[gmx-users] NMR restrained MD

Rama Krishna Koppisetti ramkishna72 at gmail.com
Mon Sep 9 20:49:29 CEST 2013


Hi Justin ,

I prepared .rtp files for lipid. what is the exact command  to merge two
chains in gromacs.




On Fri, Sep 6, 2013 at 4:37 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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<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 <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 <jalemkul at outerbanks.umaryland.edu> | (410)
> 706-7441
>
> ==============================**====================
> --
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