Pseudo atoms

A 'P' line should look like:

P Pseudo_atom_index Pseudo_atom_type Numb_real_atoms Real_atom_indices

These parameters encode the pseudo atom information as given in Section 5.3.2. Pseudo_atom_index is the atom index, which should be a number between NATM+1 and NATM+NPSEUDO, where NATM is the number of real atoms in the model, and NPSEUDO the number of pseudo atoms. Pseudo_atom_type is the numerical pseudo atom type, as given in Table B.3. The pseudo atom is defined as an average of Numb_real_atoms, of indices Real_atom_indices. For example,

P    144   1   3    120 121 122

creates a pseudo atom at index 144, which is a gravity center of the 3 atoms 120, 121 and 122.

Table B.3: Numerical pseudo atom types

Numeric pseudo atom type	Pseudo atom type
1	pseudo_atom.GravityCenter
2	virtual_atom.CH1
3	virtual_atom.CH1A
4	pseudo_atom.CH2
5	virtual_atom.CH2
6	pseudo_atom.CH31
7	pseudo_atom.CH32