In the interests of transparency and for someone else reading this, my PRES looked like this:

Code
*Additional PRESs for Tf
*
36  1

[...]

PRES TYD         -1.00 !
GROUP
ATOM CZ   CA     -0.18 !
ATOM OH   OH1    -0.82 !
!ATOM HH   H      0.00 !
DELETE ATOM HH

[...]

And corresponding PATCHs in the input file:

Code
*QM/MM calculation of protein, water box
*

BOMBLEV -1

! Read topology and parameter files
stream toppar.str
!##################################
!    COORDINATES
!#################################

!    Read in protein

open read card unit 10 name "prep/6ctc_bp1_prep_prot.pdb"
read sequence pdb resi unit 10
generate Tf setup warn first nter last cter

! Termini, disulfide bonds
patch NTER Tf 1 setup warn
patch CTER Tf 330 setup warn
patch disu Tf 7 Tf 46 setup warn
patch disu Tf 17 Tf 37 setup warn

[...]

open read card unit 10 name "prep/6ctc_bp1_prep_prot.pdb"
read coor pdb resi unit 10

!     Read in metal and counter ions

open read card unit 10 name "prep/6ctc_bp1_prep_FeCO3.pdb"
read sequence pdb unit 10
generate Tf2 setup warn

! Patch Fe-TYR bond
patch TYD  Tf 186 Tf2 331 setup warn

open read card unit 10 name "prep/6ctc_bp1_prep_FeCO3.pdb"
read coor pdb unit 10

[...]

Last edited by Corey Taylor; 08/01/20 08:45 AM.