
and you can use the lattice custom command in LAMMPS.

the talk slides below are not for lammps but a DFT code,
but the principle is the same:

- get a book with the tables of crystal structures
- look up the space group
- compute the positions of all symmetry operations
- eliminate redundant positions
- multiply with the lattice constant, if needed
- convert to a conventional cell, if needed
- create a lammps data file from the resulting coordinates

http://www.vlab.msi.umn.edu/events/download/tutorial_wyckoff.pdf

axel.

4

I'm not an expert on this at all. CIF (and mmCIF) was a popular
comparatively modern alternative to the aging PDB file format (which I
loath). (Since then, several newer file formats have been invented.)

I remember 10 years ago several popular protein molecule viewers
(pymol, chimera) could load mmCIF files. You could use one of these
programs to load your CIF file and look at it, (and then convert the
file to some other format with more support, such as ... PDB). Try
that.

It also looks like there was also a "CIFTr" program to convert CIF to
PDB, but I have not tried it
http://sw-tools.pdb.org/apps/CIFTr/index.html

(PDB format is more popular, and both "topotools" and "moltemplate",
for example, can convert the periodic boundaries in the the "CRYST1"
record in a PDB file into LAMMPS DATA file format. I can probably
help if you get stuck converting from PDB to LAMMPS DATA format.)

I hate PDB files.

Cheers
Andrew

P.S.
I don't know if CIF is still popular, but there was also some
discussion about import CIF files into VMD a few years ago. I don't
know what happened.
http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/10040.html