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<H2><A NAME="SECTION00072000000000000000">
The force field (.ff) file</A>
</H2>

<P>
All the lines beginning with ``#'' are considered as commentaries.

<P>
The file consists of a number of sections; each beginning with a keyword.
Each new keyword means the end of the old section and beginning of the 
new one corresponding to this keyword

<P>

<UL>
<LI><code>BONDS</code>

<P>
Contains parameters for covalent bonds. Each line consists of four or six
parameters. The first two parameters are the force field atom types.
The third parameter is the force constant <IMG
 WIDTH="13" HEIGHT="14" ALIGN="BOTTOM" BORDER="0"
 SRC="img12.png"
 ALT="$k$"> of the harmonic potential
(<A HREF="node7.html#harm">4</A>) and the fourth parameter is the equilibrium
distance <IMG
 WIDTH="19" HEIGHT="30" ALIGN="MIDDLE" BORDER="0"
 SRC="img11.png"
 ALT="$r_0$">. The presence of 5-th and 6-th parameters means that
the corresponding bond should be described by a Morse potential,
they have a sense of <IMG
 WIDTH="18" HEIGHT="14" ALIGN="BOTTOM" BORDER="0"
 SRC="img14.png"
 ALT="$D$"> and <IMG
 WIDTH="13" HEIGHT="30" ALIGN="MIDDLE" BORDER="0"
 SRC="img16.png"
 ALT="$\rho$"> parameters of the Morse potential 
(<A HREF="node7.html#morse">5</A>) correspondingly. 

<P>
</LI>
<LI><code>ANGLES</code>

<P>
Contains parameters for covalent bonds. Each line consists of 5 or 7
parameters. The first three parameters are the force field atom types.
The fourth parameter is the equilibrium angle, the 5th parameter
is the force constant <IMG
 WIDTH="13" HEIGHT="14" ALIGN="BOTTOM" BORDER="0"
 SRC="img12.png"
 ALT="$k$">. The 6-th and 7-th parameters are optional,
if they are present, they define the Urey-Bradley (UB) potential which
is in fact a distance-dependent harmonic potential between 1st and 3rd
atoms. The equilibrium distance for UB potential is given as a 6-th
parameter and the force constant as a 7-th. <code>makemol</code> puts the 
UB term into the ``bond'' section of the <code>.mmol</code> file.

<P>
</LI>
<LI><code>TORSIONS</code>

<P>
Contains parameter for torsion potentials of ``standard'' type (<A HREF="node9.html#tors-0">7</A>).
Each line consists of 7 parameters, the first four define the force field
atom types, and parameters from 5-th to 7-th are <IMG
 WIDTH="18" HEIGHT="14" ALIGN="BOTTOM" BORDER="0"
 SRC="img24.png"
 ALT="$\Delta$">, <IMG
 WIDTH="26" HEIGHT="30" ALIGN="MIDDLE" BORDER="0"
 SRC="img47.png"
 ALT="$K_\phi$">
and <IMG
 WIDTH="22" HEIGHT="14" ALIGN="BOTTOM" BORDER="0"
 SRC="img26.png"
 ALT="$M$"> correspondingly.

<P>
This section allows definition of multiple torsions and wildcards 
(denotes as ``X''). The wildcards can be used only for the 1st and 4-th
atoms in the list. The following rules are applied. If an explicit torsion   
(without wildcards) is specified, lines with wildcards matching this 
torsion are ignored. If lines with explicit torsions are repeated 
for the same set of atom types, they define multiple torsions, that 
is the total torsion potential is a sum of several terms of type 
(<A HREF="node9.html#tors-0">7</A>).

<P>
</LI>
<LI><code>NONBONDED</code>

<P>
Contains Lennard-Jones parameters for non-bonded interactions.
Each line consists of 3 or 5 parameters. The first parameter is the
force field atom type. The second and third parameters are 
<IMG
 WIDTH="14" HEIGHT="13" ALIGN="BOTTOM" BORDER="0"
 SRC="img7.png"
 ALT="$\sigma$"> and <IMG
 WIDTH="11" HEIGHT="13" ALIGN="BOTTOM" BORDER="0"
 SRC="img8.png"
 ALT="$\epsilon$"> of the Lennard-Jones potential. If the 4-th and
5-th parameters are present, they define <IMG
 WIDTH="14" HEIGHT="13" ALIGN="BOTTOM" BORDER="0"
 SRC="img7.png"
 ALT="$\sigma$"> and <IMG
 WIDTH="11" HEIGHT="13" ALIGN="BOTTOM" BORDER="0"
 SRC="img8.png"
 ALT="$\epsilon$"> parameters
for 1-4 Lennard-Jones interactions.  

<P>
</LI>
</UL>

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<ADDRESS>
<I>Alexander Lyubartsev <BR>
2006-12-28</I>
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