The property file is where the parameters of the particles, bonds, angles, torsions and improper torsions are kept. It is used as an input for the connectivity program which build the molecular connectivity file The property file is build from sequential sections which MUST come in the following order: PRTC - individual particle properties BOND - bond parameters ANGLE - angle parameters TORSION - torsion parameters IMPROPER - improper torsion parameters It is possible not to provide all the information i.e. a property file with PRTC only is legal, however PRTC and ANGLE is not. If you provide only PRTC the program will issue a warning (yellow alert), ignore it unless you want to provide bonds and something happened. Each subsection (e.g. PRTC, BOND, TORSION) must end with DONE The file must end with *EOD The DONE and *EOD are general termination features used in other datafile. Another general feature shared between different data files is the comment line. ~ ANYWHERE in the line makes it a comment. This line is ignored by the program. Below details on the syntax are provided: The explanations will be written as comment lines as in a "real" property file ~ This is a first line of a property file. The first exe line must be PRTC ~ The following line lists properties of an individual particle ~ name mass charge epsilon sigma PNAM=(NX) PMAS=14. PCHG=-0.3 PEPS=0.170 PSGM=3.250 ~ The example above provides the data for the particle type NX (Nitrogen ~ of the N-terminal. characters (like PNAM - the name of particle ~ type) must be enclosed in brackets. Each of the expressions (i.e. ~ A=B) must be seprated from other expressions by space(s). No spaces ~ within an expression are allowed. ~ espilon and sigma are the van der Waals well depth ~ and the hard core radius respectively. Obvioulsy this type of ~ line is repeated as needed for different particle types. ~ The data base for particle properties is based on the OPLS potential ~ Jorgensen and Tirado-Rives JACS 110,1657(1988) ~ ~ Now end the particle part by DONE DONE ~ ~ The next part lists the bond properties. The first Bond line must be BOND ~ Bond energy is set to be K(r - req)^2 ~ Below we provide the names of the two particle types, the force constant ~ (in kcal/mol angstrom^-2) and the equilibrium distance in angstrom ~ Note the different style of i/o different expression are still ~ separated by spaces but no equality is used. This requires the data ~ to be placed in exactly the same order. I.e. do not exchange equilibrium ~ position and force constant. ~ The covalent part of the potential (excluding improper torsions) ~ is taken from AMBER ~ Weiner et al JACS 106,765(1984) ~ particle particle force-constant equilbrium distance NX HX 434.0 1.01 CANX NX 337.0 1.449 ~ ~ Pictorialy NX-HX ~ end the BOND with DONE DONE ~ ~ Angles are similar to bonds in format style ANGLE ~ K (theta -theta(eq))^2 ~ name name name K(kcal/mol radians^-2) theta(eq) (degrees) HX NX HX 35.0 109.5 ~ ~ Pictorially HX-NX-HX DONE ~ ~ And here are the torsions. The format style is similar to BOND and ANGLE TORSION ~ (Pictorially CAH-CO-NH-CAH) ~ however the energy function is more complex: ~ E = sum k(n)*(1 + cos(n*phi+gamma) ~ (gamma should be a function of n too and will be added to the program ~ soon). Currently the format is ~ name name name name k(1) k(2) k(3) n cos(gamma) CAH CO NH CAH 0.0 2.5 0.0 2 -1.0 ~ There is an option in TORSION (only) to use a wild card by X, e.g. X CANX CX X 0.0 0.0 0.0 3 0.0 ~ where X means "any atom". ~ **** ALL TORSIONS MUST BE DEFINED IN THE PROPERTY FILE *** ~ However in many cases the energy is set identically to zero. ~ This is done by setting cos(gamma)=0. When the program matched ~ this torsion, it is skipped and NOT included finally in the ~ connectivity file ~ DONE ~ ~ Improper torsions are four body interactions in which one atom is sitting ~ in the center, Pictorially ~ B ~ | ~ A ~ / \ ~ C D IMPROPER ~ The internal degree of freeom - phi, is the angle between the normal ~ to the ABC plane and the normal to the BCD plane. To obtain consistent ~ values A must be first and D must be last ~ ~ The energy function is rather messy... ~ If the equilibrium angle is far from zero we use simply harmonic term ~ E = K1(phi-phi(eq))^2 (K1 kcal/mol radian^-2 ; phi(eq) degrees) ~ If the equilibrium angle equals zeo then the above energy expression ~ is singular, we therefore use ~ E = K2(cos(phi) - cos(phi(eq))^2 (K2 kcal/mol ; phi(eq) degrees) ~ Note that the units for K is different in both cases. Note also ~ that at phi(eq)=0, Taylor exapnsion shows that E is quartic in phi ~ therfore to maintain comparable restoring force K2 > k1 ~ ~ The atom in the center is always first, the last atom must also be chosen ~ with care since it determines the sign. The other two in the middle ~ can be interchange ~ name name name name K1/K2 phi(eq) CANX NX CO CH3 55.0 35.26 DONE ~ End it all *EOD An example for a property file can be found in the directory bully:/store/us/ron/moil.mop/ALL.PROP