!
! Compute the binding free energy of Neuraminidase-inhibitor system
!
! Files: desol_110.inp - this file
!        2qwe_prot.qcd - coords for protein oppa with charges and radii
!        GNA.qcd       - coords for ligand peptide with charges and radii
!

!
! read in the coords., charges, and radii in CHARMM qcard
! format
!
read mol 1 file "2qwe_prot.qcd" qcard end ! protein neuraminidase N9 mutant
read mol 2 file "GNA.qcd" qcard end       ! inhibitor GNA , Relenza

!step 1
! Regular Runs:
!               compute the potential on a coarse grid for
!               molecule 1
!

elec calc mol 1
 pdie   2.00                          ! internal dielectric=2
 sdie  78.00                          ! solvent  dielectric=78
 temp 298.00                          ! temperature in K
 ions 150.00                          ! ionic strength
 rion   1.5                           ! ionic radius
 nmap   1.4                           ! use probe-accessible surface
 nsph 400                             ! use 400 sphere points for surface cal.  
 bcfl   2                             ! boundary condition - each atom
                                      ! is a Debye-Huckel sphere
 efld    .00                          ! external electric field
 grid    .80                          ! grid spacing
 dime  110  110  110                  ! grid dimension (size of oppa is 60A)
 mcenter 2                            ! center on molecule 2
 maxit 400                            ! maximum # of iteration for FDPBE
end

print elec phizero mol1 end           ! zero out the phisite accumulator
print elec phisave mol1 end           ! compute and store phi at atoms on grid

!  
!               compute the potential on a fine grid
!               molecule 1 using the coarse grid to set the
!               boundary potentials for this grid.
!

elec calc mol 1
 pdie   2.00                          ! internal dielectric=2
 sdie  78.00                          ! solvent  dielectric=78
 temp 298.00                          ! temperature in K
 ions 150.00                          ! ionic strength
 rion   1.5                           ! ionic radius
 nmap   1.4                           ! use probe-accessible surface
 nsph 400                             ! use 400 sphere points for surface cal.  
 bcfl   4                             ! focusing - use the coarse grid to
                                      ! set the boundary potential of this
                                      ! focused grid.
 efld    .00                          ! external electric field
 grid   0.225                         ! spacing for focused grid
 dime  110  110  110                    ! grid dimension
 mcenter 2                            ! center on molecule 2
 maxit 400                            ! maximum # of iteration for FDPBE
end

print elec phisave mol1 end
!print elec phiwrite mol1 end          ! write the phisite potentials to the output
print elec phinrg mol1 end            ! compute and save to a user variable the
                                      ! phi energy
assign e1 = $phinrg end               ! assign the phi energy to a local variable 
                                      ! for later use

!
! step 3
! Regular Runs:
!               coarse grid
!               molecule 2
!
elec calc mol 2
 pdie   2.00                          ! internal dielectric=2
 sdie  78.00                          ! solvent  dielectric=78
 temp 298.00                          ! temperature in K
 ions 150.00                          ! ionic strength
 rion   1.5                           ! ionic radius
 nmap   1.4                           ! use probe-accessible surface
 nsph 400                             ! use 400 sphere points for surface cal.  
 bcfl   2                             ! boundary condition - each atom
                                      ! is a Debye-Huckel sphere
 efld    .00                          ! external electric field
 grid    .80                          ! grid spacing
 dime  110  110  110                  ! grid dimension
 mcenter  2                           ! center the grid on the molecule
 maxit 400                            ! maximum # of iteration for FDPBE
end

print elec phizero mol2 end           ! zero out the phisite accumulator
print elec phisave mol2 end           ! compute and store phi at atoms on grid

!  
!               fine grid
!               molecule 2
!

elec calc mol 2
 pdie   2.00                          ! internal dielectric=2
 sdie  78.00                          ! solvent  dielectric=78
 temp 298.00                          ! temperature in K
 ions 150.00                          ! ionic strength
 rion   1.5                           ! ionic radius
 nmap   1.4                           ! use probe-accessible surface
 nsph 400                             ! use 400 sphere points for surface cal.  
 bcfl   4                             ! focusing - use the coarse grid to
                                      ! set the boundary potential of this
                                      ! focused grid.
 efld    .00                          ! external electric field
 grid   0.225                         ! spacing for focused grid
 dime  110  110  110                  ! grid dimension
 mcenter 2
 maxit 400                            ! maximum # of iteration for FDPBE
end

print elec phisave mol2 end
print elec phinrg mol2 end  
assign e3 = $phinrg end
!
! step 2
! run on complex
! zero ligand charge
!               coarse grid
!               
!
edit mol 2 charge 0.0 end
print apar mol2 end
!
elec calc all 
 pdie   2.00                          ! internal dielectric=2
 sdie  78.00                          ! solvent  dielectric=78
 temp 298.00                          ! temperature in K
 ions 150.00                          ! ionic strength
 rion   1.5                           ! ionic radius
 nmap   1.4                           ! use probe-accessible surface
 nsph 400                             ! use 400 sphere points for surface cal.  
 bcfl   2                             ! boundary condition - each atom
                                      ! is a Debye-Huckel sphere
 efld    .00                          ! external electric field
 grid    .80                          ! grid spacing
 dime  110  110  110                    ! grid dimension
 mcenter 2                            ! center the grid on the molecule
 maxit 400                            ! maximum # of iteration for FDPBE
end

print elec phizero all end            ! zero out the phisite accumulator
print elec phisave all end            ! compute and store phi at atoms on grid

!  
!               fine grid
!               molecule complex , with zero ligand charge
!
elec calc all 
 pdie   2.00                          ! internal dielectric=2
 sdie  78.00                          ! solvent  dielectric=78
 temp 298.00                          ! temperature in K
 ions 150.00                          ! ionic strength
 rion   1.5                           ! ionic radius
 nmap   1.4                           ! use probe-accessible surface
 nsph 400                             ! use 400 sphere points for surface cal.  
 bcfl   4                             ! focusing - use the coarse grid to
                                      ! set the boundary potential of this
                                      ! focused grid.
 efld    .00                          ! external electric field
 grid   0.225                         ! spacing for focused grid
 dime  110  110  110                    ! grid dimension
 mcenter 2
 maxit 400                            ! maximum # of iteration for FDPBE
end

print elec phisave all end
print elec phinrg all end  
assign e2 = $phinrg end

!
! Now compute the solvation energies of mol1, mol2

assign
  esolv1 = $e1 $e2 -
end
assign
  esolv2 = $e3
end

stop