dictin dictionary form input stream

neibor radius to calculate interactions

treltr¹ tree length, torsion and rotational information

trecal¹ tree interatomic energy terms

endict² end dictionary information

linkin input special tree or linkage information

disulf³ residue pair involved in disulfide linkage

mspair³ atoms of master/slave pair

noauto³ turn off automatic assignment of masters and slaves

endlin² end of linkage information

1These lines must be sorted by residue type. First atom of amino-acid residues should be N (peptide nitrogen), and last two atoms should be C and O of the peptide group.

2Required only if previous major control line present. Multiple lines permitted.

3Required only if related major control line present.

PRECED

neibor1 radius to calculate interactions (Å) 6.0

dictinCodeOption

del delete old residue dictionary from bdf

nod do not use information from standard dictionary

treltr1 residue name

2 atom label

3 previous atom to which the residue is covalently bonded

4 forwardmost atom to which this atom is bonded

5 group type key (1,0,-1 or -9)

6 bond distance to previous atom

7 angle involving two previous atoms of tree

8 torsion angle involving previous three atoms of tree

9 secondary dihedral angle (chirality)

10 number of rotational minima for flexible dihedral

11 dihedral angle with minimum energy

A blank back or forward name means no bond exists in that direction.

trecal1 residue name

2 atom label

3 force associated with stretching of bond

4 force associated with distortion of the angle

5 force associated with torsion angle bending

6 force associated with the secondary dihedral angle

7 force barrier to rotation (if single bond)

8 Lennard-Jones coefficient A

9 Lennard-Jones coefficient B

10 partial charge on atom

11 Lennard-Jones coef. A for 1-4 interactions

12 Lennard-Jones coef. B for 1-4 interactions

13 key for hydrogen bonding (1, 0, -1 or -9)

14 mass of atom or pseudo atom

endictend of the dictionary information

linkinbeginning of the linkage information

disulf1 residue number* of the first CYS involved in disulfide

2 residue number* of the second CYS involve in disulfide

mspair1 residue number* and atom name of master atom

2 resiude number* and atom name of slave atom

newchn1 residue number* of start of new chain

noauto1 residue number* where auto master/slave assignments halted

* Residue number can be decribed in several ways.

a) residue number or residue number with insertion code; e.g. 27 or 126A

b) residue number preceded by RES (nospaces); e.g. RES27

c) if chain must be designated the chain name, as well as, the residue number must be preceded by designator; e.g. RES126A CHN1

endlinend of the linkage information