There are virtual and pseudo atoms. A virtual atom is an atom that occurs in the actual molecule, but whose position is not represented explicitly in the MODEL and topology file. A pseudo atom is a position that does not correspond to an actual atom in a molecule, but is some sort of an average of positions of real atoms. MODELLER follows GROMOS definitions for the seven types of pseudo and virtual atoms: gravity center, V41, V31, P2, V42, P3, and P6. These names are constructed using the following rules: 'V' and 'P' indicate virtual and pseudo atoms, respectively. The second digit indicates the number of substituents on the central atom (for 'V') and the number of protons whose positions are averaged (for 'P'). The last digit indicates the number of protons on the central atom (for 'V').
GROMOS ROUTINE #DEF DESCRIPTION
TYPE NAME ATM
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1 PSD N gravity center
2 VCH1 4 virtual aliphatic proton on a tetrahedral carbon (->CH),
defined by the central C and the three other substituents;
3 VCH1A 3 virtual aromatic proton on a trigonal carbon (=CH),
defined by the central C and the two C atoms bonded
to the central C;
4 PCH2 3 pseudo aliphatic proton on a tetrahedral carbon (>CH2)
not assigned stereospecifically; its position is
between the two real protons; defined by the central
C and the other two substituents;
5 VCH2 3 virtual aliphatic proton on a tetrahedral carbon (>CH2)
assigned stereospecifically; defined by the central
tetraedral atom and the other two substituents on it;
6 PCH31 2 pseudo aliphatic proton on a tetrahedral carbon (-CH3),
defined by the central C and the heavy atom X in X-CH3;
its position is the average of the three real protons;
7 PCH32 3 pseudo aliphatic proton between two unassigned -CH3
groups; defined by X in CH3 - X - CH3 and the two
C atoms from the two CH3 groups (Val, Leu!);
its position is the average of the six real protons;
0 - - delta and epsilon protons on rapidly flipping aromatic
rings should refer directly to real gamma and delta C
atoms, respectively.
In a restraints file, pseudo atoms are indexed from NATM+1 to NATM+NPSEUDO where NPSEUDO is the number of pseudo atoms. The restraints (the R entries) are exactly the same as for the real atoms, except that the pseduo atom integer indices are used (indices are larger than NATM). The pseudo atoms are defined in the P entries:
P i j k a1 a2 a3
where i is atom index of pseudo atom i, j is the type of the pseudo atom i (see the table above), k is the number of real atoms defining the current pseudo atom (3 in this case), and a1 a2 a3 are the integer indices of real atoms defining the current pseudo atom.
For example, if you want to define a pseudo atom which is a gravity center of atoms 4, 7, and 10, and there are 101 real atoms in the protein:
P 102 1 3 4 7 10