[gmx-users] NMR restrained MD
Justin Lemkul
jalemkul at vt.edu
Fri Sep 6 23:37:34 CEST 2013
On 9/6/13 5:35 PM, Rama Krishna Koppisetti wrote:
> H
> 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.
-Justin
>
>
> 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:
>>
>>> 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 at outerbanks.umaryland.**edu <jalemkul at outerbanks.umaryland.edu> | (410)
>> 706-7441
>>
>> ==============================**====================
>>
>> --
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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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