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tleap.in
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tleap.in
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# AmberTools leap script to generate
# Amber prmtop and inpcrd MD files
source oldff/leaprc.ff14SB
source leaprc.gaff
source leaprc.lipid17
loadamberprep ubiquinone.prepi
loadamberparams ubiquinone.frcmod
loadoff heme.lib
loadamberparams heme.frcmod
loadamberparams mcpbpy.frcmod
protein = loadpdb combined_renum.pdb
bond protein.445.CA protein.3.CB1
bond protein.238.CA protein.3.CB
bond protein.1.CA protein.3.C2A
bond protein.2.CA protein.3.C3D
bond protein.497.CA protein.6.CB
bond protein.4.CA protein.6.C2A
bond protein.5.CA protein.6.C3D
bond protein.71.CA protein.8.CB
bond protein.7.CA protein.8.C2A
check protein
savepdb protein protein.pdb
saveamberparm protein protein.prmtop protein.inpcrd
addions protein Na+ 0 Cl- 0 ## replace this with number of atoms needed to neutralize the system
solvatebox protein TIP3PBOX 15.0
addions protein Na+ 94 Cl- 94 ## this is to set the ionic concentration
#setbox protein vdw
savepdb protein protein_solv.pdb
saveamberparm protein protein_solv.prmtop protein_solv.rst7
quit