Authors: Keith Watenpaugh, Michael Carson & Jan Hermans
Contact: Keith Watenpaugh, The Upjohn Company,
Physical and Analytical Chemistry, Kalamazoo, MI 49007, USA
PRECED loads a macromolecular sequence, bonding and force restraints, and special linkage information onto the binary data file for programs such as CEDAR. In addition, the program will calculate positions for those atoms missing from the input binary data file based on the restraint information.
The primary function of the program is to prepare the proper logical records on the binary data file for the program CEDAR. PROATM is used to load atom and sequence information. PRECED must be run after any new atoms are loaded with PROATM, but the residue dictionary does not need reloading unless new or modified dictionary information is needed. However, the dictionary is easily and usually loaded. The program sets up an atom array based on the sequence information and loads the atom parameters. Missing atoms are checked for and their coordinates calculated from the information in the dictionary, if possible. Pointers to the dictionary entries are added to the atom logical record, as well as keys needed for the refinement and linkage of the atoms. Finally, information dealing with complex linkages is added to a master/slave logical record, lrslav:, that controls information such as disulfide bonds, metal clusters and closed ring systems.
The neibor line is needed only if the non-bonded energy terms ( i.e., van der Waals and partial charges) are going to be used. It causes the program to link for all symmetry and translationally related atoms that are within a defined distance of the atoms in lratom:. The required symmetry operators are stored in lrsymm: after the crystallographic symmetry operators. These will be carried along in the bdf until deleted. The neibor line does not need to be included in PRECED every time.
The dictionary information sets up the geometric information and forces involved in maintaining (or distorting) the model. The standard dictionary resides in the main XTAL directory under the name assigned by the macro prodict:. Any special residues that are a replacement of a standard residue from the input lines takes precedence over that in the standard dictionary. In other words, if a residue ALA is input by the user, the ALA in the PROTDICT: file will be ignored when read. The first line (treltr) of the pair of lines treltr/trecal primarily contains the expected bond length, angle and torsion angle information (hence L-Theta-Rho). The second (trecal) contains the force information associated with stretching, bending, etc: i.e., the geometry. It also contains the forces of non-bonded interactions, hydrogen bonding parameters and atomic masses. The information is based on parameters values for previous atoms in the tree structure from the end of branches back to the trunk. Rings are closed using master/slave atom relationships. For example, has bond length, ; bond angle, ; and torsion angle, as fields 6-8. Field 9 is a pseudo dihedral angle for chirality. The group type key (treltr line, field 5) has values 1 = start of fixed dihedral group, 0 = member of fixed group, -1 = no group (flexible dihedral), -9 = dummy (slave) atom. The hydrogen bonding key (trecal, field 13) has values -3 = water oxygen, -2 = negatively charged atom; +2 = positively charged atom; +1 other polar group (C of C=O, for example), and 0 = non-polar group. If building a new dictionary entry, the values from the current ones can generally be used for approximate values. Other generally available dictionaries exist for related molecular dynamics programs, such as AMBER (Peter Kollman) or GROMOS (Wilfred van Gunsteren). Always check any modifications using printer priority 4 in both PRECED and CEDAR. Also, in CEDAR, large and possibly erroneous parameters can be detected by activating the listing of bad energy terms with field 10 an the weight line in CEDAR.
The lines linkin through endlin provide special directives for beginnings of chains, disulfide linkages, linkage into metal clusters or other covalent bonds not known from a simple sequence. Usually, the disulf line is the only directive needed for most proteins. The beginning and ending of chains are defined in PROATM. To print the dictionary and atom coordinate information enter reset psta 4
neibor 6.0 :find the symmetry operators of neighbouring atoms
dictin delete :enter new dictionary
disulf 27 126
disulf 29 45
disulf 44 105
disulf 50 133
disulf 51 98
disulf 61 91
disulf 84 96
This is an example of entering a standard dictionary and the linkage information for a number of disulfide bridges. PROATM had previously added the atom and sequence information.
reset psta 4
dictin delete :enter new dictionary
remark ala replace residue in standard dictionary
treltr ala n c ca 1 1.31 117.1 180. 62.0
trecal ala n 1090. 120. 0. 81. 0. 49.4 1300. -0.28 49.4 1300. 1 14
treltr ala h n *5 0 1. 123. 0. 57.0
trecal ala h 895. 70. 1.4 44. 0. 0. 0. 0.280 0. 0. 1 1
treltr ala ca n c -1 1.460 120.0 180. 57. 3. 0.0
trecal ala ca 760. 124. 10. 44. .6 111.8 8470.4 0. 54. 1933. 0 13
treltr ala cb ca *5 -1 1.530 110. 60. 55.0
trecal ala cb 600. 112. 0. 55. 0. 94.20 5114. 0. 82.80 3472. 0 15
treltr ala c ca n 1 1.510 110.7 180. 55. 3. 180.0
trecal ala c 740. 112. 0. 57. 0.2 48.4 1837. 0.38 48.4 1837. 1 12
treltr ala o c *5 0 1.240 120.8 0. 62.0
trecal ala o 1390. 124. 8.1 81. 0. 47.6 861. -0.38 47.6 861. 1 16
disulf res27 chn0 res126 chn0
disulf res29 chn0 res45 chn0
disulf res27 chn1 res126 chn1
disulf res29 chn1 res45 chn1
In this example, symmetry and translational operators will be searched for atoms that could have non-bonded interactions with the parent molecule. The dictionary for ALA will use that read from the input lines, rather than in the standard dictionary. Two chains are present and thus disulfides must be further described with a chain name. Printer priority is set to 4 to output the dictionary and atom parameters.
K.D. Watenpaugh, "Conformational Energy as a Restraint in Refinement", Molecular Dynamics and Protein Structure (ed. J.Hermans), University of North Carolina, Chapel Hill, 77-80, 1985.
Force constants and non-bonded interactions:
S. Lifson and A. Warshel, J. Chem. Phys. 49, 5116-5129, 1968.
A. Warshel and S. Lifson, J. Chem. Phys. 53, 582-594, 1970.
A. Warshel, M. Levitt and S. Lifson, J. Mol. Spectrosc. 33, 84-99, 1970.
H.A. Scheraga, Adv. Phys. Org. Chem. 6, 103, 1968.
F.A. Momany, R.F. McGuire, A.W. Burgess & H.A. Scheraga, J. Phys. Chem. 79, 2361-2381,1975.