[gmx-users] Protein in GdmCl solution

Biswajit Gorai biswajit.ju at gmail.com
Mon Feb 18 12:29:41 CET 2013


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
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

[ 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.
Sorry for reposting. Thanking all.

Regards
Biswajit



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