Hello all Earlier also I posted a query regarding FEP for protein ligand complex, but I dint not help much. Again I would like to share detailed information regarding the protocol I am following for calculation the binding free energy between protein and ligand using FEP(free energy perturbation) method. Please correct me if I am wrong anywhere....as the values of *dVpot/dlambda dEkin/dlambda dG/dl constr *are continuously coming zero(0).
I followed the gromacs tutorial of protien-ligand complex ( http://cinjweb.umdnj.edu/~kerrigje/pdf_files/trp_drug_tutor.pdf) for preparing the coordinate and topology file for the whole system. For Free energy Calculation I followed the tutorial ( http://www.dillgroup.ucsf.edu/group/wiki/index.php/Free_Energy:_Tutorial) for lambda value ranging from zero(0) to 1 and setup 11 independent job for each lambda value for 5 ns. But the* dVpot/dlambda dEkin/dlambda dG/dl constr* values in the *.log are continuously coming zero. Any help will be highly appreciated. For convenience I am also pasting my pro_constV.mdp (please let me know if any parameter is wrong of missing...which is leading to such problem) ; RUN CONTROL PARAMETERS = integrator = md ; start time and timestep in ps = tinit = 0 dt = 0.002 nsteps = 5000000 ; number of steps for center of mass motion removal = nstcomm = 100 ; OUTPUT CONTROL OPTIONS = ; Output frequency for coords (x), velocities (v) and forces (f) = nstxout = 50000 nstvout = 50000 nstfout = 0 ; Output frequency for energies to log file and energy file = nstlog = 500 nstenergy = 500 energygrps = protein non-protein ; Output frequency and precision for xtc file = nstxtcout = 5000 xtc-precision = 1000 ; This selects the subset of atoms for the xtc file. You can = ; select multiple groups. By default all atoms will be written. = ;xtc_grps = ; NEIGHBORSEARCHING PARAMETERS = ; nblist update frequency = nstlist = 10 ; ns algorithm (simple or grid) = ns_type = grid ; Periodic boundary conditions: xyz or none = ;pbc = xyz ; nblist cut-off = rlist = 1.0 ;domain-decomposition = no ; OPTIONS FOR ELECTROSTATICS AND VDW = ; Method for doing electrostatics = coulombtype = pme ;rcoulomb-switch = 0 rcoulomb = 1.0 ; Dielectric constant (DC) for cut-off or DC of reaction field = epsilon-r = 1 ; Method for doing Van der Waals = vdw-type = cut-off ; cut-off lengths = ;rvdw-switch = 0.8 rvdw = 1.4 ; Apply long range dispersion corrections for Energy and Pressure = DispCorr = EnerPres ; Spacing for the PME/PPPM FFT grid = fourierspacing = 0.1 ; FFT grid size, when a value is 0 fourierspacing will be used = fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 ; EWALD/PME/PPPM parameters = pme_order = 6 ewald_rtol = 1e-06 epsilon_surface = 0 optimize_fft = yes ;restraints ;dihre=yes ;dihre-fc=1 ;nstdihreout=1000 ;disre=simple ;disre_fc=1 ; Berendsen temperature coupling is on Tcoupl = berendsen tau_t = 0.1 0.1 tc_grps = protein non-protein ref_t = 300 300 ;OPTIONS FOR PRESSURE COUPLING Pcoupl = berendsen tau_p = 0.5 compressibility = 4.5e-05 ref_p = 1.0 ; Free energy control stuff free_energy = yes init_lambda = 0.0 delta_lambda = 0 sc_alpha = 0.5 sc-power = 1.0 sc-sigma = 0.3 ; GENERATE VELOCITIES FOR STARTUP RUN = gen_vel = yes gen_temp = 300 gen_seed = 173529 ; OPTIONS FOR BONDS = constraints = hbonds ; Type of constraint algorithm = constraint-algorithm = Lincs ; Do not constrain the start configuration = unconstrained-start = no ; Relative tolerance of shake = shake-tol = 0.0001 ; Highest order in the expansion of the constraint coupling matrix = lincs-order = 12 ; Lincs will write a warning to the stderr if in one step a bond = ; rotates over more degrees than = lincs-warnangle = 30 -- Best Regards SUNITA GUPTA Member Research Team LeadInvent Technology TBIU, IIT Delhi, India Email- sun...@leadinvent.com Ph- +9111 26581524 (Ex-6)
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