ITITL : title
FORMAT(12i6) 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
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 : currently not used
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
FORMAT(20a4) (IGRAPH(i), i=1,NATOM)
IGRAPH : the user atoms names
FORMAT(5E16.8) (CHRG(i), i=1,NATOM)
CHRG : the atom charges. (Divide by 18.2223 to convert to units of
electron charge)
FORMAT(5E16.8) (AMASS(i), i=1,NATOM)
AMASS : the atom masses
FORMAT(12I6) (IAC(i), i=1,NATOM)
IAC : index for the atom types involved in Lennard Jones (6-12)
interactions. See ICO below.
FORMAT(12I6) (NUMEX(i), i=1,NATOM)
NUMEX : total number of excluded atoms for atom "i". See
NATEX below.
FORMAT(12I6) (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).
FORMAT(20A4) (LABRES(i), i=1,NRES)
LABRES : the residue labels
FORMAT(12I6) (IPRES(i), i=1,NRES)
IPRES : the atom number of the first atom in residue "i"
FORMAT(5E16.8) (RK(i), i=1,NUMBND)
RK : force constant for the bonds of each type, kcal/mol
FORMAT(5E16.8) (REQ(i), i=1,NUMBND)
REQ : equilibrium bond length for the bonds of each type, angstroms
FORMAT(5E16.8) (TK(i), i=1,NUMANG)
TK : force constant for the angles of each type, kcal/mol A**2
FORMAT(5E16.8) (TEQ(i), i=1,NUMANG)
TEQ : the equilibrium angle for the angles of each type, degrees
FORMAT(5E16.8) (PK(i), i=1,NPTRA)
PK : force constant for the dihedrals of each type, kcal/mol
FORMAT(5E16.8) (PN(i), i=1,NPTRA)
PN : periodicity of the dihedral of a given type
FORMAT(5E16.8) (PHASE(i), i=1,NPTRA)
PHASE : phase of the dihedral of a given type
FORMAT(5E16.8) (SOLTY(i), i=1,NATYP)
SOLTY : currently unused (reserved for future use)
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))).
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 arrays which follow that describe bonds,
angles, and dihedrals are obfuscated by the following formula (for
runtime speed in indexing arrays). The true atom number equals the
absolute value of the number divided by three, plus one. In the case
of the dihedrals, if the third atom is negative, this implies an
improper torsion and if the fourth atom is negative, this implies that
end group interactions are to be ignored. End group interactions are
ignored, for example, in dihedrals of various ring systems (to prevent
double counting) and in multiterm dihedrals.
FORMAT(12I6) (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
FORMAT(12I6) (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
FORMAT(12I6) (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)
FORMAT(12I6) (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)
FORMAT(12I6) (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, and PHASE for
dihedral IPH(i)-JPH(i)-KPH(i)-LPH(i)
FORMAT(12I6) (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, and PHASE 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.
FORMAT(12I6) (NATEX(i), i=1,NEXT)
NATEX : 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 NATEX(IEXCL) to NATEX(IEXCL+NUMEX(i)).
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
-(NTYPES*(IAC(i)-1)+IAC(j)).
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.
FORMAT(5E16.8) (HBCUT(i), i=1,NPHB)
HBCUT : no longer in use
FORMAT(20A4) (ISYMBL(i), i=1,NATOM)
ISYMBL : the AMBER atom types for each atom
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
FORMAT(12I6) (JOIN(i), i=1,NATOM)
JOIN : tree joining information, potentially used in ancient
analysis programs. Currently unused in sander or gibbs.
FORMAT(12I6) (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.
===============================================================================
**** The following are only present if IFBOX .gt. 0 ****
FORMAT(12I6) IPTRES, NSPN, 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"
FORMAT(12I6) (NSP(i), i=1,NSPM)
NSP : the total number of atoms in each molecule,
necessary to correctly determine the pressure scaling
FORMAT(5E16.8) BETA, BOX(1), BOX(2), BOX(3)
BETA : periodic box, angle between the XY and YZ planes in
degrees.
BOX : the periodic box lengths in the X, Y, and Z directions
===============================================================================
**** The following are only present if IFCAP .gt. 0 ****
FORMAT(12I6) NATCAP
NATCAP : last atom before the start of the cap of waters
placed by edit
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 are 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.
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)
IPTER : 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 ***
FORMAT(5E18.8) (ATPOL(i), i=1,NATOM)
ATPOL : atomic polarizabilities
**** The following is only present if IPOL .eq. 1 .and. IFPERT .eq. 1 ****
FORMAT(5E18.8) (ATPOL1(i), i=1,NATOM)
ATPOL1 : atomic polarizabilities at lambda = 1 (above is at lambda = 0)