
1.  Specifying a force field

     Amber  is designed to work with several simple types of
force field, although it is most commonly used with  parame-
terizations  developed  by Peter Kollman and his co-workers.
One significant recent development is that there are  now  a
variety of such parameterizations, with no obvious "default"
value.  The "traditional" parameterization uses  fixed  par-
tial charges, centered on atoms.  Examples of this are ff86,
ff94, ff96, ff98 and ff99 (described below).  The default in
versions 5 and 6 of Amber was ff94; a comparable default now
would probably be ff99, but users should consult the  papers
listed  below  to  see  a detailed discussion of the changes
made.

     Less extensively used, but very promising, recent modi-
fications  add  polarizable  dipoles  to  atoms, so that the
charge description depends upon the environment; such poten-
tials  are called "polarizable" or "non-additive".  Examples
are ff02 and ff02EP: the former has atom-based  charges  (as
in the traditional parameterization), and the latter adds in
off-center charges (or "extra points"),  primarily  to  help
describe  better  the  angular dependence of hydrogen bonds.
Again, users should consult the papers cited  below  to  see
details of how these new force fields have been developed.

     In  order to tell LEaP which force field is being used,
the four types of information described  below  need  to  be
provided.   This  is  generally accomplished by selecting an
appropriate leaprc file, which loads the information  needed
for a specific force field.  (See section 2.2, below).

 (1)   A  listing of the atom types, what elements they cor-
       respond to, and their hybridizations.  This  informa-
       tion  is  encoded  as  a set of LEaP commands, and is
       normally read from a leaprc file.

 (2)   Residue descriptions (or "topologies") that  describe
       the  chemical nature of amino acids, nucleotides, and
       so on.  These files specify the connectivities,  atom
       types,  charges,  and other information.  These files
       have a "prep" format (a now-obsolete part  of  Amber)
       and  have  a  ".in" extension.  Standard libraries of
       residue descriptions are in the  amber7/dat/leap/prep
       directory.   The  antechamber  program may be used to
       generate prep files for other organic molecules.

 (3)   Parameter files  give  force  constants,  equilibrium
       bond  lengths  and  angles, Lennard-Jones parameters,
       and the like.  Standard files have  a  ".dat"  exten-
       sion, and are found in amber6/dat/leap/parm.

 (4)   Extensions  or  changes  to  the  parameters  can  be
       included in frcmod files.  The  expectation  is  that
       the  user  will  load  a  large, "standard" parameter
       file, and (if needed)  a  smaller  frcmod  file  that
       keeps  track of any changes to the default parameters
       that are needed.  The frcmod files for  changing  the
       default water model (which is TIP3P) into other water
       models are in  files  like  amber7/dat/leap/parm/frc-
       mod.tip4p.  The parmchk program (part of Antechamber)
       can also generate frcmod files.

1.1.  Description of the database files

     The following files are in the  amber7/dat/leap  direc-
tory.   Files  with a ".in" extension are in the prep subdi-
rectory, those with a ".dat" extension are in the parm  sub-
directory, as are the "frcmod" files.
____________________________________________________________


     Amber 1999 and 2002 force fields
       parm99.dat       Force field, for amino acids and some organic molecules;
                             can be used with either additive or
                             non-additive treatment of electrostatics
       parm99EP.dat       Like parm99.dat, but with "extra-points": off-center
                             atomic charges, somewhat like lone-pairs
       gaff.dat           Newer (and still experimental) force field for quite
                             general organic molecules.

       all_nuc02.in       Nucleic acid input for building database, for a non-
                        additive (polarizable) force field without extra points.
       all_amino02.in     Amino acid input ...
       all_aminoct02.in   COO- amino acid input ...
       all_aminont02.in   NH3+ amino acid input ....

       all_nuc02EP.in     Nucleic acid input for building database, for a non-
                          additive (polarizable) force field with extra points.
       all_amino02EP.in     Amino acid input ...
       all_aminoct02EP.in   COO- amino acid input ...
       all_aminont02EP.in   NH3+ amino acid input ....

     Amber 1994 (Cornell et al.) force field
       all_nuc94.in       Nucleic acid input for building database.
       all_amino94.in     Amino acid input for building database.
       all_aminoct94.in   COO- amino acid input for database.
       all_aminont94.in   NH3+ amino acid input for database.
       nacl.in            Ion file
       parm94.dat         1994 force field file.
       parm96.dat         modified version of 1994 force field, for proteins
       parm98.dat        modified version of 1994 force field, for nucleic acids

     Amber 1984, 1986 (Weiner et al.) force fields
       all.in             All atom database input.

       allct.in           All atom database input, COO- Amino acids.
       allnt.in           All atom database input, NH3+ Amino acids.
       uni.in             United atom database input.
       unict.in           United atom database input, COO- Amino acids.
       unint.in           United atom database input, NH3+ Amino acids.
       parm91X.dat        Parameters for 1984, 1986 force fields

     Solvent models:
       water.in           topology definition for several water models
       meoh.in            topology file for methanol
       chcl3.in           topology file for chloroform
       nma.in             topology file for N-methylacetamide

       frcmod.tip4p       parameter changes from TIP3P -> TIP4P
       frcmod.tip5p       parameter changes from TIP3P -> TIP5P
       frcmod.spce        parameter changes from TIP3P -> SPC/E
       frcmod.pol3        parameter changes from TIP3P -> POL3
       frcmod.meoh        paramters for methanol
       frcmod.chcl3       paramters for chloroform
       frcmod.nma         paramters for N-methyacetamide

     Miscellaneous:
       nucgen.dat         Nucgen nucleic acid conformations.
       PROTON_INFO*       Files needed for protonate
       map.DG-AMBER       needed for NMR input generation.

____________________________________________________________



1.2.  Specifying which force field you want in LEaP

     Various combinations of the above files make sense, and
we have moved to an "ff" (force field) nomenclature to iden-
tify  these;  examples  would  then  be  ff94 (which was the
default in Amber 5 and 6), ff99, etc.  The most straightfor-
ward way to specify which force field you want is to use one
of the leaprc files in $AMBERHOME/dat/leap/cmd.   The  sytax
is:

     xleap -s -f <filename>


Here,  the  -s  flag tells LEaP to ignore any leaprc file it
might find, and the -f flag tells it to start with  commands
for  some  other file.  Here are the combinations we support
and recommend:

+-------------------------------------------------------------+
|            How to specify force fields in LEaP              |
|  filename                topology               parameters  |
+-------------------------------------------------------------+
|leaprc.ff86          Weiner et al. 1986         parm91X.dat  |
|leaprc.ff94          Cornell et al. 1994        parm94.dat   |
|leaprc.ff96                   "                 parm96.dat   |
|leaprc.ff98                   "                 parm98.dat   |
|leaprc.ff99                   "                 parm99.dat   |
|leaprc.ff02     reduced (polarizable) charges   parm99.dat   |
|leaprc.ff02EP         " + extra points          parm99EP.dat |
|leaprc.gaff                 none                gaff.dat     |
+-------------------------------------------------------------+
Notes:

 (1)   Unlike  previous  versions  of  Amber,  there  is  no
       default leaprc file anymore.  If you make a link from
       one of the files above to a file named  leaprc,  then
       that will become the default.  For example:

            cd $AMBERHOME/dat/leap/cmd
            ln -s leaprc.ff99 leaprc

       will  provide  a  good  default for many users; after
       this you could just invoke tleap or xleap without any
       arguments,  and  it would automatically load the ff99
       force field.  If you put  leaprc.ff94  in  the  above
       link  command, you would be making the Cornell et al.
       force field the default, which was  the  behavior  of
       versions  5  and 6 of Amber.  Note also that a leaprc
       file in the current  directory  overrides  any  other
       such  files that might be present in the search path.

 (2)   The first five choices in the  above  table  are  for
       additive  (non-polarizable)  simulations;  you should
       use saveAmberParm (or saveAmberParmPert) to save  the
       prmtop file, and keep the default ipol=0 in sander or
       gibbs.

 (3)   The ff02 entries in the above table are for non-addi-
       tive  (polarizable) force fields.  Use saveAmberParm-
       Pol to save the prmtop file, and set  ipol=1  in  the
       sander  or  gibbs  input  file.   Note that POL3 is a
       polarizable water model, so you need to  use  saveAm-
       berParmPol for it as well.

 (4)   The files above assume that nucleic acids are DNA, if
       not   explicitly   specified.     Use    the    files
       leaprc.rna.ff98,  leaprc.rna.ff99, leaprc.rna.ff02 or
       leaprc.rna.ff00EP to make the default  RNA.   If  you
       have  mixture  of  DNA and RNA, you will need to edit
       your  PDB  file,  or  use  the   loadPdbUsingSequence

       command  in LEaP (see that chapter) in order to spec-
       ify which nucelotide is which.

 (5)   There is also a leaprc.gaff file, which sets  you  up
       for the "general" Amber force field.  This is primar-
       ily for use with Antechamber (see that chapter),  and
       does not load any topology files.

 (6)   The leaprc.ff86 files gives the 1986 all-atom parame-
       ters; Amber no  longer  directly  supports  the  1984
       united atom parameter set.

 (7)   Our  experience  with generalized Born simulations is
       all with ff94 or ff99; the current GB models are  not
       compatible  with  polarizable  force  fields.  The GB
       options igb=3 or 4 (see Chapter 5) were  derived  for
       use  with  ff94.   Replacing explicit water with a GB
       model is equivalent to specifying a  different  force
       field,  and users should be aware that none of the GB
       options (in Amber or elsewhere)  is  as  "mature"  as
       simulations with explicit solvent; user discretion is
       advised!


1.3.  1999 and 2002 force fields

     The ff99 force field [1] represents a new direction for
Amber-related   force  fields,  pointing  towards  "general"
organic and bioorganic systems.  The atom types  are  mostly
those  of  Cornell et al. (see below), but changes have been
made in many torsional parameters, and this parameterization
supports  both additive and non-additive (polarizable) force
fields.  The topology and coordinate  files  for  the  small
molecule  test  cases  used in the development of this force
field are in the parm99_lib subdirectory.   The  ff99  force
field  uses  these parameters, along with the topologies and
charges from the Cornell et al. force field,  to  create  an
all-atom nonpolarizable force field for proteins and nucleic
acids.  This is probably the best  "general  purpose"  force
field included here for biomolecules.

     The  ff02 force field is a polarizable variant of ff99.
Here,  the  charges  were  determined   at   the   B3LYP/cc-
pVTZ//HF/6-31g*  level,  and hence are more like "gas-phase"
charges.   During  charge   fitting   the   correction   for
intramolecular  self  polarization  has  been  included [2].
Bond polarization arising from interactions with a condensed
phase  environment  are achieved through polarizable dipoles
attached to the atoms.  These are determined from  isotropic
atomic  polarizabilities  assigned  to each atom, taken from
experimental work of Applequist.  The dipoles can either  be
determined  at each step through an iterative scheme, or can
be treated as additional dynamical variables, and propagated
through  dynamics along with the atomic positions, in a man-
ner analogous Car-Parinello  dynamics.   Derivation  of  the
polarizable force field required only minor changes in dihe-
dral terms and  a few modification  of  the  van  der  Waals
parameters.

     The user also has a choice to use the polarizable force
field with extra points on which  additional  point  charges
are  located;  this is called ff02EP.  The additional points
are located on electron donating atoms (e.g.  O,N,S),  which
mimic  the presence of electron lone pairs [3].  For nucleic
acids we chose to  use  extra  interacting  points  only  on
nucleic acid bases and not on sugars or phosphate groups.

     There  is  not  (yet)  a  full published description of
this, but a good deal of preliminary work on small molecules
is  available  [2,4].   Beyond  small  molecules, our intial
tests have focussed on small  proteins  and  double  helical
oligonucleotides,  in additive TIP3P water solution.  Such a
simulation model, (using a  polarizable  solute  in  a  non-
polarizable  solvent) gains some of the advantages of polar-
ization at only a small extra cost, compared to  a  standard
force  field  model.   In  particular, the polarizable force
field appears  better  suited  to  reproduce  intermolecular
interactions  and  directionality of H-bonding in biological
systems than the additive force field.  Initial  tests  show
ff02EP  behaves slightly better than ff02, but it is not yet
clear how significant or widespread these  differences  will
be.

     The  gaff.dat  ("general  Amber  force field") is yet a
further step towards general purpose organic molecules.   It
is  primarily  used in conjunction with the antechamber pro-
gram, and users should consult that chapter for more  infor-
mation.   A  paper describing these parameters is being pre-
pared for publication.


1.4.  The Cornell et al. (1994) force field

     Contained in ff94 are  parameters  from  the  so-called
"second  generation"  force  field  developed in the Kollman
group in the early 1990's [5].  These parameters  are  espe-
cially  derived  for solvated systems, and when used with an
appropriate 1-4 electrostatic scale factor, have been  shown
to  perform  well  at modelling many organic molecules.  The
parameters in parm94.dat omit the hydrogen bonding terms  of
earlier  force  fields.  This is an all-atom force field; no
united-atom  counterpart  is  provided.   1-4  electrostatic
interactions  are  scaled by 1.2 instead of the value of 2.0
that had been used in earlier force fields.

     Charges were derived using Hartree-Fock theory with the
6-31G* basis set, because this exaggerates the dipole moment
of most residues by 10-20%.  It thus "builds in" the  amount
of polarization which would be expected in aqueous solution.
This is necessary for carrying out condensed  phase  simula-
tions  with an effective two-body force field which does not
include explicit polarization.  The charge-fitting procedure
is described in Appendix D.

     The  ff96  force  field  [6] differs from parm94.dat in
that the torsions for  and  have been modified  in  response
to  ab  initio calculations [7] which showed that the energy
difference between conformations were quite  different  than
calculated  by Cornell et al. (using parm94.dat).  To create
parm96.dat, common V1 and V2 parameters were used for  and ,
which were empirically adjusted to reproduce the energy dif-
ference between extended and constrained alpha helical ener-
gies  for  the alanine tetrapeptide.  This led to a signifi-
cant improvement between molecular  mechanical  and  quantum
mechanical  relative  energies  for the remaining members of
the set of tetrapeptides studied by  Beachy  et  al.   Users
should  be aware that parm96.dat has not been as extensively
used as parm94.dat, and that it almost certainly has its own
biases and idiosyncracies [8,9].

     The  ff98  force  field [10] differs from parm94.dat in
torsion angle parameters involving the glycosidic torsion in
nucleic acids.  These serve to improve the predicted helical
repeat and sugar pucker profiles.


1.5.  The Weiner et al. (1984,1986) force fields

     The ff86 parameters are described in early papers  from
the Kollman and Case groups [11,12].  [The "parm91" designa-
tion is somewhat unfortunate: this file  is  really  only  a
corrected version of the paramters described in the 1984 and
1986 papers listed above.]  These parameters are not  gener-
ally  recommended any more, but may still be useful for vac-
uum simulations of nucleic acids and proteins using  a  dis-
tance-dependent  dielectric,  or  for comparisons to earlier
work.  The material in parm91X.dat is the parameter set dis-
tributed  with  Amber  4.0.  The STUB nonbonded set has been
copied from parmuni.dat; these sets of parameters are appro-
priate  for united atom calculations using the "larger" car-
bon radii referred to in the "note added in  proof"  of  the
1984 JACS paper.  If these values are used for a united atom
calculation, the parameter scnb should be set  to  8.0;  for
all-atom calculations use 2.0.  The scee parameter should be
set to 2.0 for both united atom and all-atom variants.  Note
that  the  default  value for scee is sander is now 1.2 (the
value for 1994 and later force fields; users must explicitly
change this in their inputs for the earlier force fields.

     A number of terms in the non-bonded list of parm91X.dat
should be noted.  The non-bonded terms for I(iodine),CU(cop-
per)  and  MG(magnesium) have not been carefully calibrated,
but are given as approximate values.  In  the  STUB  set  of
non-bonded  parameters,  we  have  included parameters for a
large hydrated monovalent cation (IP) that represent work by
Singh et al 1985 on large hydrated counterions for DNA. Sim-
ilar values are included for a hydrated anion (IM).

     The non-bonded potentials for  hydrogen-bond  pairs  in
ff86  uses  a Lennard-Jones 10-12 potential.  If you want to
run sander with ff86, you will need to recompile, adding the
-DHAS_10_12 flag to your MACHINE file.

1.6.  Ions

     For alkali ions with TIP3P waters, we have provided the
values of Aqvist [13], which are adjusted for  Amber's  non-
bonded  atom  pair  combining  rules to give the same ion-OW
potentials as in the original (which were designed  for  SPC
water);  these values reproduce the first peak of the radial
distribution for ion-OW and the relative  free  energies  of
solvation  in  water  of  the various ions.  Note that these
values would have to be changed if a water model other  than
TIP3P were to be used.  These potentials may also need modi-
fication if absolute free energies of solvation  are  impor-
tant [14].

1.7.  Solvent models

     Amber  now  provides  direct  support for several water
models.  The default water model is TIP3P [15].  This  model
will  be  used  for  residues with names HOH or WAT.  If you
want to use other water models, execute the  following  leap
commands after loading your leaprc file:

     WAT = PL3                    (residues named WAT in pdb file will be POL3)
     loadAmberParams frcmod.pol3  (sets the HW,OW parameters to POL3)

(The  above is obviously for the POL3 model.)  The water.lib
file contains TIP3P [15], TIP4P [15,16],  TIP5P  [17],  POL3
[18]  and SPC/E [19] models for water; these are called TP3,
T4P, T5P,  PL3  and  SPC,  respectively.   By  default,  the
residue  name  in the prmtop file will be WAT, regardless of
which water model is used.  If you want to change  this  (in
order  to  keep  track  of  which water model you are using,
say), you can change the residue name to whatever you  like.
For example,

     WAT = TP4
     set WAT.1 name "TP4"

would make a special label in PDB and prtmop files for TIP4P
water.  Note that Brookhaven  format  files  allow  at  most
three characters for the residue label.

     In  addition,  non-polarizable  models  for the organic
solvents methanol, chloroform and N-methylacetamide are pro-
vided.   The  input  files  for  a  single  molecule  are in
amber7/dat/leap/prep, and the corresponding frcmod files are
in   amber7/dat/leap/parm.   Pre-equlibrated  boxes  are  in
amber7/dat/leap/lib.  For example, to solvate a simple  pep-
tide in methanol, you could do the following:

     source leaprc.ff99                     (get a standard force field)
     loadAmberParams frcmod.meoh            (get methanol parameters)
     peptide = sequence { ACE VAL NME }     (construct a simple peptide)
     solvateBox peptide MEOHBOX 12.0 0.8    (solvate the peptide with meoh)
     saveAmberParm peptide prmtop prmcrd
     quit

Similar commands will work for other solvent models.

1.   J.  Wang,  P.  Cieplak  & P.A. Kollman. How well does a
     restrained electrostatic potential (RESP) model perform
     in  calcluating  conformational energies of organic and
     biological    molecules?.     J.     Comput.     Chem.
     21, 1049-1074(2000).

2.   P. Cieplak, J. Caldwell & P. Kollman. Molecular Mechan-
     ical Models for Organic and  Biological  Systems  Going
     Beyond  the  Atom Centered Two Body Additive Approxima-
     tion: Aqueous Solution Free Energies of Methanol and N-
     Methyl Acetamide, Nucleic Acid Base, and Amide Hydrogen
     Bonding and Chloroform/Water Partition Coefficients  of
     the   Nucleic   Acid   Bases.    J.   Computat.  Chem.
     22, 1048-1057(2001).

3.   R.W. Dixon & P.A. Kollman. Advancing Beyond  the  Atom-
     Centered  Model  in  Additive and Nonadditive Molecular
     Mechanics..  J. Computat. Chem.  18, 1632-1646(1997).

4.   E.   Meng,   P.   Cieplak,   J.W.   Caldwell   &   P.A.
     Kollman. Accurate  solvation  free  energies of acetate
     and methylammonium ions calculated with  a  polarizable
     water      model.       J.      Am.     Chem.     Soc.
     116, 12061-12062(1994).

5.   W.D. Cornell, P. Cieplak, C.I. Bayly, I.R. Gould,  K.M.
     Merz, Jr., D.M. Ferguson, D.C. Spellmeyer, T. Fox, J.W.
     Caldwell &  P.A.  Kollman. A  second  generation  force
     field  for  the  simulation of proteins, nucleic acids,
     and   organic   molecules.    J.   Am.   Chem.    Soc.
     117, 5179-5197(1995).

6.   P.A. Kollman, R. Dixon, W. Cornell, T. Fox, C. Chipot &
     A. Pohorille.  The development/application of a  'mini-
     malist'  organic/biochemical  molecular  mechanic force
     field using a combination of ab initio calculations and
     experimental data.  In Computer Simulation of Biomolec-
     ular Systems, Vol. 3, A. Wilkinson, P.  Weiner  &  W.F.
     van Gunsteren, Ed. Elsevier, (1997).   pp. 83-96.

7.   M.D.   Beachy  &  R.A.  Friesner. J.  Am.  Chem.  Soc.
     119, 5908-5920(1997).

8.   L. Wang, Y. Duan,  R.  Shortle,  B.  Imperiali  &  P.A.
     Kollman. Study of the stability and unfolding mechanism
     of BBA1 by molecular dynamics simulations at  different
     termperatures.  Prot. Sci.  8, 1292-1304(1999).

9.   J.  Higo,  N.  Ito, M. Kuroda, S. Ono, N. Nakajima & H.
     Nakamura. Energy landscape of a peptide  consisting  of
     -helix, 310 helix, -turn, -hairpin and other disordered
     conformations.  Prot. Sci.  10, 1160-1171(2001).

10.  T.E. Cheatham, III, P. Cieplak & P.A. Kollman. A  modi-
     fied  version  of  the  Cornell et al. force field with
     improved sugar pucker phases and  helical  repeat.   J.
     Biomol. Struct. Dyn.  16, 845-862(1999).

11.  S.J.  Weiner,  P.A.  Kollman, D.A. Case, U.C. Singh, C.
     Ghio, G. Alagona, S. Profeta, Jr. &  P.  Weiner. A  new
     force  field  for  molecular  mechanical  simulation of
     nucleic  acids  and  proteins.   J.  Am.  Chem.   Soc.
     106, 765-784(1984).

12.  S.J.  Weiner, P.A. Kollman, D.T. Nguyen & D.A. Case. An
     all-atom force field for simulations  of  proteins  and
     nucleic acids.  J. Computat. Chem.  7, 230-252(1986).

13.  J. qvist. Ion-water interaction potentials derived from
     free energy perturbation simulations.  J. Phys.  Chem.
     94, 8021-8024(1990).

14.  T.  Darden, D. Pearlman & L.G. Pedersen. Ionic charging
     free energies: Spherical versus periodic boundary  con-
     ditions.  J. Chem. Phys.  109, 10921-10935(1998).

15.  W.L.  Jorgensen,  J.  Chandrasekhar,  J.  Madura & M.L.
     Klein. Comparison of  Simple  Potential  Functions  for
     Simulating    Liquid    Water.     J.    Chem.   Phys.
     79, 926-935(1983).

16.  W.L.   Jorgensen    &    J.D.    Madura. Mol.    Phys.
     56, 1381(1985).

17.  M.W.  Mahoney  &  W.L. Jorgensen. A five-site model for
     liquid  water  and  the  reproduction  of  the  density
     anomaly  by rigid, nonpolarizable potential functions.
     J. Chem. Phys.  112, 8910-8922(2000).

18.  J.W. Caldwell & P.A. Kollman. Structure and  properties
     of  neat  liquids using nonadditive molecular dynamics:
     Water, methanol and N-methylacetamide.  J. Phys. Chem.
     99, 6208-6219(1995).

19.  H.J.C.  Berendsen,  J.R.  Grigera & T.P. Straatsma. The
     missing term in effective pair  potentials.   J.  Phys.
     Chem.  91, 6269-6271(1987).
