X-PLOR Topology Files

An example X-PLOR topology file for protein residues shown below illustrates how the topology information is defined there:

REMARKS TOPH19.PRO ( protein topology )
REMARKS Charges and atom order modified for neutral GROUPs.
REMARKS Histidine charges set to Del Bene and Cohen sto-3g calculations.
REMARKS Amide charges set to match the experimental dipole moment.
REMARKS Default for HIStidines is the doubly protonated state 

set echo=false end
!! for use with PARAM19 parameters ( no special hydrogen bonding potential )
!! donor and acceptor terms just for analysis

AUTOGENERATE  ANGLES=TRUE  END
{*===========================*}

{* protein default masses *}
MASS   H      1.00800! hydrogen which can h-bond to neutral atom
MASS   HC     1.00800!    ="=     ="=     ="=    to charged atom
MASS   C     12.01100! carbonyl carbon
MASS   CH1E  13.01900! extended atom carbon with one hydrogen
...
MASS   S     32.06000! sulphur
MASS   SH1E  33.06800! extended atom sulfur with one hydrogen

!some empirical rules for the following topologies:
! 1. angles are taken between all permutations of atoms bonded to
!    a particular atom. Exception: 2 angles linking the THR double ring
! 2. each bond with non-terminal atoms creates one dihedral. Exception:
!    ring bonds in aromatic side chains (but not PRO).
! 3. each planar atom vertex creates one improper-planar term
!    execption: ARG head groups.
! 4. each 1-extended-H carbon atom creates one improper-tetrahedral term
!    (for chirality)
! 5. Each bond in an aromatic ring creates one improper-torsion term
!    (exception: PRO)
! 6. LYS head groups and methyl head groups create one dihedral for 
!    each hydrogen
! 7. all 1:2 and 1:3 nonbonded interactions are assumed to be excluded
! 8. All 1:4,1:5,... non-bonded interactions in aromatic rings 
!    (or double rings) are explicitly excluded
! ---------------------------------------------------------------------

RESIdue ALA
 GROUp
  ATOM N    TYPE=NH1   CHARge=-0.35   END
  ATOM H    TYPE=H     CHARge= 0.25   END
  ATOM CA   TYPE=CH1E  CHARge= 0.10   END
 GROUp
  ATOM CB   TYPE=CH3E  CHARge= 0.00   END
 GROUp
  ATOM C    TYPE=C     CHARge= 0.55   END
  ATOM O    TYPE=O     CHARge=-0.55   END
 BOND N    CA
 BOND CA   C
 BOND C    O
 BOND N    H
 BOND CA   CB
 IMPRoper  CA     N    C  CB  !tetrahedral CA
 DONOr H    N
 ACCEptor O C
 IC   N    C    *CA  CB     0.0000    0.00  120.00    0.00   0.0000
END {ALA}

!------------------------------------------------------------------
RESIdue ARG
 GROUp
...
!------------------------------------------------------------------
set echo=true end