AMBER file formats
``PARM'' parameter/topology file specification
The following section provides a good overview of the general topology file
format. A more complete prmtop specification, complete with
chamber-style sections and expanded explanations of some sections and
how they are used to calculate forces in Amber programs, is available in
PDF-form by clicking here. (This document is taken
from the appendix of Jason Swails’ doctoral dissertation.) This file is
generated by the LEaP programs, either sleap or tleap/xleap.
%FLAG TITLE
%FORMAT(20a4) (ITITL(i), i=1,20)
ITITL : title
%FLAG POINTERS
%FORMAT(10i8) NATOM, NTYPES, NBONH, MBONA, NTHETH, MTHETA,
NPHIH, MPHIA, NHPARM, NPARM, NNB, NRES,
NBONA, NTHETA, NPHIA, NUMBND, NUMANG, NPTRA,
NATYP, NPHB, IFPERT, NBPER, NGPER, NDPER,
MBPER, MGPER, MDPER, IFBOX, NMXRS, IFCAP,
NUMEXTRA, NCOPY
NATOM : total number of atoms
NTYPES : total number of distinct atom types
NBONH : number of bonds containing hydrogen
MBONA : number of bonds not containing hydrogen
NTHETH : number of angles containing hydrogen
MTHETA : number of angles not containing hydrogen
NPHIH : number of dihedrals containing hydrogen
MPHIA : number of dihedrals not containing hydrogen
NHPARM : currently not used
NPARM : used to determine if addles created prmtop
NNB : number of excluded atoms
NRES : number of residues
NBONA : MBONA + number of constraint bonds
NTHETA : MTHETA + number of constraint angles
NPHIA : MPHIA + number of constraint dihedrals
NUMBND : number of unique bond types
NUMANG : number of unique angle types
NPTRA : number of unique dihedral types
NATYP : number of atom types in parameter file, see SOLTY below
NPHB : number of distinct 10-12 hydrogen bond pair types
IFPERT : set to 1 if perturbation info is to be read in
NBPER : number of bonds to be perturbed
NGPER : number of angles to be perturbed
NDPER : number of dihedrals to be perturbed
MBPER : number of bonds with atoms completely in perturbed group
MGPER : number of angles with atoms completely in perturbed group
MDPER : number of dihedrals with atoms completely in perturbed groups
IFBOX : set to 1 if standard periodic box, 2 when truncated octahedral
NMXRS : number of atoms in the largest residue
IFCAP : set to 1 if the CAP option from edit was specified
NUMEXTRA : number of extra points found in topology
NCOPY : number of PIMD slices / number of beads
%FLAG ATOM_NAME
%FORMAT(20a4) (IGRAPH(i), i=1,NATOM)
IGRAPH : the user-specified atoms names
%FLAG CHARGE
%FORMAT(5E16.8) (CHARGE(i), i=1,NATOM)
CHARGE : the atom charges. Amber internally uses units of charge such
that E = q1*q2/r, where E is in kcal/mol, r is in Angstrom,
and q1,q2 are the values found in this section of the prmtop file.
Codes that write prmtop files need to ensure that the values
entered in this section satisfy the rule given above; similarly,
codes that read prmtop files need to interpret these values in
the same way that Amber does. (This is, after all, an "Amber"
file format!)
[Aside: Conversion of these internal values to units of electron
charge depends of what values are chosen for various fundamental
constants. For reasons lost to history, Amber force field
development has been based on the formula: q(internal units) =
q(electron charge units)*18.2223. Gromacs and some other programs
currently [2015] use a conversion factor of 18.222615, which
more closely agrees with currently-accepted values for fundamental
constants. Conversions to or from the prmtop format may need
to take account of such small differences, if they are important.]
%FLAG ATOMIC_NUMBER
%FORMAT(10I8) (ATNUM(i), i=1,NATOM)
ATNUM : the atomic number of each atom.
%FLAG MASS
%FORMAT(5E16.8) (AMASS(i), i=1,NATOM)
AMASS : the atom masses
%FLAG ATOM_TYPE_INDEX
%FORMAT(1OI8) (IAC(i), i=1,NATOM)
IAC : index for the atom types involved in Lennard Jones (6-12)
interactions. See ICO below.
%FLAG NUMBER_EXCLUDED_ATOMS
%FORMAT(10I8) (NUMEX(i), i=1,NATOM)
NUMEX : total number of excluded atoms for atom "i". Also called IBLO. See
NATEX below.
%FLAG NONBONDED_PARM_INDEX
%FORMAT(10I8) (ICO(i), i=1,NTYPES*NTYPES)
ICO : provides the index to the nonbon parameter
arrays CN1, CN2 and ASOL, BSOL. All possible 6-12
or 10-12 atoms type interactions are represented.
NOTE: A particular atom type can have either a 10-12
or a 6-12 interaction, but not both. The index is
calculated as follows:
index = ICO(NTYPES*(IAC(i)-1)+IAC(j))
If index is positive, this is an index into the
6-12 parameter arrays (CN1 and CN2) otherwise it
is an index into the 10-12 parameter arrays (ASOL
and BSOL).
%FLAG RESIDUE_LABEL
%FORMAT(20A4) (LBRES(i), i=1,NRES)
LBRES : names of each of the residues
%FLAG RESIDUE_POINTER
%FORMAT(10I8) (IPRES(i), i=1,NRES)
IPRES : atoms in each residue are listed for atom "i" in
IPRES(i) to IPRES(i+1)-1
%FLAG BOND_FORCE_CONSTANT
%FORMAT(5E16.8) (RK(i), i=1,NUMBND)
RK : force constant for the bonds of each type, kcal/(mol Angstrom**2)
%FLAG BOND_EQUIL_VALUE
%FORMAT(5E16.8) (REQ(i), i=1,NUMBND)
REQ : the equilibrium bond length for the bonds of each type, Angstroms
%FLAG ANGLE_FORCE_CONSTANT
%FORMAT(5E16.8) (TK(i), i=1,NUMANG)
TK : force constant for the angles of each type, kcal/(mol radian**2)
%FLAG ANGLE_EQUIL_VALUE
%FORMAT(5E16.8) (TEQ(i), i=1,NUMANG)
TEQ : the equilibrium angle for the angles of each type, radians
%FLAG DIHEDRAL_FORCE_CONSTANT
%FORMAT(5E16.8) (PK(i), i=1,NPTRA)
PK : force constant for the dihedrals of each type, kcal/mol
%FLAG DIHEDRAL_PERIODICITY
%FORMAT(5E16.8) (PN(i), i=1,NPTRA)
PN : periodicity of the dihedral of a given type
%FLAG DIHEDRAL_PHASE
%FORMAT(5E16.8) (PHASE(i), i=1,NPTRA)
PHASE : phase of the dihedral of a given type, radians
%FLAG SCEE_SCALE_FACTOR
%FORMAT(5E16.8) (ONE_SCEE(i), i=1,NPTRA)
ONE_SCEE : 1-4 electrostatic scaling constant. It is inverted right after
it's read in for performance reasons. This allows variable
1-4 scaling. If not present, it defaults to 1.2 for all dihedrals.
Therefore, the default ONE_SCEE value in the code is 1.0/1.2
%FLAG SCNB_SCALE_FACTOR
%FORMAT(5E16.8) (ONE_SCNB(i), i=1,NPTRA)
ONE_SCNB : 1-4 VDW scaling constant. It is inverted right after
it's read in. This allows variable 1-4 scaling. If not present,
it defaults to 2.0 for all dihedrals. Therefore, the default
ONE_SCNB value in the code is 1.0/2.0
%FLAG SOLTY
%FORMAT(5E16.8) (SOLTY(i), i=1,NATYP)
SOLTY : currently unused (reserved for future use)
%FLAG LENNARD_JONES_ACOEF
%FORMAT(5E16.8) (CN1(i), i=1,NTYPES*(NTYPES+1)/2)
CN1 : Lennard Jones r**12 terms for all possible atom type interactions,
indexed by ICO and IAC; for atom i and j where i < j, the index
into this array is as follows (assuming the value of ICO(index) is
positive): CN1(ICO(NTYPES*(IAC(i)-1)+IAC(j))).
%FLAG LENNARD_JONES_BCOEF
%FORMAT(5E16.8) (CN2(i), i=1,NTYPES*(NTYPES+1)/2)
CN2 : Lennard Jones r**6 terms for all possible
atom type interactions. Indexed like CN1 above.
NOTE: the atom numbers in the following arrays that describe bonds,
angles, and dihedrals are coordinate array indexes for runtime speed. The true
atom number equals the absolute value of the number divided by three, plus one.
In the case of the dihedrals, if the fourth atom is negative, this implies that
the dihedral is an improper. If the third atom is negative, this implies that
the end group interations are to be ignored. End group interactions are
ignored, for example, in dihedrals of various ring systems (to prevent double
counting of 1-4 interactions) and in multiterm dihedrals.
%FLAG BONDS_INC_HYDROGEN
%FORMAT(10I8) (IBH(i),JBH(i),ICBH(i), i=1,NBONH)
IBH : atom involved in bond "i", bond contains hydrogen
JBH : atom involved in bond "i", bond contains hydrogen
ICBH : index into parameter arrays RK and REQ
%FLAG BONDS_WITHOUT_HYDROGEN
%FORMAT(10I8) (IB(i),JB(i),ICB(i), i=1,NBONA)
IB : atom involved in bond "i", bond does not contain hydrogen
JB : atom involved in bond "i", bond does not contain hydrogen
ICB : index into parameter arrays RK and REQ
%FLAG ANGLES_INC_HYDROGEN
%FORMAT(10I8) (ITH(i),JTH(i),KTH(i),ICTH(i), i=1,NTHETH)
ITH : atom involved in angle "i", angle contains hydrogen
JTH : atom involved in angle "i", angle contains hydrogen
KTH : atom involved in angle "i", angle contains hydrogen
ICTH : index into parameter arrays TK and TEQ for angle
ITH(i)-JTH(i)-KTH(i)
%FLAG ANGLES_WITHOUT_HYDROGEN
%FORMAT(10I8) (IT(i),JT(i),KT(i),ICT(i), i=1,NTHETA)
IT : atom involved in angle "i", angle does not contain hydrogen
JT : atom involved in angle "i", angle does not contain hydrogen
KT : atom involved in angle "i", angle does not contain hydrogen
ICT : index into parameter arrays TK and TEQ for angle
IT(i)-JT(i)-KT(i)
%FLAG DIHEDRALS_INC_HYDROGEN
%FORMAT(10I8) (IPH(i),JPH(i),KPH(i),LPH(i),ICPH(i), i=1,NPHIH)
IPH : atom involved in dihedral "i", dihedral contains hydrogen
JPH : atom involved in dihedral "i", dihedral contains hydrogen
KPH : atom involved in dihedral "i", dihedral contains hydrogen
LPH : atom involved in dihedral "i", dihedral contains hydrogen
ICPH : index into parameter arrays PK, PN, PHASE, ONE_SCEE, and ONE_SCNB
for dihedral IPH(i)-JPH(i)-KPH(i)-LPH(i)
%FLAG DIHEDRALS_WITHOUT_HYDROGEN
%FORMAT(10I8) (IP(i),JP(i),KP(i),LP(i),ICP(i), i=1,NPHIA)
IP : atom involved in dihedral "i", dihedral does not contain hydrogen
JP : atom involved in dihedral "i", dihedral does not contain hydrogen
KP : atom involved in dihedral "i", dihedral does not contain hydrogen
LP : atom involved in dihedral "i", dihedral does not contain hydrogen
ICP : index into parameter arrays PK, PN, PHASE, ONE_SCEE, and ONE_SCNB
for dihedral IPH(i)-JPH(i)-KPH(i)-LPH(i). Note, if the
periodicity is negative, this implies the following entry
in the PK, PN, and PHASE arrays is another term in a
multitermed dihedral.
%FLAG EXCLUDED_ATOMS_LIST
%FORMAT(10I8) (INB(i), i=1,NNB)
INB : the excluded atom list. To get the excluded list for atom
"i" you need to traverse the NUMEX list, adding up all
the previous NUMEX values, since NUMEX(i) holds the number
of excluded atoms for atom "i", not the index into the
NATEX list. Let IEXCL = SUM(NUMEX(j), j=1,i-1), then
excluded atoms are INB(IEXCL) to INB(IEXCL+NUMEX(i)). Note,
this array was called NATEX at one point, and while in most
places it is now INB, it is still called NATEX in some places
(especially in pmemd)
%FLAG HBOND_ACOEF
%FORMAT(5E16.8) (ASOL(i), i=1,NPHB)
ASOL : the value for the r**12 term for hydrogen bonds of all
possible types. Index into these arrays is equivalent
to the CN1 and CN2 arrays, however the index is negative.
For example, for atoms i and j, with i < j, the index is
-ICO(NTYPES*(IAC(i)-1+IAC(j)). Note: Amber must be compiled
with -DHAS_10_12 in order to make use of this term!
%FLAG HBOND_BCOEF
%FORMAT(5E16.8) (BSOL(i), i=1,NPHB)
BSOL : the value for the r**10 term for hydrogen bonds of all
possible types. Indexed like ASOL. Note: same restriction
applies for use.
%FLAG HBCUT
%FORMAT(5E16.8) (HBCUT(i), i=1,NPHB)
HBCUT : no longer in use
%FLAG AMBER_ATOM_TYPE
%FORMAT(20A4) (ISYMBL(i), i=1,NATOM)
ISYMBL : the AMBER atom types for each atom
%FLAG TREE_CHAIN_CLASSIFICATION
%FORMAT(20A4) (ITREE(i), i=1,NATOM)
ITREE : the list of tree joining information, classified into five
types. M -- main chain, S -- side chain, B -- branch point,
3 -- branch into three chains, E -- end of the chain
%FLAG JOIN_ARRAY
%FORMAT(10I8) (JOIN(i), i=1,NATOM)
JOIN : tree joining information, potentially used in ancient
analysis programs. Currently unused in sander or gibbs.
%FLAG IROTAT
%FORMAT(10I8) (IROTAT(i), i = 1, NATOM)
IROTAT : apparently the last atom that would move if atom i was
rotated, however the meaning has been lost over time.
Currently unused in sander or gibbs.
%FLAG RADIUS_SET
%FORMAT(1a80) TYPE
TYPE : the radius set chosen inside LEaP
%FLAG RADII
%FORMAT(5E16.8) (RBORN(i), i=1,NATOM)
RBORN : Generalized Born intrinsic dielectric radii
%FLAG SCREEN
%FORMAT(5E16.8) (FS(i), i=1,NATOM)
FS : Screening parameters used in Generalized Born
The following are only present if IFBOX .gt. 0
%FLAG SOLVENT_POINTERS
%FORMAT(3I8) IPTRES, NSPM, NSPSOL
IPTRES : final residue that is considered part of the solute,
reset in sander and gibbs
NSPM : total number of molecules
NSPSOL : the first solvent "molecule"
%FLAG ATOMS_PER_MOLECULE
%FORMAT(10I8) (NSP(i), i=1,NSPM)
NSP : the total number of atoms in each molecule,
necessary to correctly perform the pressure
scaling.
%FLAG BOX_DIMENSIONS
%FORMAT(5E16.8) OLDBETA, BOX(1), BOX(2), BOX(3)
OLDBETA : periodic box, angle between the XY and YZ planes in
degrees. This is now redundant, as it is present in the
inpcrd files. It is ignored here.
BOX : the periodic box lengths in the X, Y, and Z directions.
This is now redundant, as it is present in the inpcrd files.
It is ignored here.
The following are only present if IFCAP .gt. 0
%FLAG CAP_INFO
%FORMAT(10I8) NATCAP
NATCAP : last atom before the start of the cap of waters
placed by edit
%FLAG CAP_INFO2
%FORMAT(5E16.8) CUTCAP, XCAP, YCAP, ZCAP
CUTCAP : the distance from the center of the cap to the outside
XCAP : X coordinate for the center of the cap
YCAP : Y coordinate for the center of the cap
ZCAP : Z coordinate for the center of the cap
The following is only present if IFPERT .gt. 0 Note that
the initial state, or equivalently the prep/link/edit state, is
represented by lambda=1 and the perturbed state, or final state
specified in parm, is the lambda=0 state. This information is only used for
GIBBS and is unused in either SANDER or PMEMD.
FORMAT(12I6) (IBPER(i), JBPER(i), i=1,NBPER)
IBPER : atoms involved in perturbed bonds
JBPER : atoms involved in perturbed bonds
FORMAT(12I6) (ICBPER(i), i=1,2*NBPER)
ICBPER : pointer into the bond parameter arrays RK and REQ for the
perturbed bonds. ICBPER(i) represents lambda=1 and
ICBPER(i+NBPER) represents lambda=0.
FORMAT(12I6) (ITPER(i), JTPER(i), KTPER(i), i=1,NGPER)
IPTER : atoms involved in perturbed angles
JTPER : atoms involved in perturbed angles
KTPER : atoms involved in perturbed angles
FORMAT(12I6) (ICTPER(i), i=1,2*NGPER)
ICTPER : pointer into the angle parameter arrays TK and TEQ for
the perturbed angles. ICTPER(i) represents lambda=0 and
ICTPER(i+NGPER) represents lambda=1.
FORMAT(12I6) (IPPER(i), JPPER(i), KPPER(i), LPPER(i), i=1,NDPER)
IPPER : atoms involved in perturbed dihedrals
JPPER : atoms involved in perturbed dihedrals
KPPER : atoms involved in perturbed dihedrals
LPPER : atoms involved in pertrubed dihedrals
FORMAT(12I6) (ICPPER(i), i=1,2*NDPER)
ICPPER : pointer into the dihedral parameter arrays PK, PN and
PHASE for the perturbed dihedrals. ICPPER(i) represents
lambda=1 and ICPPER(i+NGPER) represents lambda=0.
FORMAT(20A4) (LABRES(i), i=1,NRES)
LABRES : residue names at lambda=0
FORMAT(20A4) (IGRPER(i), i=1,NATOM)
IGRPER : atomic names at lambda=0
FORMAT(20A4) (ISMPER(i), i=1,NATOM)
ISMPER : atomic symbols at lambda=0
FORMAT(5E16.8) (ALMPER(i), i=1,NATOM)
ALMPER : unused currently in gibbs
FORMAT(12I6) (IAPER(i), i=1,NATOM)
IAPER : IAPER(i) = 1 if the atom is being perturbed
FORMAT(12I6) (IACPER(i), i=1,NATOM)
IACPER : index for the atom types involved in Lennard Jones
interactions at lambda=0. Similar to IAC above.
See ICO above.
FORMAT(5E16.8) (CGPER(i), i=1,NATOM)
CGPER : atomic charges at lambda=0
The following is only present if IPOL .eq. 1
%FLAG POLARIZABILITY
%FORMAT(5E18.8) (ATPOL(i), i=1,NATOM)
ATPOL : atomic polarizabilities
The following is only present if
IPOL == 1 .and. IFPERT == 1
FORMAT(5E18.8) (ATPOL1(i), i=1,NATOM)
ATPOL1 : atomic polarizabilities at lambda = 1 (above is at lambda = 0)
AMBER coordinate/restart file specification
The 'coord' version of this file is generated by the PARM or
LEaP programs. The 'restrt' version is the result of energy
minimization or molecular dynamics in SANDER or
GIBBS and may contain velocity and periodic box information.
FORMAT(20A4) ITITL
ITITL : the title of the current run, from the AMBER
parameter/topology file
FORMAT(I5,5E15.7) NATOM,TIME
NATOM : total number of atoms in coordinate file
TIME : option, current time in the simulation (picoseconds)
FORMAT(6F12.7) (X(i), Y(i), Z(i), i = 1,NATOM)
X,Y,Z : coordinates
IF dynamics
FORMAT(6F12.7) (VX(i), VY(i), VZ(i), i = 1,NATOM)
VX,VY,VZ : velocities (units: Angstroms per 1/20.455 ps)
IF constant pressure (in 4.1, also constant volume)
FORMAT(6F12.7) BOX(1), BOX(2), BOX(3)
BOX : size of the periodic box
Note: in AMBER 4.1 if the EWALD option is turned on, the box angles will
also be written out in the same format.
AMBER trajectory (coordinate or velocity) file specification
This file is optionally written during dynamics in SANDER or
GIBBS.
FORMAT(20A4) ITITL
ITITL : the title of the current run, from the AMBER
parameter/topology file
The following snapshot is written every NTWX steps in the
trajectory (specified in the control input file):
FORMAT(10F8.3) (X(i), Y(i), Z(i), i=1,NATOM)
X,Y,Z : coordinates or velocities (velocity units: Angstroms per 1/20.455 ps)
IF constant pressure (in 4.1, also constant volume), for each
snapshot:
FORMAT(10F8.3) BOX(1), BOX(2), BOX(3)
BOX : size of periodic box
AMBER Trajectory NetCDF Convention
Beginning with AMBER 9, a binary file format for trajectory data based on
NetCDF is
supported by sander, pmemd and ptraj. This format is supported by
VMD beginning with version
1.8.4.
The AMBER Trajectory NetCDF Convention,
describes the layout of dimensions, variables and attributes within the file.
It is also available as a PDF.
Force field parameter file specification
Force field information on the file frcfld: The following sec-
tion of this document describes the format of the AMBER Force
Field Parameter File. It is not expected that the user will
ordinarily modify this file; rather modifications should ordi-
narily be entered through the frcmod file described further
below. Of course, major changes, such as using the AMBER/OPLS
force field rather than the AMBER one, would best be made by
changing this file. WARNING: multiple entries for the same atom
symbols within a single frcfld or frcmod file can lead to unde-
fined results, e.g. if there are two definitions of angle ener-
gies between atom types A, B and C one of them is picked arbi-
trarily.
- 1 - ITITL
FORMAT(20A4)
ITITL A title for identification of the parameter set.
------------------------------------------------------------------------
- 2 - ***** INPUT FOR ATOM SYMBOLS AND MASSES *****
KNDSYM , AMASS, ATPOL
FORMAT(A2,2X,F10.2x,f10.2)
KNDSYM The unique atom symbol used in the system.
AMASS Atomic mass of the center having the symbol "KNDSYM".
ATPOL The atomic polarizability for each atom (in A**3)
This is the type of polarizability used in sander
and gibbs. No parameters are supplied for this since
the feature is still in development (Amber 4.1).
NOTE: All the unique atomic symbols and their masses must
be read. The input is terminated by a blank card.
------------------------------------------------------------------------
- 3 - ***** INPUT FOR ATOM SYMBOLS THAT ARE HYDROPHILIC *****
JSOLTY(I)
FORMAT(20(A2,2X))
JSOLTY(I) The atom symbols which are hydrophilic in solution.
This information is read but not used.
The input is terminated when a blank value is read for
the atom symbol.
------------------------------------------------------------------------
- 4 - ***** INPUT FOR BOND LENGTH PARAMETERS *****
IBT , JBT , RK , REQ
FORMAT(A2,1X,A2,2F10.2)
IBT,JBT Atom symbols for the two bonded atoms.
RK The harmonic force constant for the bond "IBT"-"JBT".
The unit is kcal/mol/(A**2).
REQ The equilibrium bond length for the above bond in Angstroms
The input is terminated by a blank card.
------------------------------------------------------------------------
- 5 - ***** INPUT FOR BOND ANGLE PARAMETERS *****
ITT , JTT , KTT , TK , TEQ
FORMAT(A2,1X,A2,1X,A2,2F10.2)
ITT,... The atom symbols for the atoms making an angle.
TK The harmonic force constants for the angle "ITT"-"JTT"-
"KTT" in units of kcal/mol/(rad**2) (radians are the
traditional unit for angle parameters in force fields).
TEQ The equilibrium bond angle for the above angle in degrees.
The input is terminated by a blank card.
------------------------------------------------------------------------
- 6 - ***** INPUT FOR DIHEDRAL PARAMETERS *****
IPT , JPT , KPT , LPT , IDIVF , PK , PHASE , PN
FORMAT(A2,1X,A2,1X,A2,1X,A2,I4,3F15.2)
IPT, ... The atom symbols for the atoms forming a dihedral
angle. If IPT .eq. 'X ' .and. LPT .eq. 'X ' then
any dihedrals in the system involving the atoms "JPT" and
and "KPT" are assigned the same parameters. This is
called the general dihedral type and is of the form
"X "-"JPT"-"KPT"-"X ".
IDIVF The factor by which the torsional barrier is divided.
Consult Weiner, et al., JACS 106:765 (1984) p. 769 for
details. Basically, the actual torsional potential is
(PK/IDIVF) * (1 + cos(PN*phi - PHASE))
PK The barrier height divided by a factor of 2.
PHASE The phase shift angle in the torsional function.
The unit is degrees.
PN The periodicity of the torsional barrier.
NOTE: If PN .lt. 0.0 then the torsional potential
is assumed to have more than one term, and the
values of the rest of the terms are read from the
next cards until a positive PN is encountered. The
negative value of pn is used only for identifying
the existence of the next term and only the
absolute value of PN is kept.
The input is terminated by a blank card.
------------------------------------------------------------------------
- 7 - ***** INPUT FOR IMPROPER DIHEDRAL PARAMETERS *****
IPT , JPT , KPT , LPT , IDIVF , PK , PHASE , PN
FORMAT(A2,1X,A2,1X,A2,1X,A2,I4,3F15.2)
The input is the same as in for the dihedrals except that
the torsional barrier height is NOT divided by the factor
idivf. The improper torsions are defined between any four
atoms not bonded (in a successive fashion) with each other
as in the case of "regular" or "proper" dihedrals. Improper
dihedrals are used to keep certain groups planar and to
prevent the racemization of certain centers in the united
atom model. Consult the above reference for details.
Important note: all general type improper dihedrals
(e.g. x -x -ct-hc) should appear before all
specifics (ct-ct-ct-hc) in the parm list.
Otherwise the generals will override the
specific with no warning.
The input is terminated by a blank card.
------------------------------------------------------------------------
- 8 - ***** INPUT FOR H-BOND 10-12 POTENTIAL PARAMETERS *****
KT1 , KT2 , A , B , ASOLN , BSOLN , HCUT , IC
FORMAT(2X,A2,2X,A2,2x,5F10.2,I2)
KT1,KT2 The atom symbols for the atom pairs for which the
parameters are defined.
A The coefficient of the 12th power term (A/(r**12)).
B The coefficient of the 10th power term (-B/(r**10)).
ASOLN Not used
BSOLN Not used
HCUT Not used
IC Not used
------------------------------------------------------------------------
- 9 - ***** INPUT FOR EQUIVALENCING ATOM SYMBOLS FOR
THE NON-BONDED 6-12 POTENTIAL PARAMETERS *****
IORG , IEQV(I) , I = 1 , 19
FORMAT(20(A2,2X))
IORG The atom symbols to which other atom symbols are to be
equivalenced in generating the 6-12 potential parameters.
IEQV(I) The atoms symbols which are to be equivalenced to the
atom symbol "IORG". If more than 19 atom symbols have
to be equivalenced to a given atom symbol they can be
included as extra cards.
It is advisable not to equivalence any hydrogen bond
atom type atoms with any other atom types.
NOTE: The input is terminated by a blank card.
------------------------------------------------------------------------
- 10 - ***** INPUT FOR THE 6-12 POTENTIAL PARAMETERS *****
LABEL , KINDNB
FORMAT(A4,6X,A2)
LABEL The name of the non-bonded input parameter to be
used. It has to be matched with "NAMNB" read through
unit 5. The program searches the file to load the
the required non-bonded parameters. If that name is
not found the run will be terminated.
KINDNB Flag for the type of 6-12 parameters.
'SK' Slater-Kirkwood parameters are input.
see "caution" below.
'RE' van der Waals radius and the potential well depth
parameters are read.
'AC' The 6-12 potential coefficients are read.
NOTE: All the non equivalenced atoms' parameters have to
be given.
The input is terminated when label .eq. 'END'
------------------------------------------------------------------------
CAUTION: the polarizabilities mentioned below are NOT the
polarizabilities used in the sander (min/md) code.
KINDNB 'SK' parameters are not currently part of
the AMBER force field. See card 2, ATPOL for sander
polarizability.
- 10A - ***** ONLY IF KINDNB .EQ. 'SK' *****
LTYNB , POL , XNEFF , RMIN
FORMAT(2X,A2,6X,3F10.6)
LTYNB Atom symbol.
POL Atomic polarizability for the atom centers having the
the above symbol.
XNEFF Effective number of electrons on the atom centers having
the above symbol.
RMIN van der Waals radius of the atom center having the above
symbol.
------------------------------------------------------------------------
- 10B - ***** ONLY IF KINDNB .EQ. 'RE' *****
LTYNB , R , EDEP
LTYNB Atom symbol.
R The van der Waals radius of the atoms having the symbol
"LTYNB" (Angstoms)
EDEP The 6-12 potential well depth. (kcal/mol)
------------------------------------------------------------------------
- 10C - ***** ONLY IF KINDNB .EQ. 'AC' *****
LTYNB , A , C
LTYNB Atom symbol.
A The coefficient of the 12th power term (A/r**12).
C The coefficient of the 6th power term (-C/r**6).
Force field parameter modification file specification
Modified force field parameters in file frcmod: This file is
normally the one that will be changed by the user. It consists
of a 1-card title, followed by a blank line, then keyword sec-
tions. The allowed keywords (appearing in columns 1-4) are:
MASS follow this card by card of type - 2 - listed in the
unit 10 instructions above. End with a blank line.
BOND follow this card by card of type - 4 - listed in the
unit 10 instructions above. End with a blank line.
ANGL follow this card by card of type - 5 - listed in the
unit 10 instructions above. End with a blank line.
DIHE follow this card by card of type - 6 - listed in the
unit 10 instructions above. End with a blank line.
IMPR follow this card by card of type - 7 - listed in the
unit 10 instructions above. End with a blank line.
HBON follow this card by card of type - 8 - listed in the
unit 10 instructions above. End with a blank line.
NONB follow this card by card of type - 10A, B or C - listed
in the unit 10 instructions above. E.g. if you specify
STDA in parm.in for the "regular" parm.dat file, this is
the convention that will be used when reading frcmod.
End with a blank line.
Any or all of the keywords may be missing, if you have no
changes for that section. The entire file can be missing if
you have no changes at all to make to the standard force field.
Restrictions: note that you cannot modify the equivalence pat-
tern set up in the standard force field.
If you have parameters in the frcmod file that modify val-
ues in the standard parameter file, and if iparml is set to 2,
then both the original and the modified parameters will be
printed to the output file. The modified parameters will be
marked with asterisks, and it is these values that will be used
in subsequent calculations.
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