Difference between revisions of "2016 AMBER tutorial with Thrombin"

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(I. Introduction)
(MM-GBSA Energy Calculation)
 
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==I. Introduction==
 
==I. Introduction==
 +
 +
Yaping
  
 
==II. Structural Preparation==
 
==II. Structural Preparation==
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====Antechamber, Parmchk, tLeap====
 
====Antechamber, Parmchk, tLeap====
  
Before beginning the Molecular Dynamics protocol using AMBER, you must first set up your files.
+
Omar, Katie
In your 001.chimera folder, you will add the following files:
 
 
 
  4TKG.lig.mol2
 
  4TKG.rec.noH.pdb
 
  4TKG.rec.noH.ZIN.pdb
 
 
 
To prepare the first two files, please see the 2025 DOCK tutorial at the following link: [http://ringo.ams.sunysb.edu/index.php/2015_DOCK_tutorial_with_Poly(ADP-ribose)_polymerase_(PARP)]
 
 
 
Note: delete any headers before the atoms/helix information.
 
 
 
In order to prepare 4TKG.rec.noH.ZIN.pdb, first open 4TKG.rec.noH.pdb and use the command "SHIFT + g" to reach the bottom of the pdb.  The last lines of your files should look like this:
 
 
 
  ATOM  1648  OE1 GLU B 205      23.839 -23.190  57.747  1.00  0.00          O
 
  TER    1649      GLU B 205
 
  HETATM 1650 ZN  ZN  B 206      28.130  -3.467  55.482  1.00  0.00          Zn
 
  END
 
 
 
To make 4TKG.rec.noH.ZIN.pdb, you will need to change the "ZN" atom ID to "ZIN" so that AMBER can read the atom type.
 
 
 
  ATOM  1648  OE1 GLU B 205      23.839 -23.190  57.747  1.00  0.00          O
 
  TER    1649      GLU B 205
 
  ATOM  1650  ZIN ZIN B 206      28.130  -3.467  55.482  1.00  0.00          Zn
 
  END
 
 
 
 
 
To run a tleap, first generate a 002.tleap file, with the command:
 
  mkdir 002.tleap
 
 
 
  cp ~/../../tleap.lig.in
 
 
*tleap.lig.in
 
source leaprc.ff14SB                                              #Load a force field
 
source leaprc.gaff                 
 
LIG = loadmol2 4TKG.lig.mol2                                      #Conformation file
 
saveamberparm LIG 4TKG.lig.gas.leap.prm7 4TKG.lig.gas.leap.rst7    #Save the ligand gas phase AMBER topology and coordinate file
 
solvatebox LIG TIP3PBOX 10.0                                      #Solvate the lig using TIP3P, solvent box radii 10 angstroms
 
saveamberparm LIG 4TKG.lig.wat.leap.prm7 4TKG.lig.wat.leap.rst7    #Save the ligand water phase AMBER topology and coordinate files
 
quit
 
 
 
  tleap –s –f tleap.lig.in > tleap.lig.out
 
The atom types which used in '4TKG.lig.mol2' file are not recognized.
 
[[Image:Screen Shot 2015-05-21 at 13.54.08.png‎|thumb|center|600px]]
 
So the name of the atoms has to be redefined based on the gaff force field, '''antechamber''' can be used to solve the error.
 
  antechamber –i 4TKG.lig.mol2 –fi mol2 –o 4TKG.lig.gaff.mol2 –fo mol2
 
Change the content of tleap.lig.in to
 
(gaff file)
 
 
 
Re-run tleap by:
 
  tleap –s –f tleap.lig.in > tleap.lig.out
 
[[Image:error2.png‎|thumb|center|600px]]
 
 
 
So now run parmchk to fix the missing parameters
 
  parmchk –i 4TKG.lig.gaff.mol2 –f mol2 –o 4TKG.lig.ante.frcmod
 
Change the content of tleap.lig.in to
 
(load amber params)
 
run tleap.lig.in, and all the errors are fixed.
 
[[Image:error1&error2 fixed.png‎|thumb|center|600px]]
 
  cp ~/../../tleap.rec.in
 
*tleap.rec.in
 
source leaprc.ff14SB                                                  #Load a force field
 
REC = loadpdb ../001.chimera/4TKG.rec.noH.ZIN.pdb                    #Conformation file for receptor
 
saveamberparm REC 4TKG.rec.gas.leap.prm7 4TKG.rec.gas.leap.rst7      #Save the receptor gas phase AMBER topology and coordinate file
 
solvateBox REC TIP3PBOX 10.0                                          #Solvate the lig using TIP3P, solvent box radii 10 angstroms
 
saveamberparm REC 4TKG.rec.wat.leap.prm7 4TKG.rec.wat.leap.rst7      #Save the receptor water phase AMBER topology and coordinate file
 
quit
 
 
tleap –s –f tleap.rec.in > tleap.rec.out
 
[[Image:rec.png‎|thumb|center|600px]]
 
 
 
For the missing parameters, cp the two ionparam from ../000.amberfiles/
 
  cp ../000.amberfiles/ions.lib
 
  cp ../000.amberfiles/ions.frcmod
 
Change the content of the tleap.rec.in to
 
(load param)
 
[[Image:rec_ion.png‎|thumb|center|600px]]
 
run tleap.rec.in, and all the errors are fixed.
 
(explain)
 
 
 
  cp ~/../../tleap.com.in
 
  tleap –s –f tleap.com.in > tleap.com.out
 
 
 
 
 
This whole process can be run on a cluster by using the following script:
 
[[Image:script.png‎|thumb|center|600px]]
 
  
 
==III. Simulation using pmemd==
 
==III. Simulation using pmemd==
  
'''PMEMD'''
+
====PMEMD====
 
 
In this part of the MD simulation, you begin with the starting coordinates for the system (typically the protein and the small molecule), and you perform a series of minimizations and short MD simulation runs to equilibrate the system. This is to remove any steric clashes and to allow the system to settle down into a natural state. Otherwise, any large steric clashes from the starting coordinates (which could be from the protein data bank or from a dock calculation) can cause the system to behave unnaturally or even come apart. Once the system is properly equilibrated, then you can begin an MD production run in which you record the trajectory.
 
 
 
There is no specific way in which equilibrations should be performed, but this is an example from the class:
 
 
 
1) The first input file is called 01mi.in and contains the following lines of code.
 
 
 
01mi.in: equilibration
 
&cntrl
 
  imin = 1, maxcyc = 1000, ntmin = 2,
 
  ntx = 1, ntc = 1, ntf = 1,
 
  ntb = 1, ntp = 0,
 
  ntwx = 1000, ntwe = 0, ntpr = 1000,
 
  cut = 8.0,
 
  ntr = 1,
 
  restraintmask = ':1-207 & !@H=',
 
  restraint_wt=5.0,
 
/
 
 
 
This describes a minimization in which we put a large 5.0 kcal/molA^2 on all the heavy atoms except the hydrogens. Thus, the hydrogens are allowed to relax and we remove any steric clashes involving hydrogens.
 
 
 
2) The second input file is called 02md.in and contains the following lines of code.
 
 
 
02md.in: equilibration (1,000,000 = 1ns)
 
&cntrl
 
  imin = 0, ntx = 1, irest = 0, nstlim = 50000,
 
  temp0 = 298.15, tempi = 298.15, ig = 71287,
 
  ntc = 2, ntf = 1, ntt = 1, dt = 0.001,
 
  ntb = 2, ntp = 1, tautp = 1.0, taup = 1.0,
 
  ntwx = 1000, ntwe = 0, ntwr = 1000, ntpr = 1000,
 
  cut = 8.0, iwrap = 1,
 
  ntr = 1, nscm = 100,
 
  restraintmask = ':1-207 & !@H=', restraint_wt = 5.0,
 
/
 
 
 
This describes an 'equilibration' or short MD simulation that is intended to bring the system into a more natural (low energy) state. Here, the same restraint is applied on all atoms except the hydrogen atoms, but this time we do an MD simulation, not a minimization.
 
  
For the next few steps, we perform 3 minimizations using exactly the same code as in 01mi.in, but we slowly decrease the restraint_wt from 5.0 to 2.0, to 1.0, to 0.05 kcal/molA^2.
+
Agatha, Beilei
 
 
After those 3 minimizations, we do 2 short MD simulations. At a high-level, they are as follows:
 
 
 
1) Perform a short MD simulation (almost the same code as in 02md.in) with the restraint_wt = 1.0
 
 
 
2) Perform another short MD simulation with same code as in 02md.in, but with restraintmask = ':1-206@ZIN, CA, C, N', restraint_wt = 0.1. This removes the restraint from the ligand and allows the ligand to equilibrate. Note: the protein residues are numbered 1-205, the zinc ion is residue 206, and the ligand is residue 207.
 
 
 
The length of these simulations can be variable, and in the class step 1) was set for 50 picoseconds and step 2) was set for 100 picoseconds. You can change the length of these simulations as necessary by editing the nstlim variable in the code.
 
 
 
Finally, to do a production run, you would use a mimic of 02md.in (perhaps modified if necessary) with nstlim set to the right number for the right length of simulation. dt is the time step, so the product of nstlim times dt gives the length of the simulation in picoseconds. In 02md.in, a time step of 1 femtosecond was used, which corresponds to 0.001 picoseconds.
 
 
 
To submit this job on seawulf, you can use the following script:
 
 
 
Note: in this submission script, there are calls to mi.in and md.in files which were not explicity mentioned above, but only described at a high level. But these input files, and the submission script, are easily modifiable. You may want to use a different number of minimization/equilibration steps, in which case modifications to these files must be done. To do the modific<nowiki>Insert non-formatted text here</nowiki>ations, you would essentially concentrate on deleting/adding lines of code focusing on the -i XXmi.in part of the lines of code.
 
 
 
replace user_name with your own username.
 
 
 
 
 
  #! /bin/tcsh
 
  #PBS -l nodes=4:ppn=2
 
  #PBS -l walltime=720:00:00
 
  #PBS -o zzz.qsub.out
 
  #PBS -e zzz.qsub.err
 
  #PBS -V
 
  #PBS -N pmemd
 
  set workdir = "/nfs/user03/fochtman/amber_tutorial/003.pmemd"
 
  cd ${workdir}
 
  cat \$PBS_NODEFILE | sort | uniq
 
  mpirun -n 8 pmemd.MPI -O -O -i 01mi.in -o 01mi.out -p ../002.tleap/4TKG.com.wat.leap.prm7 \
 
  -c ../002.tleap/4TKG.com.wat.leap.rst7 -ref ../002.tleap/4TKG.com.wat.leap.rst7 \
 
  -x 01mi.trj -inf 01mi.info -r 01mi.rst7
 
  mpirun -n 8 pmemd.MPI -O -O -i 02md.in -o 02md.out -p ../002.tleap/4TKG.com.wat.leap.prm7 \
 
  -c 01mi.rst7 -ref 01mi.rst7 -x 02md.trj -inf 02md.info -r 02md.rst7
 
  mpirun -n 8 pmemd.MPI -O -O -i 03mi.in -o 03mi.out -p ../002.tleap/4TKG.com.wat.leap.prm7 \
 
  -c 02md.rst7 -ref 02md.rst7 -x 03mi.trj -inf 03mi.info -r 03mi.rst7
 
  mpirun -n 8 pmemd.MPI -O -O -i 04mi.in -o 04mi.out -p ../002.tleap/4TKG.com.wat.leap.prm7 \
 
  -c 03mi.rst7 -ref 03mi.rst7 -x 04mi.trj -inf 04mi.info -r 04mi.rst7
 
  mpirun -n 8 pmemd.MPI -O -O -i 05mi.in -o 05mi.out -p ../002.tleap/4TKG.com.wat.leap.prm7 \
 
  -c 04mi.rst7 -ref 04mi.rst7 -x 05mi.trj -inf 05mi.info -r 05mi.rst7
 
  mpirun -n 8 pmemd.MPI -O -O -i 06md.in -o 06md.out -p ../002.tleap/4TKG.com.wat.leap.prm7 \
 
  -c 05mi.rst7 -ref 05mi.rst7 -x 06md.trj -inf 06md.info -r 06md.rst7
 
  mpirun -n 8 pmemd.MPI -O -O -i 07md.in -o 07md.out -p ../002.tleap/4TKG.com.wat.leap.prm7 \
 
  -c 06md.rst7 -ref 05mi.rst7 -x 07md.trj -inf 07md.info -r 07md.rst7
 
  mpirun -n 8 pmemd.MPI -O -O -i 08md.in -o 08md.out -p ../002.tleap/4TKG.com.wat.leap.prm7 \
 
  -c 07md.rst7 -ref 05mi.rst7 -x 08md.trj -inf 08md.info -r 08md.rst7
 
  mpirun -n 8 pmemd.MPI -O -O -i 09md.in -o 09md.out -p ../002.tleap/4TKG.com.wat.leap.prm7 \
 
  -c 08md.rst7 -ref 05mi.rst7 -x 09md.trj -inf 09md.info -r 09md.rst7
 
  mpirun -n 8 pmemd.MPI -O -O -i 10md.in -o 10md.out -p ../002.tleap/4TKG.com.wat.leap.prm7 \
 
  -c 09md.rst7 -ref 05mi.rst7 -x 10md.trj -inf 10md.info -r 10md.rst7
 
  mpirun -n 8 pmemd.MPI -O -O -i 11md.in -o 11md.out -p ../002.tleap/4TKG.com.wat.leap.prm7 \
 
  -c 10md.rst7 -ref 05mi.rst7 -x 11md.trj -inf 11md.info -r 11md.rst7
 
  exit
 
  
 
==IV. Simulation Analysis==
 
==IV. Simulation Analysis==
Line 195: Line 25:
 
===Ptraj===
 
===Ptraj===
  
You should create another work directory for this step (004.ptraj, for example).
+
Lauren, Haoyue
'''1.''' At first we want to concatenate the two 1ns trajectories together, stripping off the waters, and creating a .strip-file as an output. Below is the input file which will allow us to do so.
 
 
 
'''ptraj.1.in'''
 
trajin ../003.pmemd/10md.trj 1 1000 1
 
trajin ../003.pmemd/11md.trj 1 1000 1
 
trajout 4TKG.trj.strip nobox
 
strip :WAT
 
 
 
The two sets of numbers ''1 1000 1'' give the input information about which frames are used for the Ptraj. The first two numbers ''1'' and ''1000'' specify the starting and ending snapshots from the trajectory file. The ending number of the snapshot doesn't need to be accurate because if you actually don't have enough snapshots in your trajectory file, Ptraj will read up to the last one you have. The last number ''1'' specifies the frequency of the snapshot saved, in this case, we are saving every frame of the trajectory file. And the last line of the input file will take away all the water molecules.
 
 
 
As the input file is prepared we can launch the first analysis as follows:
 
ptraj  ../002.tleap/4TKG.com.wat.leap.parm  ptraj.1.in  > ptraj.1.log
 
 
 
As the output you will obtain '''4TKG.trj.strip''' file which contains ''2000'' snapshots of the trajectory.
 
 
 
'''2.''' Later on we want to compare the output file just obtained to our reference file '''4TKG.com.gas.leap.rst7''', using the following input file.
 
 
 
'''ptraj.2.in'''
 
trajin 4TKG.trj.strip  1 2000 1
 
trajout 4TKG.com.trj.stripfit
 
reference ../002.tleap/4TKG.com.gas.leap.rst7
 
rms reference out 4TKG.rmsd.CA.txt :1-206@CA
 
 
 
Since we have just concatenated the two trajectories, we will have ''2000'' snapshots in '''4TKG.trj.strip'''. The third line in the input specifies the reference file, we have taken away all the water molecules during the first step, hence we are working here with the gas phase complex. The last line says we are calculating the rmsd for alpha carbon number ''1'' to ''206''.
 
 
 
And as we have this file filled out, we can run this step:
 
ptraj  ../002.tleap/4TKG.com.gas.leap.parm  ptraj.2.in  > ptraj.2.log
 
 
 
The output file '''4TKG.rmsd.CA.txt''' wil contain two columns, the first one is the number of frame and the second one stands for rmsd value.
 
 
 
'''3.''' Afterwards we will generate a similar file for ligand, using the following input file. 
 
 
 
'''ptraj.3.in'''
 
trajin 4TKG.com.trj.stripfit 1 2000 1
 
reference ../002.tleap/4TKG.com.gas.leap.rst7
 
rms reference out 4TKG.lig.rmsd.txt :207@C*,N*,O*,S* nofit
 
 
 
And then run this step:
 
ptraj  ../002.tleap/4TKG.com.gas.leap.parm  ptraj.3.in  > ptraj.3.log
 
 
 
By doing this we will compare the trajectory file to '''4TKG.com.gas.leap.rst7''' as well, but working with the ligand instead of the receptor (we specified that by pointing that we want to calculate the rmsd for carbon, nitrogen, oxygen and sulfur in residue ''207''.
 
 
 
The last two steps are to obtain energetic information about the system. To do this we take a trajectory file of the gas phase complex '''4TKG.com.trj.stripfit''', and want to create two more trajectory files containing the information on only receptor and only ligand correspondingly.
 
 
 
'''4.''' At this step we consider receptor only. The input file is provided below:
 
 
 
'''ptraj.4.in'''
 
trajin 4TKG.com.trj.stripfit 1 2000 1
 
trajout 4TKG.rec.trj.stripfit
 
strip :207
 
 
 
And then run this step:
 
ptraj  ../002.tleap/4TKG.com.gas.leap.parm  ptraj.4.in  > ptraj.4.log
 
 
 
'''5.''' And the same procedure for the ligand, with the following input file:
 
 
 
'''ptraj.5.in'''
 
trajin 4TKG.com.trj.stripfit 1 2000 1
 
trajout 4TKG.lig.trj.stripfit
 
strip :1-206
 
 
 
And then run this step:
 
ptraj  ../002.tleap/4TKG.com.gas.leap.parm  ptraj.5.in  > ptraj.5.log
 
 
 
'''6.''' ''(optional)'' Visualization
 
 
 
As we've gone through all these steps, the analysis is done. If you want to visualize the trajectories, you first need to copy the trajectory files to Herbie like this, for example (being a level above '''004.PTRAJ''' directory):
 
scp 004.ptraj/ your_username@herbie.mathlab.sunysb.edu:~AMS536/amber_tutorial/004.ptraj
 
 
 
Now, launch VMD, then open one of the .prm7 files in 002.tleap. If you want to visualize the whole complex in gas state, you can open 4TKG.com.gas.leap.prm7 with AMBER7 Parm from 002.tleap and then 4TKG.com.trj.stripfit with AMBER coordinates from 004.ptraj. With these files, you can look at the real-time movement of the complex in the gas state. You can repeat this procedure to observe the real-time movement of the complex in the water state. Just open 4TKG.com.wat.leap.prm7 instead of 4TKG.com.gas.leap.prm7.
 
  
 
===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.
 
 
Create a new directory:
 
  mkdir 005.MMGBSA
 
Create an input file name
 
  vim gb.rescore.in
 
Enter the following into the input file:
 
  Single point GB energy calc
 
&cntrl
 
  ntf    = 1,        ntb    = 0,        ntc    = 2,
 
  idecomp= 0,
 
  igb    = 5,        saltcon= 0.00,
 
  gbsa  = 2,        surften= 1.0,
 
  offset = 0.09,    extdiel= 78.5,
 
  cut    = 99999.0,  nsnb  = 99999,
 
  imin  = 5,        maxcyc = 1,        ncyc  = 0,
 
  /
 
Create a tcsh/bash/csh script (run.sander.rescore.csh) with the following information:
 
  #! /bin/tcsh
 
  #PBS -l nodes=1:ppn=1
 
  #PBS -l walltime=48:00:00
 
  #PBS -o zzz.qsub.out
 
  #PBS -e zzz.qsub.err
 
  #PBS -V
 
  #PBS -N mmgbsa
 
 
 
  set workdir = /nfs/user03/kbelfon/amber_tutorial/005.mmgbsa
 
 
 
  cd $workdir
 
 
 
  sander -O -i gb.rescore.in \
 
  -o gb.rescore.out.com \
 
  -p ../002.tleap/4TKG.com.gas.leap.prm7 \
 
  -c ../002.tleap/4TKG.com.gas.leap.rst7 \
 
  -y ../004.ptraj/4TKG.com.trj.stripfit \
 
  -r restrt.com \
 
  -ref ../002.tleap/4TKG.com.gas.leap.rst7 \
 
  -x mdcrd.com \
 
  -inf mdinfo.com
 
 
  sander -O -i gb.rescore.in \
 
  -o gb.rescore.out.lig \
 
  -p ../002.tleap/4TKG.lig.gas.leap.prm7 \
 
  -c ../002.tleap/4TKG.lig.gas.leap.rst7 \
 
  -y ../004.ptraj/4TKG.lig.trj.stripfit \
 
  -r restrt.lig \
 
  -ref ../002.tleap/4TKG.lig.gas.leap.rst7 \
 
  -x mdcrd.lig \
 
  -inf mdinfo.lig
 
 
 
  sander -O -i gb.rescore.in \
 
  -o gb.rescore.out.test.rec \
 
  -p ../002.tleap/4TKG.rec.gas.leap.prm7 \
 
  -c ../002.tleap/4TKG.rec.gas.leap.rst7 \
 
  -y ../004.ptraj/4TKG.rec.trj.stripfit \
 
  -r restrt.rec \
 
  -ref ../002.tleap/4TKG.rec.gas.leap.rst7 \
 
  -x mdcrd.rec \
 
  -inf mdinfo.rec
 
 
 
  exit
 
 
Execute this script on the seawulf cluster or machine(s) of your preference
 
  qsub run.sander.rescore.csh
 
Three output files will be generated once the job is completed:             
 
'''gb.rescore.out.com''', '''gb.rescore.out.lig''', and '''gb.rescore.out.rec'''
 
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:
 
 
                                    FINAL RESULTS
 
 
 
 
 
   
 
    NSTEP      ENERGY          RMS            GMAX        NAME    NUMBER
 
      1      5.9132E+03    2.0005E+01    1.2640E+02    C        159
 
 
 
  BOND    =      661.8980  ANGLE  =    1751.7992  DIHED      =    2581.7692
 
  VDWAALS =    -1696.6585  EEL    =  -13958.9335  EGB        =    -3125.9524
 
  1-4 VDW =      747.0185  1-4 EEL =    7750.8118  RESTRAINT  =        0.0000
 
  ESURF  =    11201.4791
 
minimization completed, ENE= 0.59132314E+04 RMS= 0.200047E+02
 
'''Extracting Data from MM-GBSA calculation and calculating Free energy of Binding'''
 
From the output files above:
 
 
VDWAALS = ΔGvdw
 
 
EELS = ΔGcoul
 
 
EGB = ΔGpolar
 
 
SASA = ESURF
 
 
With this information ΔGnonpolar can be solved using equation(1):
 
 
ΔGnonpolar = SASA*0.00542 + 0.92                                                      (1)
 
 
Once ΔGnonpolar is solved then ΔGmmgbsa can be determined by equation(2):
 
 
ΔGmmgbsa = ΔGvdw + ΔGcoul + ΔGpolar + ΔGnonpolar                                      (2)
 
 
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                               
 
 
Finally ΔΔGbind can be calculated using equation (3):
 
 
ΔΔGbind = ΔGmmgbsa,complex – (ΔGmmgbsa,lig + ΔGmmgbsa,rec)                       (3)
 
 
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.
 
 
The following script (get.mmgbsa.sh) can be used to extract the energy from the three output files obtained above and calculate ΔΔGbind:
 
 
 
  #! /bin/bash
 
  # by Haoquan
 
  echo com lig rec > namelist
 
  LIST=`cat namelist`
 
  for i in $LIST ; do
 
  grep VDWAALS gb.rescore.out.$i | awk '{print $3}' > $i.vdw
 
  grep EGB    gb.rescore.out.$i | awk '{print $9}' > $i.polar
 
  grep EELS    gb.rescore.out.$i | awk '{print $6}' > $i.coul
 
  grep ESURF  gb.rescore.out.$i | awk '{print $3 * 0.00542 + 0.92}' > $i.surf
 
  paste -d " " $i.vdw $i.polar $i.surf $i.coul | awk '{print $1 + $2 + $3 + $4}' > data.$i
 
  rm $i.*
 
  done
 
  paste -d " " data.com data.lig data.rec | awk '{print $1 - $2 - $3}' > data.all
 
  for ((j=1; j<=`wc -l data.all | awk '{print $1}'`; j+=1)) do
 
  echo $j , >> time
 
  done
 
  paste -d " " time data.all > MMGBSA_vs_time.dat 
 
  rm namelist time data.*
 
 
Execute this script:
 
  bash get.mmgbsa.sh
 
 
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:
 
  
  xmgrace MMGBSA_vs_time.dat
+
Monaf
  
 
==V. Frequently Encountered Problems==
 
==V. Frequently Encountered Problems==

Latest revision as of 13:16, 6 April 2016

For additional Rizzo Lab tutorials see AMBER Tutorials.

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).

I. Introduction

Yaping

II. Structural Preparation

Antechamber, Parmchk, tLeap

Omar, Katie

III. Simulation using pmemd

PMEMD

Agatha, Beilei

IV. Simulation Analysis

Ptraj

Lauren, Haoyue

MM-GBSA Energy Calculation

Monaf

V. Frequently Encountered Problems