/set/zznotes

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  For amides, {ab initio} calculations at the HF/6-31G* level tend to
overestimate molecular dipoles by about 12%.  The origin of this inaccuracy is
largely neglect of electron correlation.  To partially account for this
tendency, and for the energetic effects of polarization (induced dipoles of
protein and solvent) and alignment of solvent dipoles, atomic multipoles have
been uniformly scaled by a factor (1/1.12).  In the neutralization of forward
groups in SET_Q2, for consistency with the reduction of the atomic multipoles
by (1.12), the target charge (chg) of a forward group is multiplied by
(1/1.12).  If this factor is changed in "dat/residue_fe", it must also be
changed in SET_Q2.

  tyr_chi3= 0 represents the correct polarization of the phenol functional
group.  Alternatively symmetry could have been imposed such that the confs
chi3= 0 and chi3=180 are equivalent.  arg_chi5= 0, asn_chi3=180, gln_chi4=180
represent the correct polarization of the corresponding functional groups.

  Data files in directory "dat" contain the 20 amino acids in forms
corresponding to amino terminal, internal, and carboxyl terminal residues.  In
addition data files contain non amino acids units, for example water.

  Variables having dimensions of distance or energy are expressed internally in
atomic units.

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    energy component      variable    functional form
  ______________________  ________  ____________________________
  [repulsion+dispersion]    Fr      3-parameter buf14-7
  [electrostatic]           Fe      multipole expansion
  [disulfide]               Fs      harmonic
  [intrinsic torsional]     Ft      2D fourier series of order 6
  [distance constraint]     Fc      harmonic
  [hydration entropy]       Fh      gaussian volume

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  Variables in the path to Fs.

  Q2sq(iQ2)= 0
            iS  When added, there exists a back group that can interact with
                the iQ2 forward group.
           -iS  There exists a forward group that, when added, interacts with
                the iQ2 back group.
  Q2sq(  0)= 0
            iS  When added, there exists a back group that can interact with
                the base forward group.
  X1sq(iX1)= 0
            iS  There exists a forward group that, when added, interacts with
                the iX1 back group.

  G2sg(iG2)= 0  when corresponding Q2sq<1
  B2sb(iB2)= 0      "       "       "
  F1sf(iF1)= 4  when corresponding Q2sq>-1 and X1sx=0

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