Principal Structure File (PSF)



The use of the CHARMM force field in Minimax requires the input of a CHARMM Principal Structure File (PSF). The PSF contains information about atom properties (atom name, atom type, partial atomic charge, mass) and lists bonds, bond angles, torsion angles, and improper torsion angles as well as information needed to generate the hydrogen bonds and the non-bonded list. PSFs will be generated automatically by the minimax command in Wit!P. Alternatively, they may be produced through Wit!P's charmm psf command.

The PSF is a formatted file, consisting of several sections. Sections are separated by a single blank line.

1. Header Line:

The first line of a PSF must contain the string 'PSF ' (in upper case) in columns 1-4.
2. Title Records:
Number of title records (ntit)  Format(I8), followed by ntit title lines, Format (A). If ntit is zero, a blank line must be given instead of a title.
3. Atom List:
Number of atoms (nat). Format: (I8), i.e. right justified in columns 1-8, followed by nat atom records with the following fields:

seqnr segid resnr resid name type charge mass fixed

Format: (I8,1X,A,1X,A,1X,A,1X,A,1X,I4,1X,2G14.6,I8)

Notes: type is a numeric field with the numeric CHARMM atom type, charge is the partial atomic charge, fixed is 1 for fixed atoms, 0 otherwise. PSFs generated by Wit!P always have fixed = 0. Only the segid, resnr and resid fields of the atom list are read into Minimax. Atom names, partial atomic charges and atom types are taken from the MOL2 file.

4. Bond List:
Number of bonds (nbond), Format(I8). Followed on subsequent lines by nbond pairs of atom numbers defining the bonds, 4 pairs per line, Format (8I8). If nbond is zero, a blank line must be given instead of the first atom pair record.

Note: in Minimax, the bond list is read from the MOL2 file.

5. Angle List:
Number of angles (nang). Format (I8). Followed on subsequent lines by nang triples of atom numbers defining bond angles to be included in the angle bend energy, 3 triples per line, Format (9I8). If nang is zero, a blank line must be given instead of the first atom triple record.
6. Torsion List:
Number of torsion angles (ntors). Format (I8). Followed on subsequent lines by ntors quadruples of atom numbers defining torsion angles to be included in the torsion angle energy, 2 quadruples per line, Format (8I8). If ntors is zero, a blank line must be given instead of the first atom quadruple record.
7. Improper List:
Number of improper dihedral angles (nimp). Format (I8). Followed on subsequent lines by nimp quadruples of atom numbers defining improper dihedral angles to be included in the improper torsion energy, 2 quadruples per line, Format (8I8). If nimp is zero, a blank line must be given instead of the first atom quadruple record.

Note: there is absolutely nothing improper about impropers! Wit!P generates an improper for every planar atom (ligance 3, non zero value of oop attribute), and for every bond in rings of 5 or 6 planar atoms.

8. H-Bond Donor List:
Number of hydrogen bond donors (ndon). Format (I8). Followed on subsequent lines by ndon pairs of atom numbers (hetero atom, hydrogen), 4 pairs per line, Format (8I8). If ndon is zero, a blank line must be given instead of the first atom pair record.
Note: Minimax does not use the hydrogen bond donor list (Hydrogen bond energy term not implemented).
9. H-Bond Acceptor List:
Number of hydrogen bond acceptors (nacc). Format (I8). Followed on subsequent lines by nacc pairs of atom numbers (hetero atom, precursor), 4 pairs per line, Format (8I8). If nacc is zero, a blank line must be given instead of the first atom pair record.
Note: Minimax does not use the hydrogen bond acceptor list (H-bond energy term not implemented).
10. Non-bonded Exclusion List:
Number of exclusions (nexcl). Format (I8). Followed on subsequent lines by nexcl atom numbers excl(.), 8 numbers per line, Format (8I8). If nexcl is zero, a blank line must be given instead of the first atom number record. The atom number records are followed by nat pointers pt(.)into the  the array excl of exclusions.

Notes: the non-bonded exclusion list is used to add specific non-bonded exclusions to the list of exclusions generated automatically, depending on the non-bonded exclusion mode (NBXMOD, -nbx option of Minimax). The interpretation of the non-bonded exclusion list is as follows: for each atom i the interactions with atoms excl(k),k=pt(i-1)+1 ... pt(i) are excluded from the non-bonded energy, where pt(0)is assumed to be 0.

11. Charge Groups List:
Number of groups (ngrp), and nbst2 (??). Format (2I8). Followed on subsequent lines by ngrp triples of integers igbp(.), ityp(.),imov(.), 3 triples per line, Format (9I8). If ngrp is zero, a blank line must be given instead of the first integer triple record.

Notes: Minimax does not use charge groups (group cutoff not implemented). If charge groups are defined for the molecule, they will be used by Wit!P to generate a charge group list with nbst2=0 and ityp=0, imov=0 for all groups. igbp is the list of group base pointers, i.e. atoms with sequence numbers in the range [igbp(i)+1,igbp(i+1)] belong to group i, where igbp(ngrp+1)=nat, by definition.


 Example of a PSF



A.Widmer, NIBR/CPC/CSG-SB