北鯤教程 | 利用Amber熱力學積分計算相對自由能變化
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save * my_case\ ben_ligand .mol2
save *\ my_case\ benfen_ligand .mol2
module add Anaconda3/2020.02
source /public/software/. local/easybuild/software/amber/aber20/amber.sh
ulimit -s unlimited
ulimit -l unlimited
antechamber -i ben_ligand.mol2 -fi mol2 -o ben_real.gaff2.mol2 -fo mol2 -rn BEN -at gaff2 -an yes -dr no -pf yes -c bcc -nc 0
antechamber -i benfen_ligand .mol2 -fi mol2 -o benfen_real .gaff2 .mol2 -fo mol2 -rn FEN -at gaff2 -an yes -dr no -pf yes -c bcc -nc 0
parmchk2 -i benfen_real .gaff2 .mol2 -f mol2 -o FEN .gaff2 .frcmod -s gaff2 -a yes
tleap -f - <<_EOF
source leaprc.gaff2
loadamberparams FEN.gaff2.frcmod
FEN = loadmol2 benfen_real.gaff2.mol2
saveoff FEN FEN.lib
savepdb FEN FEN.pdb
quit
_EOF
tleap -f - <<_EOF
source leaprc.gaff2
loadamberparams BEN.gaff2.frcmod
BEN = loadmol2 ben_real.gaff2.mol2
saveoff BEN BEN.lib
savepdb BEN BEN.pdb
quit
_EOF
pdb4amber pure_protein .pdb -o pure_check .pdb
cat pure_check_sslink
tleap -f - <<_EOF
source leaprc.protein.ff14SB
source leaprc.gaff2
source leaprc.water.tip3p
loadAmberParams frcmod.ionsjc_tip3p
loadoff BEN.lib
loadoff FEN.lib
loadamberparams BEN.gaff2.frcmod
loadamberparams FEN.gaff2.frcmod
ligands = loadpdb lig.pdb
complex = loadpdb pure_check.pdb
complex = combine {ligands complex}
check complex
solvatebox ligands TIP3PBOX 15
addions ligands Na+ 0
savepdb ligands ligands_vdw_bonded.pdb
saveamberparm ligands ligands_vdw_bonded.parm7 ligands_vdw_bonded.rst7
solvatebox complex TIP3PBOX 15
addions complex Cl- 0
savepdb complex complex_vdw_bonded.pdb
saveamberparm complex complex_vdw_bonded.parm7 complex_vdw_bonded.rst7
quit
_EOF
timask1 = ':BEN', timask2 = ':FEN',
scmask1 = ':BEN@H6', scmask2 = ':FEN@O1,H6'
ambmask -p complex_vdw_bonded .parm7 -c complex_vdw_bonded .rst7 -find :FEN
p ligands_vdw_bonded .rst7 ligands_vdw_bonded .rst7 .leap
cp press_lig .rst7 ligands_vdw_bonded .rst7
cp complex_vdw_bonded .rst7 complex_vdw_bonded .rst7 .leap
cp press_com .rst7 complex_vdw_bonded .rst7
cpptraj -p ligands_vdw_bonded .parm7 <<_ EOF
trajin ligands_vdw_bonded .rst7
strip " :1,2"
outtraj ligands_solvated .pdb onlyframes 1
unstrip
strip " :2-999999"
outtraj ligands_BEN .pdb onlyframes 1
unstrip
strip " :1,3 -999999"
outtraj ligands_FEN .pdb onlyframes 1
_ EOF
cpptraj -p complex_vdw_bonded .parm7 <<_ EOF
trajin complex_vdw_bonded .rst7
strip " :1,2"
outtraj complex_solvated .pdb onlyframes 1
unstrip
strip " :2-999999"
outtraj complex_BEN .pdb onlyframes 1
unstrip
strip " :1,3 -999999"
outtraj complex_FEN .pdb onlyframes 1
_ EOF
tleap -f - <<_EOF
# load the AMBER force fields
source leaprc.protein.ff19SB
source leaprc.gaff2
source leaprc.water.tip3p
loadAmberParams frcmod.ionsjc_tip3p
loadOff BEN.lib
loadOff FEN.lib
loadamberparams BEN.gaff2.frcmod
loadamberparams FEN.gaff2.frcmod
# coordinates for solvated ligands as created previously by MD
lsolv = loadpdb ligands_solvated.pdb
lbnz = loadpdb ligands_BEN.pdb
lphn = loadpdb ligands_FEN.pdb
# coordinates for complex as created previously by MD
csolv = loadpdb complex_solvated.pdb
cbnz = loadpdb complex_BEN.pdb
cphn = loadpdb complex_FEN.pdb
# decharge transformation
decharge = combine {lbnz lbnz lsolv}
setbox decharge vdw
savepdb decharge ligands_decharge.pdb
saveamberparm decharge ligands_decharge.parm7 ligands_decharge.rst7
decharge = combine {cbnz cbnz csolv}
setbox decharge vdw
savepdb decharge complex_decharge.pdb
saveamberparm decharge complex_decharge.parm7 complex_decharge.rst7
# recharge transformation
recharge = combine {lphn lphn lsolv}
setbox recharge vdw
savepdb recharge ligands_recharge.pdb
saveamberparm recharge ligands_recharge.parm7 ligands_recharge.rst7
recharge = combine {cphn cphn csolv}
setbox recharge vdw
savepdb recharge complex_recharge.pdb
saveamberparm recharge complex_recharge.parm7 complex_recharge.rst7
quit
_EOF
decharge_crg= ":2@H6"
vdw_crg= ":1@H6 | :2@O1,H6"
recharge_crg= ":1@O1,H6"
decharge= " ifsc = 0, crgmask = '$decharge_crg',"
vdw_bonded= " ifsc=1, scmask1=':1@H6', scmask2=':2@O1,H6', crgmask='$vdw_crg'"
recharge= " ifsc = 0, crgmask = '$recharge_crg',"
python run_mpi .py ligands 500000 mpi
pip2 install matplotlib
pip2 install scipy
pip2 install numpy
pip2 install pymbar== 3.0 .3
mkdir -p ana_recharge && cd ana_recharge
../../alchemical-analysis/alchemical_analysis/alchemical_analysis.py -a AMBER -d . -p ../recharge/[01]*/ti00[1-9] -q out -o . -t 300 -v -r 5 -u kcal -f 50 -g -w
mkdir -p ../ana_decharge && cd ../ana_decharge
../../alchemical-analysis/alchemical_analysis/alchemical_analysis.py -a AMBER -d . -p ../decharge/[01]*/ti00[1-9] -q out -o . -t 300 -v -r 5 -u kcal -f 50 -g -w
mkdir -p ../ana_vdw && cd ../ana_vdw
../../alchemical-analysis/alchemical_analysis/alchemical_analysis.py -a AMBER -d . -p ../vdw_bonded/[01]*/ti00[1-9] -q out -o . -t 300 -v -r 5 -u kcal -f 50 -g -w
vim /home/cloudam/. local/lib/python2.7/site-packages/pymbar/timeseries.py
load *.pdb
cmd.wizard( "mutagenesis")
cmd.do( "refresh_wizard")
cmd.get_wizard().set_mode( "GLN")
cmd.get_wizard().do_select( "86/")
cmd.get_wizard().apply()
cmd.set_wizard( "done")
save *\out_name.pdb, enabled
tleap
source leaprc.protein.ff14SB
source leaprc.gaff2
source leaprc.water.tip3p
loadamberparams frcmod.ionsjc_tip3p
zn = loadpdb WT.pdb
check zn
solvateBox zn TIP3PBOX 10
addIons zn Cl- 0
savepdb zn box_check.pdb
quit
python dry_for_TI .py box_check .pdb wat .pdb WT_receptor .pdb
tleap
source leaprc.protein.ff14SB
source leaprc.gaff2
source leaprc.water.tip3p
loadamberparams frcmod.ionsjc_tip3p
zn = loadpdb L86Q.pdb
check zn
solvateBox zn TIP3PBOX 10
addIons zn Cl- 0
savepdb zn L86Q_leap.pdb
quit
python dry_for_TI.py L86Q_leap.pdb wat1.pdb L86Q_dry.pdb
python check_diff_online .py L84Q L86Q_dry .pdb WT_receptor .pdb 84 L86Q_check .pdb WT_check .pdb
tleap
source leaprc.protein.ff14SB
source leaprc.gaff2
loadOff FEN.lib
loadamberparams FEN.gaff2.frcmod
source leaprc.water.tip3p
loadamberparams frcmod.ionsjc_tip3p
ligand = loadmol2 FEN.gaff2.mol2
m1 = loadpdb L86Q_check.pdb
m2 = loadpdb WT_check.pdb
w = loadpdb wat1.pdb
protein = combine {m1 m2 w}
complex = combine {m1 m2 ligand w}
set default nocenter on
setBox protein vdw {39.415 43.577 52.292}
savepdb protein protein.pdb
saveamberparm protein protein.parm7 protein.rst7
setBox complex vdw {39.415 43.577 52.292}
savepdb complex complex.pdb
saveamberparm complex complex.parm7 complex.rst7
quit
parmed protein .parm7 <<_ EOF
loadRestrt protein .rst7
setOverwrite True
tiMerge :1-162 :163-324 :84&!@ CA, C, O, N, H, HA, CB : 246&!@CA,C,O,N,H,HA,CB
outparm merged_L86Q_protein.parm7 merged_L86Q_protein.rst7
quit
_EOF
parmed complex.parm7 <<_EOF
loadRestrt complex.rst7
setOverwrite True
tiMerge : 1- 162 : 163- 324 : 84&!@CA,C,O,N,H,HA,CB : 246&!@CA,C,O,N,H,HA,CB
outparm merged_L86Q_complex.parm7 merged_L86Q_complex.rst7
quit
_EOF
python auto_gene_inp_run .py 84 162 CA, C, O, N, H, HA, CB L86Q
tleap
source leaprc.protein.ff14SB
source leaprc.gaff
source leaprc.water.tip3p
loadamberparams frcmod.ionsjc_tip3p
zn = loadpdb omi_SS.pdb
bond zn.333.SG zn.358.SG
bond zn.376.SG zn.429.SG
bond zn.388.SG zn.522.SG
bond zn.477.SG zn.485.SG
bond zn.637.SG zn.645.SG
bond zn.848.SG zn.865.SG
bond zn.1034.SG zn.1046.SG
check zn
solvateBox zn TIP3PBOX 10
addIons zn Na+ 0
addIons zn Na+ 80
addIons zn Cl- 0
savepdb zn box_check.pdb
quit
python dry_for_TI.py box_check.pdb wat1.pdb omi_rbd.pdb,omi_ace2.pdb
tleap
source leaprc.protein.ff14SB
source leaprc.gaff
source leaprc.water.tip3p
loadamberparams frcmod.ionsjc_tip3p
m1 = loadpdb omi_rbd.pdb
bond m1.4.SG m1.29.SG
bond m1.47.SG m1.100.SG
bond m1.59.SG m1.193.SG
bond m1.148.SG m1.156.SG
check m1
solvateBox m1 TIP3PBOX 10
addIons m1 Na+ 0
addIons m1 Na+ 28
addIons m1 Cl- 0
savepdb m1 ligands_recharge.pdb
quit
python dry_for_TI.py ligands_recharge.pdb rbd_wat.pdb test_rbd.pdb
python check_diff_online .py A152E A484E_rbd .pdb omi_rbd .pdb 152 A484E_check .pdb omi_check .pdb
tleap
source leaprc.protein.ff14SB
source leaprc.gaff
source leaprc.water.tip3p
loadamberparams frcmod.ionsjc_tip3p
ligand = loadpdb omi_ace2.pdb
bond ligand.308.SG ligand.316.SG
bond ligand.519.SG ligand.536.SG
bond ligand.705.SG ligand.717.SG
m1 = loadpdb omi_check.pdb
bond m1.4.SG m1.29.SG
bond m1.47.SG m1.100.SG
bond m1.59.SG m1.193.SG
bond m1.148.SG m1.156.SG
m2 = loadpdb A484E_check.pdb
bond m2.4.SG m2.29.SG
bond m2.47.SG m2.100.SG
bond m2.59.SG m2.193.SG
bond m2.148.SG m2.156.SG
w1 = loadpdb rbd_wat.pdb
w2 = loadpdb wat1.pdb
protein = combine {m1 m2 w1}
complex = combine {m1 m2 ligand w2}
set default nocenter on
setBox protein vdw {43.215 53.421 59.922}
savepdb protein protein.pdb
saveamberparm protein protein.parm7 protein.rst7
setBox complex vdw {64.171 75.490 114.587}
savepdb complex complex.pdb
saveamberparm complex complex.parm7 complex.rst7
quit
parmed protein .parm7 <<_ EOF
loadRestrt protein .rst7
setOverwrite True
tiMerge :1-193 :194-386 :152&!@ CA, C, O, N, H, HA, CB : 345&!@CA,C,O,N,H,HA,CB
outparm merged_A484E_protein.parm7 merged_A484E_protein.rst7
quit
_EOF
parmed complex.parm7 <<_EOF
loadRestrt complex.rst7
setOverwrite True
tiMerge : 1- 193 : 194- 386 : 152&!@CA,C,O,N,H,HA,CB : 345&!@CA,C,O,N,H,HA,CB
outparm merged_A484E_complex.parm7 merged_A484E_complex.rst7
quit
_EOF
python auto_gene_inp_run .py 152 193 CA, C, O, N, H, HA, CB A484E
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