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Nirmatrelvir_REAC.nw
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title "nirmatrelvir"
start nirmatrelvir
echo
charge 0
memory total 1000 mb
#print debug
SCRATCH_DIR /tmp
PERMANENT_DIR .
prepare
directory_3 ../
system nirmatrelvir
source ./nirmatrelvir-F.pdb
amber
new_top new_seq
new_rst
modify atom 401:_NK quantum
modify atom 401:_HK quantum
modify atom 401:_CK1 quantum
modify atom 401:_OK1 quantum
modify atom 401:_CK2 quantum
modify atom 401:_HK2 quantum
modify atom 401:_CK3 quantum
modify atom 401:2HK3 quantum
modify atom 401:3HK3 quantum
modify atom 401:_CK4 quantum
modify atom 401:2HK4 quantum
modify atom 401:3HK4 quantum
modify atom 401:_CK5 quantum
modify atom 401:2HK5 quantum
modify atom 401:3HK5 quantum
modify atom 401:_CK6 quantum
modify atom 401:_HK6 quantum
modify atom 401:_CK7 quantum
modify atom 401:_NK7 quantum
modify atom 401:_NK8 quantum
modify atom 401:_HK8 quantum
modify atom 401:_CK8 quantum
modify atom 401:_OK8 quantum
modify atom 401:_CK9 quantum
modify atom 401:_HK9 quantum
modify atom 401:_NL1 quantum
modify atom 401:_CL2 quantum
modify atom 401:2HL2 quantum
modify atom 401:3HL2 quantum
modify atom 401:_CL3 quantum
modify atom 401:_HL3 quantum
modify atom 401:_CL4 quantum
modify atom 401:_HL4 quantum
modify atom 401:_CL5 quantum
modify atom 401:_CL6 quantum
modify atom 401:2HL6 quantum
modify atom 401:3HL6 quantum
modify atom 401:4HL6 quantum
modify atom 401:_CL7 quantum
modify atom 401:2HL7 quantum
modify atom 401:3HL7 quantum
modify atom 401:4HL7 quantum
modify atom 401:_CM1 quantum
modify atom 401:_OM1 quantum
modify atom 401:_CM2 quantum
modify atom 401:_HM2 quantum
modify atom 401:_NM3 quantum
modify atom 401:_HM3 quantum
modify atom 401:_CM4 quantum
modify atom 401:_OM4 quantum
modify atom 401:_CM5 quantum
modify atom 401:2FM5 quantum
modify atom 401:3FM5 quantum
modify atom 401:4FM5 quantum
modify atom 401:_CN1 quantum
modify atom 401:_CN2 quantum
modify atom 401:2HN2 quantum
modify atom 401:3HN2 quantum
modify atom 401:4HN2 quantum
modify atom 401:_CN3 quantum
modify atom 401:2HN3 quantum
modify atom 401:3HN3 quantum
modify atom 401:4HN3 quantum
modify atom 401:_CN4 quantum
modify atom 401:2HN4 quantum
modify atom 401:3HN4 quantum
modify atom 401:4HN4 quantum
modify atom 25:_CA quantum
modify atom 25:_HA quantum
modify atom 25:_CB quantum
modify atom 25:_HB quantum
modify atom 25:_CG2 quantum
modify atom 25:2HG2 quantum
modify atom 25:3HG2 quantum
modify atom 25:4HG2 quantum
modify atom 25:_OG1 quantum
modify atom 25:_HG1 quantum
modify atom 25:_C quantum
modify atom 25:_O quantum
modify atom 26:_N quantum
modify atom 26:_H quantum
modify atom 26:_CA quantum
modify atom 26:_HA quantum
modify atom 26:_C quantum
modify atom 26:_O quantum
modify atom 27:_N quantum
modify atom 27:_H quantum
modify atom 27:_CA quantum
modify atom 27:_HA quantum
modify atom 41:_CA quantum
modify atom 41:_HA quantum
modify atom 41:_CB quantum
modify atom 41:2HB quantum
modify atom 41:3HB quantum
modify atom 41:_CG quantum
modify atom 41:_ND1 quantum
modify atom 41:_HD1 quantum
modify atom 41:_CD2 quantum
modify atom 41:_HD2 quantum
modify atom 41:_CE1 quantum
modify atom 41:_HE1 quantum
modify atom 41:_NE2 quantum
modify atom 41:_HE2 quantum
modify atom 141:_CA quantum
modify atom 141:_HA quantum
modify atom 141:_C quantum
modify atom 141:_O quantum
modify atom 142:_N quantum
modify atom 142:_H quantum
modify atom 142:_CA quantum
modify atom 142:_HA quantum
modify atom 142:_CB quantum
modify atom 142:2HB quantum
modify atom 142:3HB quantum
modify atom 142:_CG quantum
modify atom 142:_OD1 quantum
modify atom 142:_ND2 quantum
modify atom 142:2HD2 quantum
modify atom 142:3HD2 quantum
modify atom 142:_C quantum
modify atom 142:_O quantum
modify atom 143:_N quantum
modify atom 143:_H quantum
modify atom 143:_CA quantum
modify atom 143:2HA quantum
modify atom 143:3HA quantum
modify atom 143:_C quantum
modify atom 143:_O quantum
modify atom 144:_N quantum
modify atom 144:_H quantum
modify atom 144:_CA quantum
modify atom 144:_HA quantum
modify atom 144:_CB quantum
modify atom 144:2HB quantum
modify atom 144:3HB quantum
modify atom 144:_OG quantum
modify atom 144:_HG quantum
modify atom 144:_C quantum
modify atom 144:_O quantum
modify atom 145:_N quantum
modify atom 145:_H quantum
modify atom 145:_CA quantum
modify atom 145:_HA quantum
modify atom 145:_CB quantum
modify atom 145:2HB quantum
modify atom 145:3HB quantum
modify atom 145:_SG quantum
modify atom 145:_C quantum
modify atom 145:_O quantum
modify atom 146:_N quantum
modify atom 146:_H quantum
modify atom 146:_CA quantum
modify atom 146:2HA quantum
modify atom 146:3HA quantum
modify atom 146:_C quantum
modify atom 146:_O quantum
modify atom 147:_N quantum
modify atom 147:_H quantum
modify atom 147:_CA quantum
modify atom 147:_HA quantum
modify atom 147:_CB quantum
modify atom 147:2HB quantum
modify atom 147:3HB quantum
modify atom 147:_OG quantum
modify atom 147:_HG quantum
modify atom 147:_C quantum
modify atom 147:_O quantum
modify atom 148:_N quantum
modify atom 148:_H quantum
modify atom 148:_CA quantum
modify atom 148:_HA quantum
modify atom 162:_CA quantum
modify atom 162:_HA quantum
modify atom 162:_C quantum
modify atom 162:_O quantum
modify atom 163:_N quantum
modify atom 163:_H quantum
modify atom 163:_CA quantum
modify atom 163:_HA quantum
modify atom 163:_CB quantum
modify atom 163:2HB quantum
modify atom 163:3HB quantum
modify atom 163:_CG quantum
modify atom 163:_ND1 quantum
modify atom 163:_CE1 quantum
modify atom 163:_HE1 quantum
modify atom 163:_NE2 quantum
modify atom 163:_HE2 quantum
modify atom 163:_CD2 quantum
modify atom 163:_HD2 quantum
modify atom 163:_C quantum
modify atom 163:_O quantum
modify atom 164:_N quantum
modify atom 164:_H quantum
modify atom 164:_CA quantum
modify atom 164:_HA quantum
modify atom 164:_CB quantum
modify atom 164:2HB quantum
modify atom 164:3HB quantum
modify atom 164:_CG quantum
modify atom 164:_ND1 quantum
modify atom 164:_CD2 quantum
modify atom 164:_HD2 quantum
modify atom 164:_CE1 quantum
modify atom 164:_HE1 quantum
modify atom 164:_NE2 quantum
modify atom 164:_HE2 quantum
modify atom 164:_C quantum
modify atom 164:_O quantum
modify atom 165:_N quantum
modify atom 165:_H quantum
modify atom 165:_CA quantum
modify atom 165:_HA quantum
modify atom 501:2HW quantum
modify atom 501:_OW quantum
modify atom 501:3HW quantum
modify atom 504:2HW quantum
modify atom 504:_OW quantum
modify atom 504:3HW quantum
modify atom 505:2HW quantum
modify atom 505:_OW quantum
modify atom 505:3HW quantum
modify atom 506:2HW quantum
modify atom 506:_OW quantum
modify atom 506:3HW quantum
modify atom 509:2HW quantum
modify atom 509:_OW quantum
modify atom 509:3HW quantum
modify atom 1774:2HW quantum
modify atom 1774:_OW quantum
modify atom 1774:3HW quantum
modify atom 1775:2HW quantum
modify atom 1775:_OW quantum
modify atom 1775:3HW quantum
modify atom 1776:2HW quantum
modify atom 1776:_OW quantum
modify atom 1776:3HW quantum
modify atom 1778:2HW quantum
modify atom 1778:_OW quantum
modify atom 1778:3HW quantum
modify atom 1779:2HW quantum
modify atom 1779:_OW quantum
modify atom 1779:3HW quantum
update lists
ignore
write nirmatrelvir.rst
write nirmatrelvir.pdb
end
task prepare
driver
tight
end
md
system nirmatrelvir
noshake solute
cutoff 10 qmmm 10
msa 30000
end
basis
* library "6-31G*"
end
dft
disp vdw 3
maxiter 250
xc pbe0
direct
grid
end
qmmm
region qmlink mm_solute
method bfgs lbfgs
maxiter 5 100
density espfit
ncycles 50
convergence 1d-7
bqzone 200
end
constraints
# spring bond 122 123 1.0 4.0
# spring bond 18 147 1.0 6.0
end
task qmmm dft optimize
prepare
system nirmatrelvir
read rst nirmatrelvir.rst
write solute pdb nirmatrelvir-F.pdb
end
task prepare