%%file solvate.tleap
source leaprc.ff99SB_spce
loadAmberPrep Acetate.prp
loadAmberPrep Ammonium.prp
ammparms = loadAmberParams Ammonium.frcmod
x = loadPdb "solv1AHO.pdb"
bond x.11.SG x.62.SG
bond x.15.SG x.35.SG
bond x.21.SG x.45.SG
bond x.25.SG x.47.SG
bond x.204.SG x.255.SG
bond x.208.SG x.228.SG
bond x.214.SG x.238.SG
bond x.218.SG x.240.SG
bond x.397.SG x.448.SG
bond x.401.SG x.421.SG
bond x.407.SG x.431.SG
bond x.411.SG x.433.SG
bond x.590.SG x.641.SG
bond x.594.SG x.614.SG
bond x.600.SG x.624.SG
bond x.604.SG x.626.SG
set x box {45.900 40.700 30.100}
set default nocenter on
saveAmberParm x solv1AHO.top solv1AHO.crd
quit
Overwriting solvate.tleap
In [9]:
! tleap -f solvate.tleap > solvate.out
In [10]:
! tail -20 solvate.out
<ACT 777>: CB OA1 CA OA2
<ACT 778>: CB OA1 CA OA2
<ACT 779>: CB OA1 CA OA2
total 883 improper torsions applied
7 improper torsions in old prep form
Building H-Bond parameters.
Incorporating Non-Bonded adjustments.
Not Marking per-residue atom chain types.
Marking per-residue atom chain types.
(Residues lacking connect0/connect1 -
these don't have chain types marked:
res total affected
CHID 4
NVAL 4
WAT 695
)
(no restraints)
Quit