Aspherical Atom Databank

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Analytical Fit to Relativistic Scattering Factors for Ions

Analytical Wave Functions for Relativistic Atoms

 

    

The databank contains all atom-types present in natural amino acid residues and other biologically relevant molecules. Each atom-type results from averaging over a family of the theoretical density of chemically unique pseudoatoms, taking into account both first and second neighbors. A spawning procedure is used to assure that close transferability is obeyed.  The databank parameters will be listed on this website in the near future. Examples of the deformation densities of aspherical nitrogen atoms are shown below:

                                                                            

Deformation densities of the nitrogen atom types in the UBDB: (left) in the plane of two neighboring atoms, contour levels at 0.05 e/3; (right) 3D representation, contour levels at 0.2 and 0.3 e/3. Positive contours, blue, negative contours, red, zero contour, black.


Download University at Buffalo Pseudoatom Databank (UBDB) :

  Use of UBDB implies that the user will adhere to the following terms and conditions:

    • The use of UBDB should be acknowledged in any publications, which use results obtained with UBDB

    • The acknowledgment should be of the form:

    Volkov, A., Li, X., Koritsanszky, T. S. & Coppens, P., J. Phys. Chem. A 108, 4283-4300, (2004).
    Dominiak, P. M., Volkov, A., Li, X., Messerschmidt, M. & Coppens, P., J. Chem. Theory Comput.,
    3, 232-247 (2007).
    Volkov, A.,
    Messerschmidt, M. & Coppens, P., Acta Crystallogr. D
    63, 160-170(2007).


    Download databank in WINDOWS format

    Download databank in UNIX format


    Download program LSDB :

    Use of the program LSDB implies that the user will adhere to the following terms and conditions:

     

    • The use of the program of LSDB should be acknowledged in any publications, which use results obtained with LSDB


    • The acknowledgment should be of the form:

    Volkov, A., Li, X., Koritsanszky, T. S. & Coppens, P., J. Phys. Chem. A 108, 4283-4300 (2004).
    Dominiak, P. M., Volkov, A., Li, X., Messerschmidt, M. & Coppens, P., J. Chem. Theory Comput.,
    3, 232-247 (2007).
    Volkov, A.,
    Messerschmidt, M. & Coppens, P., Acta Crystallogr. D
    63, 160-170(2007).

    Download statically linked x86 LINUX executable of the program LSDB

    Download WINDOWS executable of the program LSDB


    LSDB usage notes:

      1. LSDB requires input file called lsdb.inp

      2. Running LSDB executable with '-h' option will printout the sample lsdb.inp file with     

        explanation of each of the options (see below)

      3. Download and run example (files are in WINDOWS format)

      4. Sample lsdb.inp file :

    <>!
    ! Example of LSDB input file (lsdb.inp) :
    !
    FORMAT  *shelx xd aim2tab platon
    ! for SHELX :
    INPUT   l-dopa.shelx   rename 0 toxd
    ! for XD :
    !INPUT   xd.mas xd.inp
    ! etc :
    !INPUT file.inp
    ! printout level (higher number gives more printout) :
    VERBOSE  4
    ! tolerances for bonds / planar rings / planar groups
    TOLS bond 0.4 ring 0.1 group 0.1
    ! modify covalent radii
    !RADII  H 0.1  He 0.2  Li 0.3 ....
    ! number of cells in each direction for complete fragment search
    ! comment it out or set to -1 to turn off search
    NCELLS  1
    ! how to handle disordered part
    DISORD  extendH  db
    ! generation of keys
    KEYGEN  XYZUIJ all ordered  MULT all ordered
    ! use simple model for determination of chemical equivalency
    SIMPLE
    ! use/do_not_use chemical/kappa contraints for H/non-H atoms
    CHEMCON  *hydrogen   *other
    ! extend H-atoms to neutron/standard distance
    Extend_H
    ! search for 3-8 membered rings
    RINGS  3  8  *special
    ! assign pseudoatom parameters from COPPENS LAB databank
    DATABANK /usr/local/UBDB_Oct10_2006_unix.db
    ! select method for scaling of Pv's
    SCALE *sigma diff fract
    ! number of fragments
    NFRAG 1
    ! fragment specifications
    !FRAG 1 1 -25
    !FRAG 2 26 -50
    ! net charges of fragments
    !CHFRAG 0. 0.