- 1 - TITLE
FORMAT(20A4)
TITLE Title for identification.
------------------------------------------------------------------------
- 2 - NTX , NTXO , NRC , NRCX , NGRPX , KFORM
FORMAT(5I)
NTX Format of coordinates.
= \1 Formatted (inpcrd, unit 21)
= 2 \Unformatted (inpcrd, unit 21)
NTXO Read but not used
NRC Option to read position constraints.
= 0 no constraints
= 1 constrained minimization
The atoms to be constrained are read as groups with
different harmonic force constants for each group.
Consult the section on GROUP in the Appendices for
group specification format.
When using positional constraints, the constrained
groups are given first in the group input followed
by the groups for energy analysis.
NRCX Format of constraint coordinates. The constraint
coordinate file has the same organization as the structure
coordinates.
= 0 Formatted (refc, unit 24)
= 1 Binary (refc, Unit 24)
NGRPX Maximum number of groups that the structure can be
divided into for analysis. Note that if any atoms are not
explicitly included in a group, they will automatically
be put in an additional group.
= 0 Default = 70
= N Structure may be partitioned into N different groups
KFORM The Flag for the type of Topology File
= 0 Binary (prmtop, unit 20)
= 1 Formatted (prmtop, unit 20)
------------------------------------------------------------------------
- 3 - NTB , BOX(1) , BOX(2) , BOX(3) , BETA
FORMAT(I,4F)
NTB Flag for periodic boundary conditions.
( not yet operational )
=-n Periodicity is applied. Box is truncated octahedron
(BETA = 90)
= 0 No periodicity is applied
=+n Periodicity is applied. Box is rectangular or monoclinic
depending on the value of BETA
BOX(1..3) Lengths of the edges of the periodic box
BETA Angle between the X- and Z- axes of the box in degrees.
the Y- axis is assumed to be orthogonal to the other
axes. ( 0 < BETA < 180 )
------------------------------------------------------------------------
- 4 - NTF , NTID , NTN , NTNB , NSNB , IDIEL
FORMAT(6I)
NTF Flag for force evaluation.
= 1 complete interaction is calculated
= 2 bond interactions involving H-atoms omitted
= 3 all the bond interactions are omitted
= 4 angle involving H-atoms and all bonds are omitted
= 5 all bond and angle interactions are omitted
= 6 dihedrals involving H-atoms and all bonds and all angle
interactions are omitted
= 7 all bond, angle and dihedral interactions are omitted
= 8 all bond, angle, dihedral and non-bonded interactions
are omitted
NTID Flag for improper dihedral contribution (read but not used).
NTN Read but not used
Note: non-bonded interactions are now always calculated
using a residue based cutoff. The nb pairs are stored as
residue pairs. This uses substantially less memory than
the atom pairlist in the minimizer.
NTNB Read but not used
NSNB Read but not used
IDIEL Flag for the type of dielectric function to be used in
calculating the electrostatic energy.
= 0 distance dependent dielectric function
= 1 constant dielectric function
------------------------------------------------------------------------
- 5 - CUT , SCNB , SCEE , DIELC
FORMAT(4F)
CUT The cutoff distance for the non-bonded pairs.
SCNB 1-4 vdw interactions are divided by SCNB.
if SCNB .le. 0.0 then SCNB = 2.0
SCEE 1-4 electrostatic interactions are divided by SCEE
if SCEE .le. 0.0 then SCEE = 2.0
DIELC Dielectric multiplicative constant for the electrostatic
interactions. If DIELC .le. 0.0 then DIELC = 1.0. DIELC
and IDIEL are coupled. For example to obtain a dielectric
'constant' of 4rij set DIELC=4 and IDIEL=0.
------------------------------------------------------------------------
- 6 - Printout of energies beyond specified values. You
must use the ENERGY keyword to obtain output.
IMAX , EMAX(I) , I = 1, 9
FORMAT(I,9F)
IMAX Flag for printing the energy contributions.
= 0 no printing
= 1 energy contributions will be printed
EMAX(1) All the bonds whose energy contribution is greater
than EMAX(1) will be printed.
EMAX(2) All the angles whose energy contribution is greater
than EMAX(2) will be printed.
EMAX(3) All the dihedrals whose energy contribution is
greater than EMAX(3) will be printed.
EMAX(4) All the 1-4 vdw whose energy contribution is greater
than EMAX(4) will be printed.
EMAX(5) All the 1-4 eel whose energy contribution is greater
than EMAX(5) will be printed.
EMAX(6) All the vdw nb pairs whose energy contribution is
greater than EMAX(6) will be printed.
EMAX(7) All the eel nb-pairs with absolute value of energy
greater than EMAX(7) will be printed.
EMAX(8) All the H-bond pairs whose energy contribution is
greater than EMAX(8) will be printed.
EMAX(9) All the constrained atoms whose energy contribution
is greater than EMAX(9) will be printed.
------------------------------------------------------------------------
INPUT FOR PROGRAM OPTIONS
------------------------------------------------------------------------
- 7 - The control for doing the desired options. When a
control word is encountered the program reads the
needed input for that option, then looks for the
next control word. This process continues until
the word STOP is read.
IOPT
FORMAT(A)
IOPT The control word for the option.
'ENERGY' Energy decomposition into groups
'PUCKER' Sugar puckering analysis
'HELIX' DNA/RNA helical parameters analysis
'RMS' RMS fit between two structures of identical topology
'VOLUME' Compaction analysis
'HBOND' Hydrogen bond analysis
'GAUSS' Punch the Z-matrix for GAUSSIAN 80 (to unit 7)
Note: be careful to check the connectivity especially
for the first dihedral angle.
'PDB' Write the coordinates in pdb format (to unit 33)
'TELL' Output of internal coordinates for the entire system.
(TELL in the edit module gives a more complete description)
'TORSION' Output of torsion angles only for specified torsions.
(avoids the voluminous output of TELL)
'STOP' Control to terminate the run
------------------------------------------------------------------------
and TELL require no further input. TheENERGY
following section describes additional input for those
options that require it.
------------------------------------------------------------------------
------------------------------------------------------------------------
Parts of the molecule for which interaction energies
are to be calculated are entered in GROUP format. See
the section on GROUP in the Appendices for details.
Groups are read sequentially in any order. Each group
is terminated by an "END" card.
The ENERGY option is terminated by another "END" card.
------------------------------------------------------------------------
------------------------------------------------------------------------
PUCKER 1: NMIS
FORMAT(I)
NMIS The number of unique non-standard or modified bases in
the DNA molecule. "Standard" means DNA from the Amber
United Atom database. Anything else (including residues
from the Amber all-atom database) is considered nonstandard.
Important: If any of the standard names ADE, CYT, GUA,
THY, or URA are used with other than standard united atom
topology, make NMIS NEGATIVE. If any of the standard
names are redefined, they all must be.
------------------------------------------------------------------------
PUCKER 2: NAMBAS(I), NRA(I), (KRA(J,I), J = 1, 20), I = 1, abs(NMIS)
***** THIS CARD READ ONLY IF abs(NMIS) .GT. 0 *****
FORMAT(A,21I)
NAMBAS Residue name of the non-standard base.
NRA The number of sugar atoms in base (I) to be used for
the puckering analysis.
KRA The atom numbers to be used, relative to the first
atom in the base residue.
------------------------------------------------------------------------
------------------------------------------------------------------------
HELIX 1: IBPGEN , NMIS , NBASP , NMISF , NFOSP
FORMAT(5I)
IBPGEN Flag for the base pair generation.
= 0 DNA is standard. This means that the DNA
bases are from the AMBER united atom data base.
The base pairing will be generated automatically
= 1 Non-standard DNA. The base pairing must be read
explicitly from the following four parameters and
lines below.
NMIS The number of types of non-standard or modified
bases in the DNA molecule.
Important: If any of the standard names ADE, CYT, GUA,
THY, or URA are used with other than standard united atom
topology, make NMIS NEGATIVE. If any of the standard
names are redefined, they all must be.
NBASP The total number of base pairs in the molecule
if any nonstandard residues are present.
NMISF The number of types of non-standard or modified
phosphate residues in the DNA molecule.
NFOSP The total number of phosphate pairs in the DNA
molecule if any non-standard residues (either base
or phosphate) are present.
------------------------------------------------------------------------
HELIX 2: NAMBAS(I), NRA(I), (KRA(J,I), J = 1, 20), I = 1, abs(NMIS)
***** THIS CARD READ ONLY IF abs(NMIS) .GT. 0 *****
FORMAT(A,21I)
NAMBAS Residue name of the non-standard base.
NRA The number of atoms in base (I) to be used for
calculating the mean plane of the base.
KRA The atom numbers to be used, relative to the first
atom in the base residue.
------------------------------------------------------------------------
HELIX 3: NAMF(I) , NFRA(I) , KFRA(I) , I = 1, NMISF
***** THIS CARD READ ONLY IF NMISF .GT. 0 *****
FORMAT(A,2I)
NAMF Residue name of the non-standard phosphate.
NFRA The number of atoms to be considered for finding
the helical twist. (it is always 1 since the twist
is taken as the angle between two phosphate pairs)
KFRA The relative position of the P atoms in the residue.
------------------------------------------------------------------------
HELIX 4: KBASA(I) , KBASB(I) , I = 1, NBASP
***** THIS CARD READ ONLY IF NBASP .GT. 0 *****
FORMAT(2I)
Residue numbering for DNA analysis is sequential from
the 5' end of the first chain to the 3' end, continuing
from 5' end of the second chain and ending at the 3'
end of the second chain. All bases must be paired in
this way if NBASP = 0.
KBASA The residue number of the first base in a pair.
KBASB The residue number of the second base in a pair.
------------------------------------------------------------------------
HELIX 5: KFA(I) , KFB(I) , I = 1, NFOSP
***** THIS CARD READ ONLY IF NFOSP .GT. 0 *****
FORMAT(2I)
See note on residue numbering above.
KFA The residue number of the first phosphate in a pair.
KFB The residue number of the second phosphate in a pair.
------------------------------------------------------------------------
------------------------------------------------------------------------
RMS 1: NTXP , FACT , JGROUP, IPDB , IMOVE
FORMAT(I,F,3I)
NTXP Format of the reference set of conformer coordinates to be
read for the rms fit.
= 0 Formatted input
= 1 Unformatted input (same as the initial binary coordinates)
FACT The threshold for printing the deviation of individual
atoms. The default is 0.02.
JGROUP
= 0 Compare all atoms for rms fit
= 1 Compare only those atoms read in GROUP format from unit 5
IPDB
= 0 No output of the rotated coordinate sets.
= 1 Output the rotated coordinate sets.
IMOVE
= 0 The molecules are NOT rotated to the principal axes
= 1 The molecules ARE oriented along the principal axes
NOTE: principal axis transformation is not required
for RMS fitting.
------------------------------------------------------------------------
------------------------------------------------------------------------
VOLUME 1: NTXP
FORMAT(I)
NTXP Flag for type of format of the reference coordinates
of the conformer whose compaction is to be calculated.
= 0 Formatted input
= 1 Binary input (same as the initial binary coordinates).
------------------------------------------------------------------------
------------------------------------------------------------------------
HBOND 1: CUTHB
FORMAT(F)
CUTHB The cut off distance for chosing the hydrogen bond
pairs. The default is 4.0 Angstroms
------------------------------------------------------------------------
------------------------------------------------------------------------
TORSION 1: Four atom names, free format. All torsion angles between
atoms with these names will be reported. This card may
be repeated.
------------------------------------------------------------------------
TORSION 2: 'END' to end TORSION input.
------------------------------------------------------------------------
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