[gmx-users] NMR restrained MD
Rama Krishna Koppisetti
ramkishna72 at gmail.com
Mon Sep 9 20:57:24 CEST 2013
Ok..I got it
Thanks Justin...
--Rama
On Mon, Sep 9, 2013 at 1:49 PM, Rama Krishna Koppisetti <
ramkishna72 at gmail.com> wrote:
>
> 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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