Targeted MD of Complex

Directory for Complex Setup

% mkdir tgtmd
% cp complex_setup/vm1_complex_target.prmtop tgtmd
% cp complex_setup/vm1_complex_min.inpcrd tgtmd
%

Download mdtgt.in

If you need these, download:
vm1_complex_target.prmtop
vm1_complex_min.inpcrd
vm1_complex_target.inpcrd

Try running the simulation with targeted md

inpcrd->refcrd tgtmd: regular vacuum md, backbone restrained
 &cntrl
        imin = 0, ntx = 1, nstlim = 5000, irest=0,
        dt = 0.002, ntc = 2, ntf = 2, tol = 0.000001,
        tempi = 100.0, temp0 = 300.0,
        scee = 1.2, cut = 10.0,
        ntpr = 50, ntwx = 50, ntwr = 500,
        ntb = 0, ntt = 1, tautp = 0.5, ntp = 0,
        igb = 1, nscm = 0, nmropt = 1, 
        ntr = 1, restraint_wt=0.02, 
        restraintmask=":TAZ | :40-51,73-85,96-113,136-147,207-220@CA",
        itgtmd = 1, tgtrmsd = 5.516, tgtmdfrc = 1.0,
        tgtrmsmask=":TAZ & @S1,C2,C3,N4",
 /
 &wt
        TYPE='TGTRMSD', istep1=1, istep2=1000,
        value1 = 1.000, value2 = 0.0,
 /
  &wt
        TYPE='TGTRMSD', istep1=1000, istep2=0,
        value1 = 0.0, value2 = 0.0,
 /
&wt
   type="END",
 /

You will probably want to run on a compute engine, preferable parallel, such as jonas.psc.edu to get a decent number of steps.

Now try modifying the force constants and find out what the effects of turning on and off ntr and itgtmd are. See if you can get the ligand docked. For each test, run a lot more steps and adjust your output parameters to suit the size of the run. q

Finally, try adding in QMMM for the ligand, with and without targeted MD. Once it is "docked", turn off all restraints and targeting and run with and without QMMM. Analyze results with the vmd and with analysis tools used in the earlier tutorials.

Amber9 on Jonas is in /usr/users/4/walkerr/amber9

QMMM documentation on Jonas is in /usr/users/4/walkerr/amber9/QMMM_DOCS

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