[gmx-users] Protein in GdmCl solution
Justin Lemkul
jalemkul at vt.edu
Mon Feb 18 14:25:17 CET 2013
On 2/18/13 6:29 AM, Biswajit Gorai wrote:
> Dear GMX Users,
>
> Past few months I am struggling to unfold my protein using Guanidinium
> (GDM) solutions (3,4,5,6 M).
> I already did temperature (upto 498 K) induced unfolding, and able to get
> expected results in 60 ns.
> For GDM (6M), I did simulation upto 120 ns but my target protein is intact
> (rmsd ~2 A).
> It seems chemical denaturants take comparatively more time, so I increased
> the temperature to 423 K to speed-up the process.
> Now m worried, even after 80 ns simulation in 6M GDM and 423 K, target not
> showing any remarkable structural change.
> Also I tried by changing the temperature coupling groups, such as:
> a) Protein Non-Protein
I would stick with (a) here, as there is no definitive reason to change it.
> b) System
> c) Protein+GDM Water+Ions
>
> But all seems waste.
>
> *Brief workflow of my work is:*
>
> a) Build GDM topology from AmberTools and partial charge was imported from *J.
> Phys. Chem. B 2011, 115, 12521–1252.
>
> gdm.itp::
>
> [ moleculetype ]
> ; Name nrexcl
> GDM 3
>
> [ atoms ]
> ; nr type resnr residue atom cgnr charge mass
> typeB ch
> argeB
> 1 CA 1 GDM C1 1 0.99610 12.000000
> 2 N2 1 GDM N1 2 -0.94930 14.000000
> 3 H 1 GDM H1 3 0.47530 1.000000
> 4 H 1 GDM H2 4 0.47530 1.000000
> 5 N2 1 GDM N2 5 -0.94930 14.000000
> 6 H 1 GDM H3 6 0.47530 1.000000
> 7 H 1 GDM H4 7 0.47530 1.000000
> 8 N2 1 GDM N3 8 -0.94930 14.000000
> 9 H 1 GDM H5 9 0.47530 1.000000
> 10 H 1 GDM H6 10 0.47530 1.000000
>
The masses on all your atoms are incorrect here. Check atomtypes.atp for your
force field for correct values.
> [ bonds ]
> ; ai aj funct r k
> 2 3 1 1.0140e-01 3.3572e+05
> 2 4 1 1.0140e-01 3.3572e+05
> 5 6 1 1.0140e-01 3.3572e+05
> 5 7 1 1.0140e-01 3.3572e+05
> 8 9 1 1.0140e-01 3.3572e+05
> 8 10 1 1.0140e-01 3.3572e+05
> 1 2 1 1.3390e-01 4.0819e+05
> 1 5 1 1.3390e-01 4.0819e+05
> 1 8 1 1.3390e-01 4.0819e+05
>
> [ pairs ]
> ; ai aj funct
> 2 6 1
> 2 7 1
> 2 9 1
> 2 10 1
> 5 3 1
> 8 3 1
> 5 4 1
> 8 4 1
> 5 9 1
> 5 10 1
> 8 6 1
> 8 7 1
>
> [ angles ]
> ; ai aj ak funct theta cth
> 1 2 3 1 1.2124e+02 4.0827e+02
> 1 2 4 1 1.2124e+02 4.0827e+02
> 1 5 6 1 1.2124e+02 4.0827e+02
> 1 5 7 1 1.2124e+02 4.0827e+02
> 1 8 9 1 1.2124e+02 4.0827e+02
> 1 8 10 1 1.2124e+02 4.0827e+02
> 3 2 4 1 1.1485e+02 3.3514e+02
> 6 5 7 1 1.1485e+02 3.3514e+02
> 9 8 10 1 1.1485e+02 3.3514e+02
> 2 1 5 1 1.2017e+02 6.1061e+02
> 2 1 8 1 1.2017e+02 6.1061e+02
> 5 1 8 1 1.2017e+02 6.1061e+02
>
> [ dihedrals ]
> ;i j k l func C0 ... C5
> 2 1 5 6 3 5.64840 0.00000 -5.64840
> 0.00000
> 0.00000 0.00000 ;
> 2 1 5 7 3 5.64840 0.00000 -5.64840
> 0.00000
> 0.00000 0.00000 ;
> 2 1 8 9 3 5.64840 0.00000 -5.64840
> 0.00000
> 0.00000 0.00000 ;
> 2 1 8 10 3 5.64840 0.00000 -5.64840
> 0.00000
> 0.00000 0.00000 ;
> 5 1 2 3 3 5.64840 0.00000 -5.64840
> 0.00000
> 0.00000 0.00000 ;
> 8 1 2 3 3 5.64840 0.00000 -5.64840
> 0.00000
> 0.00000 0.00000 ;
> 5 1 2 4 3 5.64840 0.00000 -5.64840
> 0.00000
> 0.00000 0.00000 ;
> 8 1 2 4 3 5.64840 0.00000 -5.64840
> 0.00000
> 0.00000 0.00000 ;
> 5 1 8 9 3 5.64840 0.00000 -5.64840
> 0.00000
> 0.00000 0.00000 ;
> 5 1 8 10 3 5.64840 0.00000 -5.64840
> 0.00000
> 0.00000 0.00000 ;
> 8 1 5 6 3 5.64840 0.00000 -5.64840
> 0.00000
> 0.00000 0.00000 ;
> 8 1 5 7 3 5.64840 0.00000 -5.64840
> 0.00000
> 0.00000 0.00000 ;
> 1 3 2 4 3 9.20480 0.00000 -9.20480
> 0.00000
> 0.00000 0.00000 ;
> 1 6 5 7 3 9.20480 0.00000 -9.20480
> 0.00000
> 0.00000 0.00000 ;
> 1 9 8 10 3 9.20480 0.00000 -9.20480
> 0.00000
> 0.00000 0.00000 ;
> 8 1 5 2 3 9.20480 0.00000 -9.20480
> 0.00000
> 0.00000 0.00000 ;
>
>
> *b) Build small equilibrated (NVT at 310 K) boxes at 3, 4, 5, 6 M of GDM+
> ion.
> c) Protein in GDM
> i) Solvate the protein in 6M GDM
> ii) Add CL to neutralize the system
> iii) Minimize using SD followed by CG.
> iv) NVT (2 ns) and NPT (5 ns) equilibration
> v) Finally production run.
>
> *md.mdp::*
>
> *title = Gdm-Amber-CTX-6M
> ; Run parameters
> integrator = sd
> nsteps = 20000000
> dt = 0.002
> ; Output control
> nstxout = 5000
> nstvout = 5000
> nstxtcout = 5000
> nstenergy = 5000
> nstlog = 5000
> ; Bond parameters
> continuation = yes
> constraint_algorithm = lincs
> constraints = all-bonds
> lincs_iter = 1
> lincs_order = 4
> ; Neighborsearching
> ns_type = grid
> nstlist = 5
> rlist = 1.0
> rcoulomb = 1.0
> rvdw = 1.0
> ; Electrostatics
> coulombtype = PME
> pme_order = 4
> fourierspacing = 0.16
> ; Temperature coupling is on
> tcoupl = V-rescale
> tc-grps = protein_gdm Water_and_ions ; Protein Non-Protein ;
> System (also tried)
> urate
> tau_t = 0.1 0.1
> ref_t = 423 423
> ; Pressure coupling is on
> pcoupl = Parrinello-Rahman
> pcoupltype = isotropic
> tau_p = 5.0
> ref_p = 1.0
> compressibility = 4.5e-5
> ; Periodic boundary conditions
> pbc = xyz
> ; Dispersion correction
> DispCorr = EnerPres
> ; Velocity generation
> gen_vel = no *
>
>
> I am using AMBER99SB-ILDN and TIP3P in GROMACS 4.5.4v. I really need the
> valuable sugestions.
What does your assessment of the literature tell you? Denaturation simulations
have been done before with a variety of chemicals like urea and SDS. How long
did they take and what were the simulation conditions? Is your protein
comparable in size to others that have been assessed before, or is it much
larger (thus implying it would take longer)? What makes you think that chemical
denaturation would be observed on the time scale of tens of ns, when in reality
it may take far longer?
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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