[gmx-users] NMR restrained MD
Justin Lemkul
jalemkul at vt.edu
Fri Sep 6 23:30:33 CEST 2013
On 9/6/13 5:27 PM, Rama Krishna Koppisetti wrote:
> Sorry ..,here are my distance restraints file:
>
Without context as to what these numbers are, there's little useful information
here. I suspect you're trying to implement restraints between protein and lipid
atoms, which will not work for reasons described in my last mail.
-Justin
> [ 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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--
==================================================
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 at outerbanks.umaryland.edu | (410) 706-7441
==================================================
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