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| | ==I. Introduction== | | ==I. Introduction== |
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| | + | Yaping |
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| | ==II. Structural Preparation== | | ==II. Structural Preparation== |
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| | ====Antechamber, Parmchk, tLeap==== | | ====Antechamber, Parmchk, tLeap==== |
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| | + | Omar, Katie |
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| | ==III. Simulation using pmemd== | | ==III. Simulation using pmemd== |
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| | ====PMEMD==== | | ====PMEMD==== |
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| | + | Agatha, Beilei |
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| | ==IV. Simulation Analysis== | | ==IV. Simulation Analysis== |
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| | ===Ptraj=== | | ===Ptraj=== |
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| | + | Lauren, Haoyue |
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| | ===MM-GBSA Energy Calculation=== | | ===MM-GBSA Energy Calculation=== |
| − | Molecular Mechanics-Generalized Born Surface Area (MM-GBSA) is a great method to calculate or estimate relative binding affinity of a ligand(s) to a receptor. The binding energy calculated from this method are also known as free energies of binding, where the more negative values indicate stronger binding. For this section, the topology files for the ligand, receptor and complex are needed.
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| − | Create a new directory:
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| − | mkdir 005.MMGBSA
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| − | Create an input file name
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| − | vim gb.rescore.in
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| − | Enter the following into the input file:
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| − | Single point GB energy calc
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| − | &cntrl
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| − | ntf = 1, ntb = 0, ntc = 2,
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| − | idecomp= 0,
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| − | igb = 5, saltcon= 0.00,
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| − | gbsa = 2, surften= 1.0,
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| − | offset = 0.09, extdiel= 78.5,
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| − | cut = 99999.0, nsnb = 99999,
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| − | imin = 5, maxcyc = 1, ncyc = 0,
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| − | /
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| − | Create a tcsh/bash/csh script (run.sander.rescore.csh) with the following information:
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| − | #! /bin/tcsh
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| − | #PBS -l nodes=1:ppn=1
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| − | #PBS -l walltime=48:00:00
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| − | #PBS -o zzz.qsub.out
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| − | #PBS -e zzz.qsub.err
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| − | #PBS -V
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| − | #PBS -N mmgbsa
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| − |
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| − | set workdir = /nfs/user03/kbelfon/amber_tutorial/005.mmgbsa
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| − |
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| − | cd $workdir
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| − |
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| − | sander -O -i gb.rescore.in \
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| − | -o gb.rescore.out.com \
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| − | -p ../002.tleap/4TKG.com.gas.leap.prm7 \
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| − | -c ../002.tleap/4TKG.com.gas.leap.rst7 \
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| − | -y ../004.ptraj/4TKG.com.trj.stripfit \
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| − | -r restrt.com \
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| − | -ref ../002.tleap/4TKG.com.gas.leap.rst7 \
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| − | -x mdcrd.com \
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| − | -inf mdinfo.com
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| − |
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| − | sander -O -i gb.rescore.in \
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| − | -o gb.rescore.out.lig \
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| − | -p ../002.tleap/4TKG.lig.gas.leap.prm7 \
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| − | -c ../002.tleap/4TKG.lig.gas.leap.rst7 \
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| − | -y ../004.ptraj/4TKG.lig.trj.stripfit \
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| − | -r restrt.lig \
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| − | -ref ../002.tleap/4TKG.lig.gas.leap.rst7 \
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| − | -x mdcrd.lig \
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| − | -inf mdinfo.lig
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| − |
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| − | sander -O -i gb.rescore.in \
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| − | -o gb.rescore.out.test.rec \
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| − | -p ../002.tleap/4TKG.rec.gas.leap.prm7 \
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| − | -c ../002.tleap/4TKG.rec.gas.leap.rst7 \
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| − | -y ../004.ptraj/4TKG.rec.trj.stripfit \
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| − | -r restrt.rec \
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| − | -ref ../002.tleap/4TKG.rec.gas.leap.rst7 \
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| − | -x mdcrd.rec \
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| − | -inf mdinfo.rec
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| − |
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| − | exit
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| − |
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| − | Execute this script on the seawulf cluster or machine(s) of your preference
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| − | qsub run.sander.rescore.csh
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| − | Three output files will be generated once the job is completed:
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| − | '''gb.rescore.out.com''', '''gb.rescore.out.lig''', and '''gb.rescore.out.rec'''
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| − | These files represent the single point energy calculation results for the complex (.com), the ligand (.lig) and the receptor (.rec). The energy will be output by the program Sander for each frame specified in the input file. The final results for one frame in one of the three files should look as the following:
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| − | FINAL RESULTS
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| − |
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| − | NSTEP ENERGY RMS GMAX NAME NUMBER
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| − | 1 5.9132E+03 2.0005E+01 1.2640E+02 C 159
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| − |
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| − | BOND = 661.8980 ANGLE = 1751.7992 DIHED = 2581.7692
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| − | VDWAALS = -1696.6585 EEL = -13958.9335 EGB = -3125.9524
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| − | 1-4 VDW = 747.0185 1-4 EEL = 7750.8118 RESTRAINT = 0.0000
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| − | ESURF = 11201.4791
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| − | minimization completed, ENE= 0.59132314E+04 RMS= 0.200047E+02
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| − | '''Extracting Data from MM-GBSA calculation and calculating Free energy of Binding'''
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| − | From the output files above:
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| − |
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| − | VDWAALS = ΔGvdw
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| − |
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| − | EELS = ΔGcoul
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| − |
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| − | EGB = ΔGpolar
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| − |
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| − | SASA = ESURF
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| − |
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| − | With this information ΔGnonpolar can be solved using equation(1):
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| − |
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| − | ΔGnonpolar = SASA*0.00542 + 0.92 (1)
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| − |
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| − | Once ΔGnonpolar is solved then ΔGmmgbsa can be determined by equation(2):
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| − |
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| − | ΔGmmgbsa = ΔGvdw + ΔGcoul + ΔGpolar + ΔGnonpolar (2)
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| − |
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| − | Solve equation 2 and 3 using the extracted information from all three output files. So therefore you should have ΔGmmgbsa for the complex, ligand and receptor
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| − |
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| − | Finally ΔΔGbind can be calculated using equation (3):
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| − | ΔΔGbind = ΔGmmgbsa,complex – (ΔGmmgbsa,lig + ΔGmmgbsa,rec) (3)
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| − |
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| − | Plot your ΔΔGbind and examine the plot for changes in the ligand position and the ΔΔGbind. Also, you should calculate the mean and standard deviation for your ΔΔGbind.
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| − |
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| − | The following script (get.mmgbsa.sh) can be used to extract the energy from the three output files obtained above and calculate ΔΔGbind:
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| − |
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| − | #! /bin/bash
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| − | # by Haoquan
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| − | echo com lig rec > namelist
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| − | LIST=`cat namelist`
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| − | for i in $LIST ; do
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| − | grep VDWAALS gb.rescore.out.$i | awk '{print $3}' > $i.vdw
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| − | grep EGB gb.rescore.out.$i | awk '{print $9}' > $i.polar
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| − | grep EELS gb.rescore.out.$i | awk '{print $6}' > $i.coul
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| − | grep ESURF gb.rescore.out.$i | awk '{print $3 * 0.00542 + 0.92}' > $i.surf
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| − | paste -d " " $i.vdw $i.polar $i.surf $i.coul | awk '{print $1 + $2 + $3 + $4}' > data.$i
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| − | rm $i.*
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| − | done
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| − | paste -d " " data.com data.lig data.rec | awk '{print $1 - $2 - $3}' > data.all
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| − | for ((j=1; j<=`wc -l data.all | awk '{print $1}'`; j+=1)) do
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| − | echo $j , >> time
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| − | done
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| − | paste -d " " time data.all > MMGBSA_vs_time.dat
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| − | rm namelist time data.*
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| − |
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| − | Execute this script:
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| − | bash get.mmgbsa.sh
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| − | A text file called MMGBSA_vs_time.dat with x and y values separated by a space and comma should be created. Use XMGRACE to plot this dat file using the following command in Linux:
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| − | xmgrace MMGBSA_vs_time.dat
| + | Monaf |
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| | ==V. Frequently Encountered Problems== | | ==V. Frequently Encountered Problems== |
In this tutorial, we will learn how to run a molecular dynamics simulation of a protein-ligand complex. We will then post-process that simulation by calculating structural fluctuations (with RMSD) and free energies of binding (MM-GBSA).
