Energies of Nonbonded Interactions.

Synopsis

pamoc.exe   [-ecryst]   [-ecd <ECD input data file name>]   [-(lmx|MaxMulOrd) <(0||1||2||3||4)>]
[-usedma <(1||2||3||4||5||6||7||8)>]
[-(em|ecm|ecmdl) <(1||2||3||4||5||6)>]   [-(arp|rap|repar) <(1||2||3||4||5)>]   [-(adp|dap|dispar) <(1||2||3||4||5)>]
[-(dfd|damp|dampdsp) <(1||2||3||4||5||6)>]   [-(sm|shift|shiftmom) <(0||1||2||3)>]
[[-epmm]   [-(pet|pent|penthrs) <penetration energy threshold>]]   [-csize <a-length b-length c-length>]
[-(ecprt|ecrystprt)]   [-LooseHB]
<   (<input-file>||/dev/null)   >&   <output-file>   &

Keywords and Options

The ECD input data file

C     ------------------------------------------------------------------
C     Keyword     Arguments                Meaning
C     ----------- ------------------------ -----------------------------
C     MOLE[CULE]  m [<options>]            Estimate intramolecular
C                                          interaction energies in
C                                          molecule 'm' (sequence number
C                                          of the molecule in the
C                                          asymmetric unit).
C
C     MOLP[AIR]   m1 m2 [<options>]        Estimate intermolecular
C                                          interaction energies between
C                                          a pair of molecules, whose
C                                          sequence numbers in the
C                                          crystal are 'm1' and 'm2'.
C
C     ATOMP[AIR]  a1 a2 m1 m2 [<options>]  Estimate interaction energies
C                                          between a pair of atoms 'a1'
C                                          and 'a2' belonging to
C                                          molecules 'm1' and 'm2',
C                                          respectively.
C
C     NEIGH[BOURS] [n]                     Print the table of nearest
C                                          neigbours (useful to know the
C                                          sequence number of a molecule
C                                          in the crystal).
C
C     ------------------------------------------------------------------
C     Option[=value]  Meaning
C     --------------  --------------------------------------------------
C     MODEL=m         Select the m-th model to evaluate electrostatic
C                     interaction energies (default MODEL=2):
C                     m=1, Exact calculation of the Coulomb integral;
C                     m=2, Spackman's model (2005):
C                          Ees = Epp + Epd + Edd;
C                     m=3, Exact partitioning of the Coulomb integral
C                          into Epp, Epd, and Edd terms;
C                     m=4, Modified Spackman's model (pseudoatoms only):
C                          Ees = Ess + Esa + Eaa;
C                     m=5, Exact partitioning of the Coulomb integral
C                          into Ess, Esa, and Eaa terms (pseudoatoms
C                          only);
C                     m=6, Spackman's model (1986);
C                     m=ALL, use all available models.
C
C     EPMM            Use either model 1 or model 2, depending on the
C                     sum of the Van der Waals radii and on Epp value.
C
C     LMX=k           Use a multipole expansion up to the k-th order.
C
C     LooseHB         Include weak hydrogen bonds in MODEL=6.
C
C     PRINT                iprint       Amount of print output:
C                             0         no print output,
C                1 ... Description of the E-Cryst model.
C                1 ... Table of interaction energies in KJ/Mol for each
C                      molecular pair with distance between centres of
C                      mass lower than 15 Angstrom.
C                2 ... Table of interaction energies in KCal/Mol for
C                      each molecular pair with distance between centres
C                      of mass lower than 15 Angstrom.
C                3 ... Table of interaction energies in Hartree for each
C                      molecular pair with distance between centres of
C                      mass lower than 15 Angstrom.
C                3 ... Table of crystallographic rotation matrices and
C                      translation vectors.
C                3 ... Table of translation vectors and rotation
C                      matrices associated to each molecular pair with
C                      distance between centres of mass lower than
C                      15 Angstrom.  For each pair the shortest contact
C                      distance is also reported, i.e. the shortest
C                      intermolecular atomic distance among those
C                      distances which are lower than the sum of Van der
C                      Waals radii times 1.1
C                1 ... Table of hydrogen bonds involved in each pair.
C                4 ... For each interacting pair which contains a
C                      contact distance (i.e. an intermolecular atomic
C                      distance lower than the sum of Van der Waals
C                      radii times 1.1):
C                      a) Table of atomic coordinates of the rotated and
C                         translated monomer.
C                      b) Tables of molecular electrostatic moments and
C                         estimated standard deviations in the BDF
C                         orientation and in the eigen-axes of the dimer
C                         inertial tensor.
C                8 ... The content of tables 2, 3, 4, and 6 is extended
C                      to all the computed pairs.
C                9 ... For each interacting pair a table of atom-atom
C                      interaction energies for all atomic pairs with
C                      distance lower than 3.0 Angstrom.
C

Print Output

Graphical Output

Interactive Usage

The interactive procedure was intended mainly for debugging and testing purposes. Based on a cascade of menus, it is rather self explaining.

Links