Hi,

I am running APBS on a mumber of transmembrane channel proteins, but for 2 proteins the program stops. In the first case, I get the error:

CALCULATION #1: MULTIGRID
  Setting up problem...
  Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
VASSERT: ASSERTION FAILURE!  filename vmem.c, line 245, (ram != ((void *)0))
Abort

In the second case, the program is just killed without explanations:

----------------------------------------
CALCULATION #1: MULTIGRID
  Setting up problem...
  Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
  Debye length:  9.58919 A
  Current memory usage:  -1552.924 MB total, 2001.830 MB high water
  Using cubic spline charge discretization.
  Grid dimensions: 257 x 225 x 193
  Grid spacings: 0.823 x 0.706 x 0.817
  Grid lengths: 210.810 x 158.200 x 156.822
  Grid center: (0.723, -1.197, -0.387)
  Multigrid levels: 4
  Molecule ID: 1
  Linearized traditional PBE
  Single Debye-Huckel sphere boundary conditions
  4 ion species (0.100 M ionic strength):
    2.000 A-radius, 1.000 e-charge, 0.100 M concentration
    2.000 A-radius, -1.000 e-charge, 0.100 M concentration
    2.000 A-radius, 2.000 e-charge, 0.000 M concentration
    2.000 A-radius, -2.000 e-charge, 0.000 M concentration
  Solute dielectric: 4.000
  Solvent dielectric: 78.000
  Using "molecular" surface definition;harmonic average smoothing
  Solvent probe radius: 1.400 A
  Temperature:  298.150 K
  Solving PDE (see io.mc* for details)...
Killed

In this case, the last lines of the io.mc files are:

Vacc_storeParms:  Surf. density = 10
Vacc_storeParms:  Max area = 286.521
Vacc_storeParms:  Using 2814-point reference sphere
Setting up PDE object...
Vpmp_ctor2:  Using meth = 0, mgcoar = 2, mgsolv = 0
Setting PDE center to local center...
Vpmg_ctor2:  PMG chose nx = 257, ny = 225, nz = 193
Vpmg_ctor2:  PMG chose nlev = 4
Vpmg_ctor2:  PMG chose nxc = 33, nyc = 29, nzc = 25
Vpmg_ctor2:  PMG chose nf = 11160225, nc = 23925
Vpmg_ctor2:  PMG chose narr = 12779664, narrc = 1619439
Vpmg_ctor2:  PMG chose n_rpc = 500, n_iz = 250, n_ipc = 500
Vpmg_ctor2:  PMG chose nrwk = 153346097, niwk = 750
Vpmg_fillco:  filling in source term.
fillcoCharge:  Calling fillcoChargeSpline2...
Vpmg_fillco:  filling in source term.
Vpmg_fillco:  marking ion and solvent accessibility.
fillcoCoef:  Calling fillcoCoefMol...
Vpmg_fillco:  done filling coefficient arrays
Vpmg_fillco:  filling boundary arrays
Vpmg_fillco:  done filling boundary arrays
Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 8.127000e+01
Vnm_tstart: starting timer 28 (Solver timer)..
Vnm_tstart: starting timer 30 (MGDRIV2: fine pro)..
Vnm_tstop: stopping timer 30 (MGDRIV2: fine pro).  CPU TIME = 4.330000e+00
Vnm_tstart: starting timer 30 (MGDRIV2: coarse pro)..


Does anybody know what could be happening?

Thanks,

Marialuisa


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Marialuisa Pellegrini-Calace, PhD
European Bioinformatics Institute
Wellcome Trust Genome Campus
Hinxton
CB10 1SD Cambridge (UK)

E-mail: marial@ebi.ac.uk
Tel: +44 (0)1223 492579
Fax: +44 (0)1223 494468
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