On 3/8/17 8:11 PM, Amir Zeb wrote:
Hello gmx users, I want to calculate binding energy for a protein-ligand complex. Obviously, this is the very first time, I'm handling umbrella sampling, so I faced the following error. WARNING 2 [file pull.mdp, line 65]: Unknown left-hand 'pull_ncoords' in parameter file WARNING 3 [file pull.mdp, line 65]: Unknown left-hand 'pull_group1_name' in parameter file WARNING 4 [file pull.mdp, line 65]: Unknown left-hand 'pull_group2_name' in parameter file WARNING 5 [file pull.mdp, line 65]: Unknown left-hand 'pull_coord1_type' in parameter file WARNING 6 [file pull.mdp, line 65]: Unknown left-hand 'pull_coord1_geometry' in parameter file WARNING 7 [file pull.mdp, line 65]: Unknown left-hand 'pull_coord1_groups' in parameter file WARNING 8 [file pull.mdp, line 65]: Unknown left-hand 'pull_coord1_dim' in parameter file WARNING 9 [file pull.mdp, line 65]: Unknown left-hand 'pull_coord1_rate' in parameter file WARNING 10 [file pull.mdp, line 65]: Unknown left-hand 'pull_coord1_k' in parameter file WARNING 11 [file pull.mdp, line 65]: Unknown left-hand 'pull_coord1_start' in parameter file There was 1 note There were 11 warnings *The pull.mdp file is this one:* title = Umbrella pulling simulation define = -DPOSRES_NAD ; Run parameters integrator = md dt = 0.002 tinit = 0 nsteps = 250000 ; 500 ps nstcomm = 10 ; Output parameters nstxout = 5000 ; every 10 ps nstvout = 5000 nstfout = 500 nstxtcout = 500 ; every 1 ps nstenergy = 500 ; Bond parameters constraint_algorithm = lincs constraints = all-bonds continuation = yes ; continuing from NPT ; Single-range cutoff scheme nstlist = 5 ns_type = grid rlist = 1.4 rcoulomb = 1.4 rvdw = 1.4 ; PME electrostatics parameters coulombtype = PME fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft = yes ; Berendsen temperature coupling is on in two groups Tcoupl = Nose-Hoover tc_grps = Protein NAD tau_t = 0.5 0.5 ref_t = 310 310 ; Pressure coupling is on Pcoupl = Parrinello-Rahman pcoupltype = isotropic tau_p = 1.0 compressibility = 4.5e-5 ref_p = 1.0 refcoord_scaling = com ; Generate velocities is off gen_vel = no ; Periodic boundary conditions are on in all directions pbc = xyz ; Long-range dispersion correction DispCorr = EnerPres ; Pull code pull = yes pull_ngroups = 2 pull_ncoords = 1 pull_group1_name = NAD pull_group2_name = Protein pull_coord1_type = umbrella ; harmonic biasing force pull_coord1_geometry = distance ; simple distance increase pull_coord1_groups = 1 2 pull_coord1_dim = N N Y pull_coord1_rate = 0.01 ; 0.01 nm per ps = 10 nm per ns pull_coord1_k = 1000 ; kJ mol^-1 nm^-2 pull_coord1_start = yes ; define initial COM distance > 0 Please let me know where I'm making the mistake.
You're using an outdated version of GROMACS that does not recognize the new syntax that was introduced in version 5.1.
-Justin -- ================================================== Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul ================================================== -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
