Hello,
I am relatively new to using AMBER, specifically the QUICK module.
I am trying to study the reaction mechanism between a ligand and the residues in the active site of a protein of interest.
The QUICK input file I am using is as follows:
&cntrl
imin=0, nstlim=1000000, ! 2ns QM/MM simulation
dt=0.002, irest=1, ntx=7, ! 2 fs time step 1ns sim
tempi = 300.0, temp0 = 300.0,
ntt = 3, gamma_ln = 1.0,
ntb = 2, pres0 = 1.0, ntp = 1,
taup = 2.0,
ntf=2, ntc=2, ! Shake hydrogen atoms
ntpr = 1000, ntwx = 1000, ntwr = 1000
cut=8.0, ! 8 angstrom classical non-bond cut off
ifqnt=1 ! Switch on QM/MM coupled potential
/
&qmmm
qmmask='.4460, 4461, 4499, 4500, 7544, 7553', !
qm_theory='quick', ! Use the PM3 semi-empirical Hamiltonian
qmcut=8.0 ! Use 8 angstrom cut off for QM region
/
&quick
method = 'B3LYP',
basis = 'def2-svp',
/
My question is: How does SHAKE work in QM/MM simulation. Are the bonds between the atoms in the 'qmmask' included in the SHAKE protocol?
I have so far obtained a 100ps long QM/MM trajectory from the above simulation. Upon visualizing the trajectory, I see that the bond lengths between the atoms specified in the qmmask do not change over time. So I am bit confused as bond length fluctuations would be necessary for a reaction to occur.
Would really appreciate it if someone could recommend the appropriate SHAKE specification for QUICK simulations. Also any advice on the input file above is welcomed!
Best,
Ankita Dutta, PhD
Postdoctoral Fellow
Icahn School of Medicine at the Mount Sinai Hospital
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Received on Fri Oct 04 2024 - 09:30:02 PDT
