[gmx-users] NMR restrained MD
Rama Krishna Koppisetti
ramkishna72 at gmail.com
Fri Sep 6 23:27:46 CEST 2013
Sorry ..,here are my distance restraints file:
[ distance_restraints ]
; ai aj type index type' low
up1 up2 fac
301 2679 1 0 1 0.0
1.6214 2.211 1.0
301 2696 1 0 1 0.0
1.6214 2.211 1.0
301 3415 1 0 1 0.0
1.6214 2.211 1.0
301 3432 1 0 1 0.0
1.6214 2.211 1.0
301 6635 1 0 1 0.0
1.6214 2.211 1.0
301 6652 1 0 1 0.0
1.6214 2.211 1.0
301 7187 1 0 1 0.0
1.6214 2.211 1.0
301 7204 1 0 1 0.0
1.6214 2.211 1.0
301 7279 1 0 1 0.0
1.6214 2.211 1.0
301 7296 1 0 1 0.0
1.6214 2.211 1.0
301 7371 1 0 1 0.0
1.6214 2.211 1.0
301 7388 1 0 1 0.0
1.6214 2.211 1.0
301 7923 1 0 1 0.0
1.6214 2.211 1.0
301 7940 1 0 1 0.0
1.6214 2.211 1.0
301 8199 1 0 1 0.0
1.6214 2.211 1.0
301 8216 1 0 1 0.0
1.6214 2.211 1.0
344 2679 1 1 1 0.0
1.5763 2.1495 1.0
344 2696 1 1 1 0.0
1.5763 2.1495 1.0
344 3415 1 1 1 0.0
1.5763 2.1495 1.0
344 3432 1 1 1 0.0
1.5763 2.1495 1.0
344 6635 1 1 1 0.0
1.5763 2.1495 1.0
344 6652 1 1 1 0.0
1.5763 2.1495 1.0
344 7187 1 1 1 0.0
1.5763 2.1495 1.0
344 7204 1 1 1 0.0
1.5763 2.1495 1.0
344 7279 1 1 1 0.0
1.5763 2.1495 1.0
344 7296 1 1 1 0.0
1.5763 2.1495 1.0
344 7371 1 1 1 0.0
1.5763 2.1495 1.0
344 7388 1 1 1 0.0
1.5763 2.1495 1.0
344 7923 1 1 1 0.0
1.5763 2.1495 1.0
344 7940 1 1 1 0.0
1.5763 2.1495 1.0
344 8199 1 1 1 0.0
1.5763 2.1495 1.0
344 8216 1 1 1 0.0
1.5763 2.1495 1.0
889 2679 1 2 1 0.0
1.8304 2.496 1.0
889 2696 1 2 1 0.0
1.8304 2.496 1.0
889 3415 1 2 1 0.0
1.8304 2.496 1.0
889 3432 1 2 1 0.0
1.8304 2.496 1.0
889 6635 1 2 1 0.0
1.8304 2.496 1.0
889 6652 1 2 1 0.0
1.8304 2.496 1.0
889 7187 1 2 1 0.0
1.8304 2.496 1.0
889 7204 1 2 1 0.0
1.8304 2.496 1.0
889 7279 1 2 1 0.0
1.8304 2.496 1.0
889 7296 1 2 1 0.0
1.8304 2.496 1.0
889 7371 1 2 1 0.0
1.8304 2.496 1.0
889 7388 1 2 1 0.0
1.8304 2.496 1.0
889 7923 1 2 1 0.0
1.8304 2.496 1.0
889 7940 1 2 1 0.0
1.8304 2.496 1.0
889 8199 1 2 1 0.0
1.8304 2.496 1.0
889 8216 1 2 1 0.0
1.8304 2.496 1.0
922 2679 1 3 1 0.0
1.5433 2.1045 1.0
922 2696 1 3 1 0.0
1.5433 2.1045 1.0
922 3415 1 3 1 0.0
1.5433 2.1045 1.0
922 3432 1 3 1 0.0
1.5433 2.1045 1.0
922 6635 1 3 1 0.0
1.5433 2.1045 1.0
922 6652 1 3 1 0.0
1.5433 2.1045 1.0
922 7187 1 3 1 0.0
1.5433 2.1045 1.0
922 7204 1 3 1 0.0
1.5433 2.1045 1.0
922 7279 1 3 1 0.0
1.5433 2.1045 1.0
922 7296 1 3 1 0.0
1.5433 2.1045 1.0
922 7371 1 3 1 0.0
1.5433 2.1045 1.0
922 7388 1 3 1 0.0
1.5433 2.1045 1.0
922 7923 1 3 1 0.0
1.5433 2.1045 1.0
922 7940 1 3 1 0.0
1.5433 2.1045 1.0
922 8199 1 3 1 0.0
1.5433 2.1045 1.0
922 8216 1 3 1 0.0
1.5433 2.1045 1.0
1113 2679 1 4 1 0.0
1.5906 2.169 1.0
1113 2696 1 4 1 0.0
1.5906 2.169 1.0
1113 3415 1 4 1 0.0
1.5906 2.169 1.0
1113 3432 1 4 1 0.0
1.5906 2.169 1.0
1113 6635 1 4 1 0.0
1.5906 2.169 1.0
1113 6652 1 4 1 0.0
1.5906 2.169 1.0
1113 7187 1 4 1 0.0
1.5906 2.169 1.0
1113 7204 1 4 1 0.0
1.5906 2.169 1.0
1113 7279 1 4 1 0.0
1.5906 2.169 1.0
1113 7296 1 4 1 0.0
1.5906 2.169 1.0
1113 7371 1 4 1 0.0
1.5906 2.169 1.0
1113 7388 1 4 1 0.0
1.5906 2.169 1.0
1113 7923 1 4 1 0.0
1.5906 2.169 1.0
1113 7940 1 4 1 0.0
1.5906 2.169 1.0
1113 8199 1 4 1 0.0
1.5906 2.169 1.0
1113 8216 1 4 1 0.0
1.5906 2.169 1.0
1123 2679 1 5 1 0.0
1.7985 2.4525 1.0
1123 2696 1 5 1 0.0
1.7985 2.4525 1.0
1123 3415 1 5 1 0.0
1.7985 2.4525 1.0
1123 3432 1 5 1 0.0
1.7985 2.4525 1.0
1123 6635 1 5 1 0.0
1.7985 2.4525 1.0
1123 6652 1 5 1 0.0
1.7985 2.4525 1.0
1123 7187 1 5 1 0.0
1.7985 2.4525 1.0
1123 7204 1 5 1 0.0
1.7985 2.4525 1.0
1123 7279 1 5 1 0.0
1.7985 2.4525 1.0
1123 7296 1 5 1 0.0
1.7985 2.4525 1.0
1123 7371 1 5 1 0.0
1.7985 2.4525 1.0
1123 7388 1 5 1 0.0
1.7985 2.4525 1.0
1123 7923 1 5 1 0.0
1.7985 2.4525 1.0
1123 7940 1 5 1 0.0
1.7985 2.4525 1.0
1123 8199 1 5 1 0.0
1.7985 2.4525 1.0
1123 8216 1 5 1 0.0
1.7985 2.4525 1.0
1148 2679 1 6 1 0.0
1.5169 2.0685 1.0
1148 2696 1 6 1 0.0
1.5169 2.0685 1.0
1148 3415 1 6 1 0.0
1.5169 2.0685 1.0
1148 3432 1 6 1 0.0
1.5169 2.0685 1.0
1148 6635 1 6 1 0.0
1.5169 2.0685 1.0
1148 6652 1 6 1 0.0
1.5169 2.0685 1.0
1148 7187 1 6 1 0.0
1.5169 2.0685 1.0
1148 7204 1 6 1 0.0
1.5169 2.0685 1.0
1148 7279 1 6 1 0.0
1.5169 2.0685 1.0
1148 7296 1 6 1 0.0
1.5169 2.0685 1.0
1148 7371 1 6 1 0.0
1.5169 2.0685 1.0
1148 7388 1 6 1 0.0
1.5169 2.0685 1.0
1148 7923 1 6 1 0.0
1.5169 2.0685 1.0
1148 7940 1 6 1 0.0
1.5169 2.0685 1.0
1148 8199 1 6 1 0.0
1.5169 2.0685 1.0
1148 8216 1 6 1 0.0
1.5169 2.0685 1.0
1418 2679 1 7 1 0.0
1.562 2.130 1.0
1418 2696 1 7 1 0.0
1.562 2.130 1.0
1418 3415 1 7 1 0.0
1.562 2.130 1.0
1418 3432 1 7 1 0.0
1.562 2.130 1.0
1418 6635 1 7 1 0.0
1.562 2.130 1.0
1418 6652 1 7 1 0.0
1.562 2.130 1.0
1418 7187 1 7 1 0.0
1.562 2.130 1.0
1418 7204 1 7 1 0.0
1.562 2.130 1.0
1418 7279 1 7 1 0.0
1.562 2.130 1.0
1418 7296 1 7 1 0.0
1.562 2.130 1.0
1418 7371 1 7 1 0.0
1.562 2.130 1.0
1418 7388 1 7 1 0.0
1.562 2.130 1.0
1418 7923 1 7 1 0.0
1.562 2.130 1.0
1418 7940 1 7 1 0.0
1.562 2.130 1.0
1418 8199 1 7 1 0.0
1.562 2.130 1.0
1418 8216 1 7 1 0.0
1.562 2.130 1.0
1425 2679 1 8 1 0.0
1.5246 2.079 1.0
1425 2696 1 8 1 0.0
1.5246 2.079 1.0
1425 3415 1 8 1 0.0
1.5246 2.079 1.0
1425 3432 1 8 1 0.0
1.5246 2.079 1.0
1425 6635 1 8 1 0.0
1.5246 2.079 1.0
1425 6652 1 8 1 0.0
1.5246 2.079 1.0
1425 7187 1 8 1 0.0
1.5246 2.079 1.0
1425 7204 1 8 1 0.0
1.5246 2.079 1.0
1425 7279 1 8 1 0.0
1.5246 2.079 1.0
1425 7296 1 8 1 0.0
1.5246 2.079 1.0
1425 7371 1 8 1 0.0
1.5246 2.079 1.0
1425 7388 1 8 1 0.0
1.5246 2.079 1.0
1425 7923 1 8 1 0.0
1.5246 2.079 1.0
1425 7940 1 8 1 0.0
1.5246 2.079 1.0
1425 8199 1 8 1 0.0
1.5246 2.079 1.0
1425 8216 1 8 1 0.0
1.5246 2.079 1.0
On Fri, Sep 6, 2013 at 4:23 PM, Rama <ramkishna72 at gmail.com> 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)./
>
> 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.
> --
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