[gmx-users] NMR restrained MD
Rama Krishna Koppisetti
ramkishna72 at gmail.com
Mon Sep 9 23:37:00 CEST 2013
Hi Justin,
I merge two molecules as a single molecule type. Now I'm trying to do
energy minimization of the system, getting errors like
Fatal error: [file topol.top, line 55130]:
No default Proper Dih. types
Any idea for this type of errors.
Thanks
--Rama
On Mon, Sep 9, 2013 at 1:57 PM, Rama Krishna Koppisetti <
ramkishna72 at gmail.com> wrote:
> 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
>>>>>
>>>>> ==============================****====================
>>>>>
>>>>>
>>>>> --
>>>>> gmx-users mailing list gmx-users at gromacs.org
>>>>> http://lists.gromacs.org/****mailman/listinfo/gmx-users<http://lists.gromacs.org/**mailman/listinfo/gmx-users>
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>>>>> >
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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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>>
>>
>
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