Hi, I'm doing NMR restrained MD simulation for protein-Bilayer system to satisfy NMR experimental data.
Without restraints there is no problem, but if I include distance restraints in topology file, getting fatal error: the lipid atom index # was not recognized by using this command: g_grompp -f md.mdp -c npt.gro -t npt.cpt -p topol.top -n index.ndx -o md.tpr -maxwarn 5 even in index file protein_DMPC atoms index is there continuously. Any one have suggestions to overcome this fatal error. Thanks / [ file beta_disres.itp, line 4 ]: Atom index (2679) in distance_restraints out of bounds (1-2513)./ md.mdp file: title = protein-bilayer complex define = -DDISRES ; NMR Distance restraints ; Run parameters integrator = md ; leap-frog integrator nsteps = 2500000 ; dt = 0.002 ; 2 fs ; Output control nstxout = 5000 ; save coordinates every 5 ps nstvout = 5000 ; save velocities every 5 ps nstxtcout = 5000 ; xtc compressed trajectory output every 5 ps nstenergy = 5000 ; save energies every 5 ps nstlog = 5000 ; update log file every 5 ps ; Bond parameters continuation = yes ; Restarting after NPT constraint_algorithm = lincs ; holonomic constraints constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Distance restraints parameters disre = simple ; simple (per-molecule) disre_fc = 1000 ; force constant for distance restraints ; Neighborsearching ns_type = grid ; search neighboring grid cels nstlist = 5 ; 10 fs rlist = 1.2 ; short-range neighborlist cutoff (in nm) rcoulomb = 1.2 ; short-range electrostatic cutoff (in nm) rvdw = 1.2 ; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling is on tcoupl = Nose-Hoover ; More accurate thermostat tc-grps = Protein non-protein non-protein ; three coupling groups - more accurate tau_t = 0.5 0.5 0.5 ; time constant, in ps ref_t = 303 303 303 ; reference temperature, one for each group, in K ; Pressure coupling is on pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT pcoupltype = semiisotropic ; uniform scaling of x-y box vectors, independent z tau_p = 2.0 ; time constant, in ps ref_p = 1.0 1.0 ; reference pressure, x-y, z (in bar) compressibility = 4.5e-5 4.5e-5 ; isothermal compressibility, bar^-1 ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr = EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = no ; Velocity generation is off ; COM motion removal ; These options remove motion of the protein/bilayer relative to the solvent/ions nstcomm = 1 comm-mode = Linear comm-grps = protein non-protein topology file: ; Include Position restraint file #ifdef POSRES #include "posre.itp" #endif ; Include Distance restraints file #ifdef DISRES #include "beta_disres.itp" #endif ; Strong position restraints for InflateGRO #ifdef STRONG_POSRES #include "strong_posre.itp" #endif ; Include DMPC topology #include "ramaLJ.ff/dmpcLJ.itp" ; Include water topology #include "ramaLJ.ff/spc.itp" #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcx fcy fcz 1 1 1000 1000 1000 #endif ; Include topology for ions #include "ramaLJ.ff/ions.itp" [ system ] ; Name Giving Russians Opium May Alter Current Situation in water [ molecules ] ; Compound #mols Protein 1 DMPC 125 SOL 8335 CL 8 -- View this message in context: http://gromacs.5086.x6.nabble.com/NMR-restrained-MD-tp5011025.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
