This appendix details the Parameter-Topology file format used extensively by the AMBER software suite for biomolecular simulation and analysis, referred to as the prmtop file for short. The format specification of the
AMBER topology file was written initially over a decade ago and posted on
http://ambermd.org/formats.html. I have recently expanded that document
to account for the drastic change to the file format that occurred with the2004 release of Amber 7. The pre-Amber 7 format (old format) is described
more briefly afterwards, although each section provided in the original format
contains exactly the same information as the newer version.
This appendix also details the format changes and additions introducedby chamber —the program that translates a CHARMM parameter file (PSF)
into a topology file that can be used with the sander and pmemd programsin AMBER.
This appendix draws from the information on http://ambermd.org/formats.html
that was added by both me and others, as well as the experience I gleaned
while writing the ParmEd program and working with the various codes in
AMBER.
As a warning, the prmtop file is a result of bookkeeping that becomesincreasingly complex as the system size increases. Therefore, hand-editing
the topology file for all but the smallest systems is discouraged—a programor script should be written to automate the procedure.

1

Layout

The first line of the Amber topology file is the version string. An example isshown below in which XX is replaced by the actual date and time.
%VERSION

VERSION_STAMP = V0001.000

DATE = XX/XX/XX

XX:XX:XX

The topology format is divided into several sections in a way that isdesigned to be parsed easily using simple Fortran code. A consequence of
this is that it is difficult for parsers written in other languages (e.g., C, C++,
Python, etc.) to strictly adhere to the standard. These parsers should try,
however, to support as much of the standard as possible.
%FLAG SECTION%COMMENT an arbitrary number of optional comments may be put here
%FORMAT(<FORTRAN FORMAT>)... data formatted according to <FORTRAN FORMAT>
1All names (e.g., atom names, atom type names, and residue names) arelimited to 4 characters and are printed in fields of width exactly 4 characterswide, left-justified. This means that names might not be space-delimited if
any of the names have 4 characters.
Requirements for prmtop parsers Parsers, regardless of the language
they are written in, should conform to a list of attributes to maximize thelikelihood that they are parsed correctly.
• Parsers should expect that some 4-character fields (e.g., atom or residue
names) may have some names that have 4 characters and therefore
might not be whitespace-delimited.
• Parsers should not expect SECTIONs in the prmtop to be in any particular order.
• Parsers should not expect or require %COMMENT lines to exist, but should
properly parse the file if any number of %COMMENT lines appear as indicated above• The topology file may be assumed to have been generated ‘correctly’
by tleap or some other credible source. No graceful error checking isrequired.
Requirements for modifying SECTIONs To minimize the impact of prmtop changes to existing, third-party parsers, the following conventions should
be followed.
• Any new SECTION should be added to the end of the topology file to
avoid conflicts with order-dependent parsers.
• The <FORTRAN FORMAT> should be as simple as possible (and avoid
adding new formats) to maintain simplicity for non-Fortran parsers.
• Avoid modifying if possible. Consider if this new section or change istruly necessary and belongs in the prmtop.

2

2

List of SECTIONs

TITLE
This section contains the title of the topology file on one line (up to 80
characters). While the title serves a primarily cosmetic purpose, this section
must be present.
%FORMAT(20a4)

POINTERSThis section contains the information about how many parameters are present
in all of the sections. There are 31 or 32 integer pointers (NCOPY might not
be present). The format and names of all of the pointers are listed below,
followed by a description of each pointer.
%FLAG POINTERS%FORMAT(10I8)
NATOM NTYPES NBONH
NNB
NRES
NBONA
IFPERT NBPER NGPERNUMEXTRA NCOPYMBONA NTHETH MTHETA NPHIH MPHIANTHETA NPHIA NUMBND NUMANG NPTRA
NDPER MBPER MGPER MDPER IFBOXNATOM Number of atoms
NTYPES Number of distinct Lennard-Jones 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 torsions containing Hydrogen
MPHIA Number of torsions not containing Hydrogen

3

NHPARM NPARM
NATYP NPHBNMXRS IFCAPNHPARM Not currently used for anything
NPARM Used to determine if this is a LES-compatible prmtop
NNB Number of excluded atoms (length of total exclusion list)
NRES Number of residues
NBONA MBONA + number of constraint bonds 1
NTHETA MTHETA + number of constraint angles 1
NPHIA MPHIA + number of constraint torsions 1
NUMBND Number of unique bond types
NUMANG Number of unique angle types
NPTRA Number of unique torsion types
NATYP Number of SOLTY terms. Currently unused.
NPHB Number of distinct 10-12 hydrogen bond pair types 2
IFPERT Set to 1 if topology contains residue perturbation information. 3
NBPER Number of perturbed bonds 3
NGPER Number of perturbed angles 3
NDPER Number of perturbed torsions 3
MBPER Number of bonds in which both atoms are being perturbed 3
MGPER Number of angles in which all 3 atoms are being perturbed 3
MDPER Number of torsions in which all 4 atoms are being perturbed 3
IFBOX Flag indicating whether a periodic box is present. Values can be 0
(no box), 1 (orthorhombic box) or 2 (truncated octahedron)
1

AMBER codes no longer support constraints in the topology file.
Modern AMBER force fields do not use a 10-12 potential
3
No AMBER codes support perturbed topologies anymore
2

4

NMXRS Number of atoms in the largest residue
IFCAP Set to 1 if a solvent CAP is being used
NUMEXTRA Number of extra points in the topology file
NCOPY Number of PIMD slices or number of beads

ATOM NAME
This section contains the atom name for every atom in the prmtop.
%FORMAT(20a4) There are NATOM 4-character strings in this section.

CHARGE
This section contains the charge
for every atom in the prmtop. Charges√
are multiplied by 18.2223 ( kele where kele is the electrostatic constant inkcal Å mol−1 q −2 , where q is the charge of an electron).
%FORMAT(5E16.8)
There are NATOM floating point numbers in this section.

ATOMIC NUMBER
This section contains the atomic number of every atom in the prmtop. Thissection was first introduced in AmberTools 12.
%FORMAT(10I8)
There are NATOM integers in this section.

MASSThis section contains the atomic mass of every atom in g mol−1 .
%FORMAT(5E16.8)
There are NATOM floating point numbers in this section.

ATOM TYPE INDEXThis section contains the Lennard-Jones atom type index. The LennardJones potential contains parameters for every pair of atoms in the system.

5

To minimize the memory requirements of storing NATOM × NATOM 4 LennardJones A-coefficients and B-coefficients, all atoms with the same σ and ε parameters are assigned to the same type (regardless of whether they have thesame AMBER ATOM TYPE). This significantly reduces the number of LJ coefficients which must be stored, but introduced the requirement for bookkeeping
sections of the topology file to keep track of what the LJ type index was foreach atom.
This section is used to compute a pointer into the NONBONDED PARM INDEX
section, which itself is a pointer into the LENNARD JONES ACOEF and LENNARD JONES BCOEF
sections (see below).
%FORMAT(10I8)
There are NATOM integers in this section.

NUMBER EXCLUDED ATOMSThis section contains the number of atoms that need to be excluded from thenon-bonded calculation loop for atom i because i is involved in a bond, angle,
or torsion with those atoms. Each atom in the prmtop has a list of excluded
atoms that is a subset of the list in EXCLUDED ATOMS LIST (see below). The
ith value in this section indicates how many elements of EXCLUDED ATOMS LIST
belong to atom i.
For instance, if the first two elements of this array is 5 and 3, then elements
1 to 5 in EXCLUDED ATOMS LIST are the exclusions for atom 1 and elements 6
to 8 in EXCLUDED ATOMS LIST are the exclusions for atom 2. Each exclusion
is listed only once in the topology file, and is given to the atom with thesmaller index. That is, if atoms 1 and 2 are bonded, then atom 2 is in the
exclusion list for atom 1, but atom 1 is not in the exclusion list for atom 2.
If an atom has no excluded atoms (either because it is a monoatomic ion or
all atoms it forms a bonded interaction with have a smaller index), then it
is given a value of 1 in this list which corresponds to an exclusion with (anon-existent) atom 0 in EXCLUDED ATOMS LIST.
The exclusion rules for extra points are more complicated. When determining exclusions, it is considered an ‘extension’ of the atom it is connected(bonded) to. Therefore, extra points are excluded not only from the atom
they are connected to, but also from every atom that its parent atom is
excluded from.
4

Only half this number would be required, since ai,j ≡ aj,i6

NOTE : The non-bonded interaction code in sander and pmemd currently(as of Amber 12) recalculates the exclusion lists for simulations of systems
with periodic boundary conditions, so this section is effectively ignored. The
GB code uses the exclusion list in the topology file.
%FORMAT(10I8)
There are NATOM integers in this section.

NONBONDED PARM INDEXThis section contains the pointers for each pair of LJ atom types into the
LENNARD JONES ACOEF and LENNARD JONES BCOEF arrays (see below). The
pointer for an atom pair in this array is calculated from the LJ atom typeindex of the two atoms (see ATOM TYPE INDEX above).
The index for two atoms i and j into the LENNARD JONES ACOEF andLENNARD JONES BCOEF arrays is calculated asindex = NONBONDED PARM INDEX [NTYPES × (ATOM TYPE INDEX(i) − 1) + ATOM TYPE INDEX(j)](1)
Note, each atom pair can interact with either the standard 12-6 LJ potential or via a 12-10 hydrogen bond potential. If index in Eq. 1 is negative,then it is an index into HBOND ACOEF and HBOND BCOEF instead (see below).
%FORMAT(10I8)
There are NTYPES × NTYPES integers in this section.

RESIDUE LABELThis section contains the residue name for every residue in the prmtop.
Residue names are limited to 4 letters, and might not be whitespace-delimited
if any residues have 4-letter names.
%FORMAT(20a4)
There are NRES 4-character strings in this section.

RESIDUE POINTER
This section lists the first atom in each residue.
%FORMAT(10i8)
There are NRES integers in this section.

7

BOND FORCE CONSTANT
Bond energies are calculated according to the equation
1
Ebond = k (~r − ~req )22(2)This section lists all of the bond force constants (k in Eq. 2) in units
kcal mol−1 Å−2 for each unique bond type. Each bond in BONDS INC HYDROGEN
and BONDS WITHOUT HYDROGEN (see below) contains an index into this array.
%FORMAT(5E16.8)
There are NUMBND floating point numbers in this section.

BOND EQUIL VALUEThis section lists all of the bond equilibrium distances (~req in Eq. 2) inunits of Åfor each unique bond type. This list is indexed the same way as
BOND FORCE CONSTANT.
%FORMAT(5E16.8)
There are NUMBND floating point numbers in this section.

ANGLE FORCE CONSTANT
Angle energies are calculated according to the equation
1
Eangle = kθ (θ − θeq )22(3)This section lists all of the angle force constants (kθ in Eq. 3) in units ofkcal mol−1 rad2 for each unique angle type. Each angle in ANGLES INC HYDROGEN
and ANGLES WITHOUT HYDROGEN contains an index into this (and the next) array.
%FORMAT(5E16.8)
There are NUMANG floating point numbers in this section.

ANGLE EQUIL VALUEThis section contains all of the angle equilibrium angles (θeq in Eq. 3) in radians. NOTE: the AMBER parameter files list equilibrium angles in degrees
and are converted to radians in tleap. This list is indexed the same way as
ANGLE FORCE CONSTANT.
8

%FORMAT(5E16.8)
There are NUMBND floating point numbers in this section.

DIHEDRAL FORCE CONSTANT
Torsion energies are calculated for each term according to the equation
Etorsion = ktor cos (nφ + ψ)

(4)This section lists the torsion force constants (ktor in Eq. 4) in units ofkcal mol−1 for each unique torsion type. Each torsion in DIHEDRALS INC HYDROGEN
and DIHEDRALS WITHOUT HYDROGEN has an index into this array.
Amber parameter files contain a dividing factor and barrier height foreach dihedral. The barrier height in the parameter files are divided by theprovided factor inside tleap and then discarded. As a result, the torsion
barriers in this section might not match those in the original parameter files.
%FORMAT(5E16.8)
There are NPTRA floating point numbers in this section.

DIHEDRAL PERIODICITYThis section lists the periodicity (n in Eq. 4) for each unique torsion type.
It is indexed the same way as DIHEDRAL FORCE CONSTANT. NOTE: only integers are read by tleap, although the AMBER codes support non-integer
periodicities.
%FORMAT(5E16.8)
There are NPTRA floating point numbers in this section.

DIHEDRAL PHASE
This section lists the phase shift (ψ in Eq. 4) for each unique torsion type inradians. It is indexed the same way as DIHEDRAL FORCE CONSTANT.
%FORMAT(5E16.8)
There are NPTRA floating point numbers in this section.

SCEE SCALE FACTOR
This section was introduced in Amber 11. In previous versions, this variable
was part of the input file and set a single scaling factor for every torsion.
9This section lists the factor by which 1-4 electrostatic interactions are
divided (i.e., the two atoms on either end of a torsion). For torsion types inwhich 1-4 non-bonded interactions are not calculated (e.g., improper torsions,multi-term torsions, and those involved in ring systems of 6 or fewer atoms),
a value of 0 is assigned by tleap. This section is indexed the same way as
DIHEDRAL FORCE CONSTANT.
%FORMAT(5E16.8)
There are NPTRA floating point numbers in this section.

SCNB SCALE FACTOR
This section was introduced in Amber 11. In previous versions, this variable
was part of the input file and set a single scaling factor for every torsion.
This section lists the factor by which 1-4 van der Waals interactions are
divided (i.e., the two atoms on either end of a torsion). This section is
analogous to SCEE SCALE FACTOR described above.
%FORMAT(5E16.8)
There are NPTRA floating point numbers in this section.

SOLTYThis section is currently unused, and while ‘future use’ is planned, this assertion has lain dormant for some time.
%FORMAT(5E16.8)
There are NATYP floating point numbers in this section.

LENNARD JONES ACOEF
LJ non-bonded interactions are calculated according to the equation
ELJ =

ai,j
bi,j
− 6
12
r
r

(5)

This section contains the LJ A-coefficients (ai,j in Eq. 5) for all pairs of
distinct LJ types (see sections ATOM TYPE INDEX and NONBONDED PARM INDEX
above).
%FORMAT(5E16.8)
There are [NTYPES × (NTYPES + 1)] /2 floating point numbers in this section.

10

LENNARD JONES BCOEF
This section contains the LJ B-coefficients (bi,j in Eq. 5) for all pairs of
distinct LJ types (see sections ATOM TYPE INDEX and NONBONDED PARM INDEX
above).
%FORMAT(5E16.8)
There are [NTYPES × (NTYPES + 1)] /2 floating point numbers in this section.

BONDS INC HYDROGEN
This section contains a list of every bond in the system in which at least
one atom is Hydrogen. Each bond is identified by 3 integers—the two
atoms involved in the bond and the index into the BOND FORCE CONSTANT
and BOND EQUIL VALUE. For run-time efficiency, the atom indexes are actually indexes into a coordinate array, so the actual atom index A is calculated
from the coordinate array index N by A = N/3 + 1. (N is the value in the
topology file)%FORMAT(10I8)
There are 3 × NBONH integers in this section.

BONDS WITHOUT HYDROGEN
This section contains a list of every bond in the system in which neither atom
is Hydrogen. It has the same structure as BONDS INC HYDROGEN describedabove.
%FORMAT(10I8)
There are 3 × NBONA integers in this section.

ANGLES INC HYDROGEN
This section contains a list of every angle in the system in which at least one
atom is Hydrogen. Each angle is identified by 4 integers—the three atoms
involved in the angle and the index into the ANGLE FORCE CONSTANT and
ANGLE EQUIL VALUE. For run-time efficiency, the atom indexes are actuallyindexes into a coordinate array, so the actual atom index A is calculated
from the coordinate array index N by A = N/3 + 1. (N is the value in the
topology file)%FORMAT(10I8)
11

There are 4 × NTHETH integers in this section.

ANGLES WITHOUT HYDROGEN
This section contains a list of every angle in the system in which no atom
is Hydrogen. It has the same structure as ANGLES INC HYDROGEN describedabove.
%FORMAT(10I8)
There are 4 × NTHETA integers in this section.

DIHEDRALS INC HYDROGEN
This section contains a list of every torsion in the system in which at least one
atom is Hydrogen. Each torsion is identified by 5 integers—the four atoms
involved in the torsion and the index into the DIHEDRAL FORCE CONSTANT,DIHEDRAL PERIODICITY, DIHEDRAL PHASE, SCEE SCALE FACTOR and SCNB SCALE FACTOR
arrays. For run-time efficiency, the atom indexes are actually indexes into
a coordinate array, so the actual atom index A is calculated from the coordinate array index N by A = N/3 + 1. (N is the value in the topology
file)
If the third atom is negative, then the 1-4 non-bonded interactions forthis torsion is not calculated. This is required to avoid double-counting these
non-bonded interactions in some ring systems and in multi-term torsions.
If the fourth atom is negative, then the torsion is improper.
NOTE: The first atom has an index of zero. Since 0 cannot be negative
and the 3rd and 4th atom indexes are tested for their sign to determine if
1-4 terms are calculated, the first atom in the topology file must be listed
as either the first or second atom in whatever torsions it is defined in. The
atom ordering in a torsion can be reversed to accommodate this requirement
if necessary.
%FORMAT(10I8)
There are 5 × NPHIH integers in this section.

DIHEDRALS WITHOUT HYDROGEN
This section contains a list of every torsion in the system in which no atom is
Hydrogen. It has the same structure as DIHEDRALS INC HYDROGEN describedabove.
12

%FORMAT(10I8)
There are 5 × NPHIA integers in this section.

EXCLUDED ATOMS LIST
This section contains a list for each atom of excluded partners in the nonbonded calculation routines. The subset of this list that belongs to each
atom is determined from the pointers in NUMBER EXCLUDED ATOMS—see that
section for more information.
NOTE: The periodic boundary code in sander and pmemd currently
recalculates this section of the topology file. The GB code, however, uses the
exclusion list defined in the topology file.
%FORMAT(10I8)
There are NNB integers in this section.

HBOND ACOEF
This section is analogous to the LENNARD JONES ACOEF array described above,
but refers to the A-coefficient in a 12-10 potential instead of the familiar 12-6
potential. This term has been dropped from most modern force fields.
%FORMAT(5E16.8)
There are NPHB floating point numbers in this section.

HBOND BCOEF
This section is analogous to the LENNARD JONES BCOEF array described above,
but refers to the B-coefficient in a 12-10 potential instead of the familiar 12-6
potential. This term has been dropped from most modern force fields.
%FORMAT(5E16.8)
There are NPHB floating point numbers in this section.

HBCUT
This section used to be used for a cutoff parameter in the 12-10 potential,
but is no longer used for anything.
%FORMAT(5E16.8)
There are NPHB floating point numbers in this section.

13

AMBER ATOM TYPE
This section contains the atom type name for every atom in the prmtop.
%FORMAT(20a4)
There are NATOM 4-character strings in this section.

TREE CHAIN CLASSIFICATIONThis section contains information about the tree structure (borrowing concepts from graph theory) of each atom. Each atom can have one of thefollowing character indicators:
M This atom is part of the “main chain”
S This atom is part of the “sidechain”
E This atom is a chain-terminating atom (i.e., an “end” atom)
3 The structure branches into 3 chains at this point
BLA If none of the above are true
%FORMAT(20a4)
There are NATOM 4-character strings in this section.

JOIN ARRAYThis section is no longer used and is currently just filled with zeros.
%FORMAT(10I8)
There are NATOM integers in this section.

IROTAT
This section is not used and is currently just filled with zeros.
%FORMAT(10I8)
There are NATOM integers in this section.

14

SOLVENT POINTERS
This section is only present if IFBOX is greater than 0 (i.e., if the system was set up for use with periodic boundary conditions). There are 3
integers present in this section—the final residue that is part of the solute (IPTRES), the total number of ‘molecules’ (NSPM), and the first solvent‘molecule’ (NSPSOL).
A ‘molecule’ is defined as a closed graph—that is, there is a pathway fromevery atom in a molecule to every other atom in the molecule by traversing
bonds, and there are no pathways to ‘other’ molecules.
%FLAG SOLVENT_POINTERS%FORMAT(3I8)IPTRESNSPMNSPSOLATOMS PER MOLECULE
This section is only present if IFBOX is greater than 0 (i.e., if the system
was set up for use with periodic boundary conditions). This section lists how
many atoms are present in each ‘molecule’ as defined in the SOLVENT POINTERS
section above.
%FORMAT(10I8)
There are NSPM integers in this section (see the SOLVENT POINTERS section
above).

BOX DIMENSIONSThis section is only present if IFBOX is greater than 0 (i.e., if the system was
set up for use with periodic boundary conditions). This section lists the box
angle (OLDBETA) and dimensions (BOX(1) × BOX(2) × BOX(3)). The values inthis section are deprecated now since newer and more accurate information
about the box size and shape is stored in the coordinate file. Since constant pressure simulations can change the box dimensions, the values in thecoordinate file should be trusted over those in the topology file.
%FLAG BOX_DIMENSIONS%FORMAT(5E16.8)
OLDBETA
BOX(1)

BOX(2)

15

BOX(3)

CAP INFOThis section is present only if IFCAP is not 0. If present, it contains a single
integer which is the last atom before the water cap begins (NATCAP)%FORMAT(10I8)

CAP INFO2
This section is present only if IFCAP is not 0. If present, it contains four
numbers—the distance from the center of the cap to outside the cap (CUTCAP),
and the Cartesian coordinates of the cap center.
%FLAG CAP_INFO2%FORMAT(5E16.8)
CUTCAP
XCAP

YCAP

ZCAP

RADIUS SETThis section contains a one-line string (up to 80 characters) describing the
intrinsic implicit solvent radii set that are defined in the topology file. The
available radii sets with their 1-line descriptions are:bondi Bondi radii (bondi)
amber6 amber6 modified Bondi radii (amber6)
mbondi modified Bondi radii (mbondi)
mbondi2 H(N)-modified Bondi radii (mbondi2)
mbondi3 ArgH and AspGlu0 modified Bondi2 radii (mbondi3)%FORMAT(1a80)
There is a single line description in this section.

RADII
This section contains the intrinsic radii of every atom used for implicit solvent
calculations (typically Generalized Born).
%FORMAT(5E16.8)
There are NATOM floating point numbers in this section.
16

IPOL
This section was introduced in Amber 12. In previous versions of Amber,this was a variable in the input file.
This section contains a single integer that is 0 for fixed-charge force fields
and 1 for force fields that contain polarization.

POLARIZABILITY
This section is only present if IPOL is not 0. It contains the atomic polarizabilities for every atom in the prmtop.
%FORMAT(5E16.8)
There are NATOM floating point numbers in this section.
%FORMAT(1I8)

3

Deprecated Sections

All of the sections of the topology file listed here are only present if IFPERT
is 1. However, no modern programs support such prmtops so these sections
are rarely (if ever) used. They are included in Table 1 for completeness, only.
More info can be found online at http://ambermd.org/formats.html

4

CHAMBER Topologies

Here we will describe the general format of topology files generated by thechamber program. The chamber program was developed to translate CHARMM
topology (PSF) files into Amber topology files for use with the AMBER program suite.
Due to differences in the CHARMM force field (e.g., the extra CMAP
and Urey-Bradley terms and the different way that improper dihedrals aretreated), chamber topologies contain more sections than Amber topologies.
Furthermore, to ensure rigorous reproduction of CHARMM energies inside
the AMBER program suites, some of the sections that are common between
AMBER and CHARMM topology files have a different format for their data
to support a different level of input data precision.
Due to the differences in the chamber topology files, a mechanism todifferentiate between chamber topologies and AMBER topologies was intro17

Table 1: List of all of the perturbed topology file sections.
FLAG name%FORMAT of values
Description
PERT BOND ATOMS
10I8
2 × NBPER
perturbed bond list
PERT BOND PARAMS
10I8
2 × NBPER perturbed bond pointers
PERT ANGLE ATOMS
10I8
3 × NGPER
perturbed angle list
PERT ANGLE PARAMS
10I8
2 × NGPER perturbed angle pointers
PERT DIHEDRAL ATOMS
10I8
4 × NDPER
perturbed torsion list
PERT DIHEDRAL PARAMS
10I8
2 × NDPER perturbed torsion pointers
PERT RESIDUE NAME
20a4
NRES
end state residue names
PERT ATOM NAME
20a4
NATOM
end state atom names
PERT ATOM SYMBOL
20a4
NATOM
end state atom types
ALMPER
5E16.8
NATOM
Unused
IAPER
10I8
NATOM
Is Atom PERturbed?
PERT ATOM TYPE INDEX
10I8
NATOM
Perturbed LJ TypePERT CHARGE
5E16.8NATOM
Perturbed charge
duced. If the topology file has a %FLAG TITLE then it is an AMBER topology.
If it has a %FLAG CTITLE instead, then it is a chamber topology.
The following sections of the chamber topology are exacly the same as
those from the AMBER topology files:• POINTERS• ATOM NAME
• MASS• ATOM TYPE INDEX• NUMBER EXCLUDED ATOMS• EXCLUDED ATOMS LIST
• NONBONDED PARM INDEX• RESIDUE LABEL• BOND FORCE CONSTANT• BOND EQUIL VALUE
18

• ANGLE FORCE CONSTANT• DIHEDRAL FORCE CONSTANT• DIHEDRAL PERIODICITY• DIHEDRAL PHASE• SCEE SCALE FACTOR• SCNB SCALE FACTOR• SOLTY• BONDS INC HYDROGEN• BONDS WITHOUT HYDROGEN• ANGLES INC HYDROGEN• ANGLES WITHOUT HYDROGEN• DIHEDRALS INC HYDROGEN• DIHEDRALS WITHOUT HYDROGEN• HBOND ACOEF• HBOND BCOEF• HBCUT• AMBER ATOM TYPE
• TREE CHAIN CLASSIFICATION 5• JOIN ARRAY• IROTAT• RADIUS SET• RADII
5

Not really supported. Every entry is BLA

19

Table 2: List of flags that are common between Amber and chamber topology
files, but have different FORMAT identifiers.
FLAG name
AMBER Format chamber Format
CHARGE
5E16.83E24.16
ANGLE EQUIL VALUE
5E16.83E25.17LENNARD JONES ACOEF
5E16.83E24.16LENNARD JONES BCOEF
5E16.83E24.16• SCREEN• SOLVENT POINTERS• ATOMS PER MOLECULEIn Table 2 is a list of sections that have the same name and the samedata, but with a different Fortran format identifier.

FORCE FIELD TYPE
This section is a description of the CHARMM force field that is parametrized
in the topology file. It is a single line (it can be read as a single string oflength 80 characters). It does not affect any numerical results.
%FORMAT(i2,a78)

CHARMM UREY BRADLEY COUNTThis section contains the number of Urey-Bradley parameters printed in the
topology file. It contains two integers, the total number of Urey-Bradleyterms (NUB) and the number of unique Urey-Bradley types (NUBTYPES).
%FLAG CHARMM_UREY_BRADLEY_COUNT%FORMAT(2i8)NUB
NUBTYPESCHARMM UREY BRADLEYThis section contains all of the Urey-Bradley terms. It is formatted exactly
like BONDS INC HYDROGEN and BONDS WITHOUT HYDROGEN.
20

%FORMAT(10i8)
There are 3 × NUB integers in this section.

CHARMM UREY BRADLEY FORCE CONSTANT
This section contains all of the force constants for each unique Urey-Bradleyterm in kcal mol−1 Å2 . It is formatted exactly the same as BOND FORCE CONSTANT.
%FORMAT(5E16.8)
There are NUBTYPES floating point numbers in this section.

CHARMM UREY BRADLEY EQUIL VALUEThis section contains all of the equilibrium distances for each unique UreyBradley term in Å. It is formatted exactly the same as BOND EQUIL VALUE.
%FORMAT(5E16.8)
There are NUBTYPES floating point numbers in this section.

CHARMM NUM IMPROPERS
This section contains the number of improper torsions in the topology file.
It contains one integer, the total number of improper torsions.
%FLAG CHARMM_NUM_IMPROPERS%FORMAT(i8)
NIMPHICHARMM IMPROPERS
This section contains all of the improper torsion terms. It is formatted exactly
like DIHEDRALS INC HYDROGEN and DIHEDRALS WITHOUT HYDROGEN.
%FORMAT(10i8)
There are 5 × NIMPHI integers in this section.

CHARMM NUM IMPROPER TYPESThis section contains the number of unique improper torsion types in the
topology file. It contains one integer, the total number of improper torsions
types.
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%FLAG CHARMM_NUM_IMPROPERS%FORMAT(i8)NIMPRTYPESCHARMM IMPROPER FORCE CONSTANT
This section contains the force constant for each unique improper torsion
type. It is formatted exactly like DIHEDRAL FORCE CONSTANT.
%FORMAT(5E16.8)
There are NIMPRTYPES integers in this section.

CHARMM IMPROPER PHASE
This section contains the phase shift for each unique improper torsion type.
It is formatted exactly like DIHEDRAL PHASE%FORMAT(5E16.8)
There are NIMPRTYPES integers in this section.

LENNARD JONES 14 ACOEF
Instead of scaling the 1-4 van der Waals interactions, the CHARMM force
field actually assigns entirely different LJ parameters to each atom type.
Therefore, chamber topologies have two extra sections that correspond to
the set of LJ parameters for 1-4 interactions. The way these tables are set
up is identical to the way LENNARD JONES ACOEF and LENNARD JONES BCOEF
are set up in chamber topologies.
%FORMAT(5E16.8)
There are [NTYPES × (NTYPES + 1)] /2 floating point numbers in this section.

LENNARD JONES BCOEF

This section contains the LJ B-coefficients for 1-4 interactions. See LENNARD JONES 14 ACOE
above.
%FORMAT(5E16.8)
There are [NTYPES × (NTYPES + 1)] /2 floating point numbers in this section.

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CHARMM CMAP COUNTThis section contains two integers—the number of total correction map (CMAP
terms and the number of unique CMAP ‘types.’%FLAG CHARMM_CMAP_COUNT%FORMAT(2i8)
CMAP_TERM_COUNT CMAP_TYPE_COUNTCHARM CMAP RESOLUTION
This section stores the resolution (i.e., number of steps along each phi/psi
CMAP axis) for each CMAP grid.
%FORMAT(20I4)
There are CMAP TERM COUNT integers in this section.

CHARMM CMAP PARAMETER
There are CMAP TYPE COUNT of these sections, where is replaced by a 2-digit
integer beginning from 01. It is a 2-dimensional Fortran array whose 1-D
sequence is stored in column-major order.
%FORMAT(8(F9.5))
There are CHARMM CMAP RESOLUTION(i)2 floating point numbers in this section, where i is the in the FLAG title.

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