[gmx-users] g_membed error - Trying to remove more lipid molecules than there are in the membrane
Carlos Navarrro Retamal
cnavarro at utalca.cl
Sun Aug 3 09:53:34 CEST 2014
Dear gromacs users,
I’m trying to embed a protein into a POPC bilayer (by using charmm27 as ff ). I was able to merged both macromolecules (including the surrounding water molecules) creating the respective top file.
When i created the .tpr (using the following command)
> grompp -f sample.mdp -c complex-solvated.gro -p membrane-protein.top -o sample.tpr
i noticed the next message:
> Velocities were taken from a Maxwell distribution at 300 K
> Analysing residue names:
> There are: 2344 Protein residues
> There are: 640 Other residues
> There are: 122500 Water residues
it is normal that the lipids are considered as ‘other residues’
Anyway, after that i ran g_memd as following:
> g_membed -f sample.tpr -p membrane-protein.top
And finally i ran mdrun as:
> mdrun -s sample.tpr -membed membed.dat -o traj.trr -c membedded.gro -e ener.edr -nt 1 -cpt -1 -mp membrane-protein.top
getting the following message:
>
> There are 42 lipids in the membrane part that overlaps the protein.
> The area per lipid is 117.8203 nm^2.
> Maximum number of lipids that will be removed is 0.
> Will resize the protein by a factor of 0.500 in the xy plane and 1.000 in the z direction.
> This resizing will be done with respect to the geometrical center of all protein atoms
> that span the membrane region, i.e. z between 7.314 and 7.712
>
> Embedding piece 0 with center of geometry: 3.000891 3.001642 7.513000
Finally i got the next error message:
> Fatal error:
> Trying to remove more lipid molecules than there are in the membrane
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
In any case, this is the .mdp file i’m using:
include =
define =
> > ; RUN CONTROL PARAMETERS
> > integrator = md
> > ; Start time and timestep in ps
> > tinit = 0
> > dt = 0.002
> > nsteps = 1000
> > init_step = 0
> > comm-mode = Linear
> > nstcomm = 1
> > comm-grps =
> >
> > ; ENERGY MINIMIZATION OPTIONS
> > ; Force tolerance and initial step-size
> > emtol = 2000
> > emstep = 0.01
> > ; Max number of iterations in relax_shells
> > niter = 20
> > ; Step size (ps^2) for minimization of flexible constraints
> > fcstep = 0
> > ; Frequency of steepest descents steps when doing CG
> > nstcgsteep = 1000
> > nbfgscorr = 10
> >
> > ; TEST PARTICLE INSERTION OPTIONS
> > rtpi = 0.05
> >
> > ; OUTPUT CONTROL OPTIONS
> > ; Output frequency for coords (x), velocities (v) and forces (f)
> > nstxout = 100000
> > nstvout = 100000
> > nstfout = 100000
> > ; Output frequency for energies to log file and energy file
> > nstlog = 100000
> > nstenergy = 50
> > ; Output frequency and precision for xtc file
> > nstxtcout = 50
> > xtc-precision =
> > ; This selects the subset of atoms for the xtc file. You can
> > ; select multiple groups. By default all atoms will be written.
> > xtc-grps =
> > ; Selection of energy groups
> > energygrps = Protein
> >
> > ; NEIGHBORSEARCHING PARAMETERS
> > ; nblist update frequency
> > nstlist = 10
> > ; ns algorithm (simple or grid)
> > ns-type = Grid
> > ; Periodic boundary conditions: xyz, no, xy
> > pbc = xyz
> > periodic_molecules = no
> > ; nblist cut-off
> > rlist = 1
> >
> > ; OPTIONS FOR ELECTROSTATICS AND VDW
> > ; Method for doing electrostatics
> > coulombtype = Cut-off
> > rcoulomb-switch = 0
> > rcoulomb = 1.4
> > ; Relative dielectric constant for the medium and the reaction field
> > epsilon_r = 1
> > epsilon_rf = 1
> > ; Method for doing Van der Waals
> > vdw-type = Cut-off
> > ; cut-off lengths
> > rvdw-switch = 0
> > rvdw = 1.4
> > ; Apply long range dispersion corrections for Energy and Pressure
> > DispCorr = No
> > ; Extension of the potential lookup tables beyond the cut-off
> > table-extension = 1
> > ; Seperate tables between energy group pairs
> > energygrp_table =
> > ; Spacing for the PME/PPPM FFT grid
> > fourierspacing = 0.12
> > ; FFT grid size, when a value is 0 fourierspacing will be used
> > fourier_nx = 0
> > fourier_ny = 0
> > fourier_nz = 0
> > ; EWALD/PME/PPPM parameters
> > pme_order = 4
> > ewald_rtol = 1e-05
> > ewald_geometry = 3d
> > epsilon_surface = 0
> > optimize_fft = no
> >
> > ; IMPLICIT SOLVENT ALGORITHM
> > implicit_solvent = No
> >
> > ; GENERALIZED BORN ELECTROSTATICS
> > ; Algorithm for calculating Born radii
> > gb_algorithm = Still
> > ; Frequency of calculating the Born radii inside rlist
> > nstgbradii = 1
> > ; Cutoff for Born radii calculation; the contribution from atoms
> > ; between rlist and rgbradii is updated every nstlist steps
> > rgbradii = 2
> > ; Dielectric coefficient of the implicit solvent
> > gb_epsilon_solvent = 80
> > ; Salt concentration in M for Generalized Born models
> > gb_saltconc = 0
> > ; Scaling factors used in the OBC GB model. Default values are OBC(II)
> > gb_obc_alpha = 1
> > gb_obc_beta = 0.8
> > gb_obc_gamma = 4.85
> > ; Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA
> > ; The default value (2.092) corresponds to 0.005 kcal/mol/Angstrom^2.
> > sa_surface_tension = 2.092
> >
> > ; OPTIONS FOR WEAK COUPLING ALGORITHMS
> > ; Temperature coupling
> > tcoupl = v-rescale
> > ; Groups to couple separately
> > tc-grps = Protein POPC SOL
> > ; Time constant (ps) and reference temperature (K)
> > tau-t = 0.1 0.1 0.1
> > ref-t = 300 300 300
> > ; Pressure coupling
> > Pcoupl = Berendsen
> > Pcoupltype = semiisotropic
> > ; Time constant (ps), compressibility (1/bar) and reference P (bar)
> > tau-p = 1 1
> > compressibility = 5.3e-05 5.3e-05
> > ref-p = 1.01325 1.01325
> > ; Scaling of reference coordinates, No, All or COM
> > refcoord_scaling = No
> > ; Random seed for Andersen thermostat
> > andersen_seed = 815131
> >
> > ; OPTIONS FOR QMMM calculations
> > QMMM = no
> > ; Groups treated Quantum Mechanically
> > QMMM-grps =
> > ; QM method
> > QMmethod =
> > ; QMMM scheme
> > QMMMscheme = normal
> > ; QM basisset
> > QMbasis =
> > ; QM charge
> > QMcharge =
> > ; QM multiplicity
> > QMmult =
> > ; Surface Hopping
> > SH =
> > ; CAS space options
> > CASorbitals =
> > CASelectrons =
> > SAon =
> > SAoff =
> > SAsteps =
> > ; Scale factor for MM charges
> > MMChargeScaleFactor = 1
> > ; Optimization of QM subsystem
> > bOPT =
> > bTS =
> >
> > ; SIMULATED ANNEALING
> > ; Type of annealing for each temperature group (no/single/periodic)
> > annealing =
> > ; Number of time points to use for specifying annealing in each group
> > annealing_npoints =
> > ; List of times at the annealing points for each group
> > annealing_time =
> > ; Temp. at each annealing point, for each group.
> > annealing_temp =
> >
> > ; GENERATE VELOCITIES FOR STARTUP RUN
> > gen-vel = yes
> > gen-temp = 300
> > gen-seed = 173529
> >
> > ; OPTIONS FOR BONDS
> > constraints = all-bonds
> > ; Type of constraint algorithm
> > constraint-algorithm = Lincs
> > ; Do not constrain the start configuration
> > continuation = no
> > ; Use successive overrelaxation to reduce the number of shake iterations
> > Shake-SOR = no
> > ; Relative tolerance of shake
> > shake-tol = 0.0001
> > ; Highest order in the expansion of the constraint coupling matrix
> > lincs-order = 4
> > ; Number of iterations in the final step of LINCS. 1 is fine for
> > ; normal simulations, but use 2 to conserve energy in NVE runs.
> > ; For energy minimization with constraints it should be 4 to 8.
> > lincs-iter = 1
> > ; Lincs will write a warning to the stderr if in one step a bond
> > ; rotates over more degrees than
> > lincs-warnangle = 30
> > ; Convert harmonic bonds to morse potentials
> > morse = no
> >
> > ; ENERGY GROUP EXCLUSIONS
> > ; Pairs of energy groups for which all non-bonded interactions are excluded
> > energygrp_excl = Protein Protein
> >
> > ; WALLS
> > ; Number of walls, type, atom types, densities and box-z scale factor for Ewald
> > nwall = 0
> > wall_type = 9-3
> > wall_r_linpot = -1
> > wall_atomtype =
> > wall_density =
> > wall_ewald_zfac = 3
> >
> > ; COM PULLING
> > ; Pull type: no, umbrella, constraint or constant_force
> > pull = no
> >
> > ; NMR refinement stuff
> > ; Distance restraints type: No, Simple or Ensemble
> > disre = No
> > ; Force weighting of pairs in one distance restraint: Conservative or Equal
> > disre-weighting = Conservative
> > ; Use sqrt of the time averaged times the instantaneous violation
> > disre-mixed = no
> > disre-fc = 1000
> > disre-tau = 0
> > ; Output frequency for pair distances to energy file
> > nstdisreout = 100
> > ; Orientation restraints: No or Yes
> > orire = no
> > ; Orientation restraints force constant and tau for time averaging
> > orire-fc = 0
> > orire-tau = 0
> > orire-fitgrp =
> > ; Output frequency for trace(SD) and S to energy file
> > nstorireout = 100
> > ; Dihedral angle restraints: No or Yes
> > dihre = no
> > dihre-fc = 1000
> >
> > ; Free energy control stuff
> > free-energy = no
> > init-lambda = 0
> > delta-lambda = 0.001
> > sc-alpha = 0
> > sc-power = 0
> > sc-sigma = 0.3
> > couple-moltype =
> > couple-lambda0 = vdw-q
> > couple-lambda1 = vdw-q
> > couple-intramol = no
> >
> > ; Non-equilibrium MD stuff
> > acc-grps =
> > accelerate =
> > freezegrps = Protein
> > freezedim =Y Y Y
> > cos-acceleration =
> > deform =
> >
> > ; Electric fields
> > ; Format is number of terms (int) and for all terms an amplitude (real)
> > ; and a phase angle (real)
> > E-x =
> > E-xt =
> > E-y =
> > E-yt =
> > E-z =
> > E-zt =
> >
> > ; User defined thingies
> > user1-grps =
> > user2-grps =
> > userint1 = 0
> > userint2 = 0
> > userint3 = 0
> > userint4 = 0
> > userreal1 = 0
> > userreal2 = 0
> > userreal3 = 0
> > userreal4 = 0
> >
>
>
is the same one that the authors used as a example on here: http://wwwuser.gwdg.de/~ggroenh/membed.html
What may be happening?
By the way, i’m using the 4.6.3 version of gromacs.
Please let me know if you need anything else.
Have a nice day,
--
Carlos Navarro Retamal
Bioinformatic engineer
Ph.D(c) in Applied Science, Universidad de Talca, Chile
Center of Bioinformatics and Molecular Simulations (CBSM)
Universidad de Talca
2 Norte 685, Casilla 721, Talca - Chile
Teléfono: 56-71-201 798,
Fax: 56-71-201 561
Email: carlos.navarro87 at gmail.com or cnavarro at utalca.cl
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