Part 3: Mutation Studies (How to set up a MD Simulation)
In the first part of the workshop you used VMD to visualise the output of molecular dynamics simulations of oseltamivir (Tamiflu) bound to the wild type and R292K mutant of H7N9 influenza neuraminidase.
In the second part of the workshop you learned how to use namd to run molecular dynamics simulations, and you performed a long simulation of zanamivir (Relenza) bound to wild type H7N9 influenza neuraminidase.
In this last part of the workshop you will learn how to set up a new molecular dynamics simulation so that you can study zanamivir bound to the R292K mutant of H7N9 neuraminidase. To do this, we will use AmberTools to mutate neuraminidase, and to build the new water box around the mutant protein.
AmberTools is a collection of free tools that can be used to build molecular models, including biomolecular models of proteins etc.
If you do not already have AmberTools installed on your computer, instructions to download and install them can be found here.
AmberTools will be installed into a directory of your computer, e.g. /usr/local/amber14. To make things easier for the rest of the workshop, set an environment variable called “AMBERHOME” to point to this directory. To do this, open a terminal (shell prompt) and then (assuming AmberTools are installed in /usr/local/amber14) type;
export AMBERHOME=/usr/local/amber14if you are using bash, or type
setenv AMBERHOME /usr/local/amber14if you are using csh or tcsh.
To test if this has worked, type;
ls $AMBERHOME/binand you should see output something like;
:-> ls $AMBERHOME/bin
AddToBox bondtype fftw-wisdom-to-conf mm_pbsa_statistics.pl parmcal rism3d.snglpnt
ChBox chamber fix_new_inpcrd_vel mmpbsa_py_energy parmchk sgldinfo.sh
FEW.pl charmmgen hcp_getpdb mmpbsa_py_nabnmode parmchk2 sgldwt.sh
MMPBSA.py charmmlipid2amber.py make_crd_hg molsurf parmed.py softcore_setup.py
MMPBSA_mods chemistry matextract nab pbsa sqm
ParmedTools compat24.py matgen nab2c pdb4amber teLeap
PropPDB compat24.pyc matmerge nc-config prepgen tinker_to_amber
UnitCell cphstats matmul nccopy process_mdout.perl tleap
acdoctor cpinutil.py mdgx ncdump process_minout.perl transform
add_pdb cpinutils mdnab ncgen pymdpbsa translate
addles cpptraj mdout2pymbar.pl ncgen3 pytleap tss_init
am1bcc database mdout_analyzer.py new2oldparm reduce tss_main
ambpdb elsize mdoutanalyzer new_crd_to_dyn residuegen tss_next
ante-MMPBSA.py espgen minab new_to_old_crd resp ucpp
antechamber ffgbsa mm_pbsa.pl nf-config respgen xparmed.py
atomtype fftw-wisdom mm_pbsa_nabnmode paramfit rism1d yaccIf you don’t see something like this, then check your AmberTools installation.
- 3a. Getting started
- 3b. Mutating the protein
- 3c. Solvating the protein
- 3d. Minimising the system
- 3e. Heating the system
- 3f. Equilibrating the system
- 3g. Running the simulation
- 3h. Comparing trajectories
- 3i. What next?