H i Justin, Thanks for your reply.
How to do that? On Fri, Sep 6, 2013 at 4:27 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 9/6/13 5:23 PM, Rama wrote: > >> 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)./ >> >> > Just like position restraints, distance restraints only work within a > [moleculetype]. Thus you're probably trying to restrain atoms between > [moleculetype] directives, which does not work. You could theoretically > make a merged [moleculetype] of whatever species need to be restrained, but > that may take a bit of effort depending on what is being restrained. > > -Justin > > > 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<http://gromacs.5086.x6.nabble.com/NMR-restrained-MD-tp5011025.html> >> Sent from the GROMACS Users Forum mailing list archive at Nabble.com. >> >> > -- > ==============================**==================== > > Justin A. Lemkul, Ph.D. > Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 601 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalemkul@outerbanks.umaryland.**edu <jalem...@outerbanks.umaryland.edu> | > (410) > 706-7441 > > ==============================**==================== > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > * Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<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? 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