[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 10:15:30 CEST 2014


Updating…
I managed to solved the previous problem (i don’t know why, but the protein was outside the membrane, so probably i used a different .gro from my protein instead of the one i originally placed on the membrane) sorry about that.
In any case, i create a new system (using the same parameters), but know i got the next messages:

> There are 582 lipids in the membrane part that overlaps the protein.
> The area per lipid is 0.6669 nm^2.
> Maximum number of lipids that will be removed is 245.
>  
> 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 12.675
>  
> Embedding piece 0 with center of geometry: 7.000156 7.000503 9.994500
>  
> Will remove 0 Protein_chain_A molecules
> Will remove 116 POPC molecules
> Will remove 3014 SOL molecules
>  

And then it crashed:


> Back Off! I just backed up membrane-protein.top to ./#membrane-protein.top.1#
> Using 1 MPI thread
> starting mdrun 'Displayed atoms in water'
> 1000 steps,      2.0 ps.
>  
> Step 0, time 0 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> rms 16248058089.363861, max 2172644884480.000000 (between atoms 106595 and 106597)
> bonds that rotated more than 30 degrees:
>  atom 1 atom 2  angle  previous, current, constraint length
>   38468  38469   90.0    0.1111   0.1555      0.1111
>   38592  38593   32.9    0.1100   0.1100      0.1100
>   38748  38749   34.1    0.1111   0.1110      0.1111
>   38798  38799   98.6    0.1510  11.2774      0.1510
>   38798  38800   98.0    0.1510   2.3274      0.1510
>   38798  38801   95.7    0.1510   2.2978      0.1510
>   38798  38802   95.7    0.1510   2.2859      0.1510
>   38799  38803   93.1    0.1080  11.0727      0.1080
>   38799  38804   92.5    0.1080  11.0809      0.1080
>   38799  38814   89.7    0.1530  98.0231      0.1530
>   38800  38805  119.6    0.1080   0.2869      0.1080
>   38800  38806  116.1    0.1080   0.2850      0.1080
>   38800  38807  125.3    0.1080   0.2972      0.1080
>   38801  38808  114.8    0.1080   0.4416      0.1080
>   38801  38809  118.3    0.1080   0.4443      0.1080
>   38801  38810  122.3    0.1080   0.4394      0.1080
>   38802  38811  120.2    0.1080   0.4746      0.1080
>   38802  38812  116.6    0.1080   0.4701      0.1080
>   38802  38813  124.1    0.1080   0.4780      0.1080
>   38814  38815   90.1    0.1111  91.7679      0.1111
>   38814  38816   89.6    0.1111  90.6432      0.1111
>   38814  38820   90.4    0.1430 313.5823      0.1430
>   38817  38818   89.8    0.1480 417.9316      0.1480
>   38817  38819   89.8    0.1480 405.8298      0.1480
>   38817  38820   89.4    0.1600 236.5796      0.1600
>   38817  38821   94.4    0.1600  34.9461      0.1600
>   38821  38822   88.6    0.1430 412.7803      0.1430


   
 so what should i do? should i perform a minimisation of each systems (protein and solvated membrane) before i run this protocol?

Greetings,


--  
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


On Sunday, August 3, 2014 at 3:47 AM, Carlos Navarrro Retamal wrote:

> 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 (mailto:carlos.navarro87 at gmail.com) or cnavarro at utalca.cl (mailto:cnavarro at utalca.cl)
>  
> --
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