[gmx-users] NMR restrained MD
jalemkul at vt.edu
Fri Sep 6 23:37:34 CEST 2013
On 9/6/13 5:35 PM, Rama Krishna Koppisetti wrote:
> i Justin,
> Thanks for your reply.
> How to do that?
If .rtp entries exist for your lipid with the force field, it's simply a matter
of pdb2gmx -merge, choosing which chains should be written as a single
[moleculetype]. If the lipids are not described by .rtp entries, you either
have to write one or modify the topology by hand (ugh) or with some script.
> On Fri, Sep 6, 2013 at 4:27 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>> On 9/6/13 5:23 PM, Rama wrote:
>>> I'm doing NMR restrained MD simulation for protein-Bilayer system to
>>> NMR experimental data.
>>> Without restraints there is no problem, but if I include distance
>>> 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.
>> 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
>>> 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
>>> 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
>>> 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,
>>> ; 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
>>> nstcomm = 1
>>> comm-mode = Linear
>>> comm-grps = protein non-protein
>>> topology file:
>>> ; Include Position restraint file
>>> #ifdef POSRES
>>> #include "posre.itp"
>>> ; Include Distance restraints file
>>> #ifdef DISRES
>>> #include "beta_disres.itp"
>>> ; Strong position restraints for InflateGRO
>>> #ifdef STRONG_POSRES
>>> #include "strong_posre.itp"
>>> ; 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
>>> ; 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.**
>>> 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 at outerbanks.umaryland.**edu <jalemkul at outerbanks.umaryland.edu> | (410)
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Justin A. Lemkul, Ph.D.
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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