* Initial topology and structure input via CHARMM followed
* by application of MMFF
*

bomlev -3

! read topology; note presence of atom type
! after the masses; essential for CHARMM to
! MMFF conversion

read rtf  card unit  5
* TOPOLOGY FILE FOR METHANOL TO METHANOL
*
   20    1                   ! Version number
MASS     1 H      1.00800  H ! Hydrogen bonding hydrogen (neutral group)
MASS     3 HA     1.00800  H ! Aliphatic or aromatic non-hydrogen bonding hydrogen
MASS     4 HT     1.00800  H ! TIPS3P water model hydrogen
MASS    10 CT    12.01100  C ! Aliphatic carbon  -sp3
MASS    45 OT    15.99940  O ! Hydroxyl oxygen (tetrahedral)/Ionizable acid oxygen
MASS    46 OW    15.99940  O ! TIP3P water model oxygen
MASS    99 DUMM   1.008   -H ! dummy atom

AUTOGENERATE ANGLES DIHEDRALS
DEFA FIRS NTER LAST CTER

RESI METH         0.0  !  methanol residue
ATOM C    CT     -0.2
ATOM HA   HA      0.2  
ATOM HB   HA      0.2  
ATOM HC   HA      0.2  
ATOM O    OT     -0.8
ATOM H    H       0.4
!DOUBLE bonds must be treated explicitly
BOND C HA   C HB   C HC    C O   O H
DONO  H O
ACCE  O
PATCH FIRST NONE LAST NONE

END

!stream MMFF parameter files and activate MMFF
stream mmff_setup.str

! generate methanol 
read sequence meth 1
generate METH setup warn first none last none

!read coordinates
read coor card unit 5
*...
*
    6
    1    1 METH C     -0.69375   0.08705   0.02506 METH 1      0.00000
    2    1 METH HA    -1.04595   0.96842  -0.51600 METH 1      0.00000
    3    1 METH HB    -1.01050   0.15222   1.06888 METH 1      0.00000
    4    1 METH HC    -1.10901  -0.81179  -0.43730 METH 1      0.00000
    5    1 METH O      0.71984   0.04198  -0.03852 METH 1      0.00000
    6    1 METH H      1.00275  -0.74985   0.44978 METH 1      0.00000

!minimize and perform various analysis
update inbfrq 10000 ihbfrq 0 cdie cutnb 999.
mini conj nstep 1000 nprint 100 step 0.1 tolg 0.0000001 tols 0.0000001
mini nrap nstep   10 nprint   2 tolg 0.0000001
coor orie mass
analys on
prnlev 6
energy
print coor

analys off
faster off
prnlev 5
vibran
diag
end

stop