Hi APBS users,
I am trying to calculate the solvation contribution to the ligand binding, I had this warning:

 
focusFillBound:  WARNING! Unusually large potential values
                   detected on the focusing boundary! 
                   Convergence not guaranteed for NPBE/NRPBE calculations!

I tried linear and non-linear solutions also I used 1.2.1 and 1.3 version of APBS.

Best regards

Safwat

Here is my input:
read
  mol pqr holo-wt-ral-qmmm-mini-complex.pqr
  mol pqr Ral.pqr
  mol pqr holo-wt-ral-qmmm-mini-receptor.pqr
end

# COMPLEX -- SOLVATED STATE (FOCUSING)
elec name complex-solv
    mg-auto
    dime   161 193 161  # number of find grid points
    cglen   112.757597 130.386602 125.512701 # coarse mesh lengths (A)
    fglen   86.327998 96.698001 93.831000 # fine mesh lengths (A)
    cgcent mol 2
    fgcent mol 2
    mol 1
    npbe
    bcfl mdh
    ion charge 1 conc 0.150 radius 2.0
    ion charge -1 conc 0.150 radius 2.0
    pdie 2.0000
    sdie 78.5400
    srfm smol
    chgm spl2
    sdens 10.00
    srad 1.40
    swin 0.30
    temp 298.15
    calcenergy total
    calcforce no
end
elec name complex-ref
    mg-auto
    dime   161 193 161  # number of find grid points
    cglen   112.757597 130.386602 125.512701 # coarse mesh lengths (A)
    fglen   86.327998 96.698001 93.831000 # fine mesh lengths (A)
    cgcent mol 2
    fgcent mol 2
    mol 1
    npbe
    bcfl mdh
    ion charge 1 conc 0.150 radius 2.0
    ion charge -1 conc 0.150 radius 2.0
    pdie 2.0000
    sdie 2.000
    srfm smol
    chgm spl2
    sdens 10.00
    srad 1.40
    swin 0.30
    temp 298.15
    calcenergy total
    calcforce no
end

# DMSO -- SOLVATED STATE (FOCUSING)
elec name lig-solv
    mg-auto
     dime   161 193 161  # number of find grid points
    cglen   112.757597 130.386602 125.512701 # coarse mesh lengths (A)
    fglen   86.327998 96.698001 93.831000 # fine mesh lengths (A)
    cgcent mol 2
    fgcent mol 2
    mol 2
    npbe
    bcfl mdh
    ion charge 1 conc 0.150 radius 2.0
    ion charge -1 conc 0.150 radius 2.0
    pdie 2.0000
    sdie 78.5400
    srfm smol
    chgm spl2
    sdens 10.00
    srad 1.40
    swin 0.30
    temp 298.15
    calcenergy total
    calcforce no
end

elec name lig-ref
    mg-auto
    dime   161 193 161  # number of find grid points
    cglen   112.757597 130.386602 125.512701 # coarse mesh lengths (A)
    fglen   86.327998 96.698001 93.831000
    cgcent mol 2
    fgcent mol 2
    mol 2
    npbe
    bcfl mdh
    ion charge 1 conc 0.150 radius 2.0
    ion charge -1 conc 0.150 radius 2.0
    pdie 2.0000
    sdie 2.000
    srfm smol
    chgm spl2
    sdens 10.00
    srad 1.40
    swin 0.30
    temp 298.15
    calcenergy total
    calcforce no
end


# 1D7H -- SOLVATED STATE (FOCUSING)
elec name ptn-solv
    mg-auto
   dime   161 193 161  # number of find grid points
    cglen   112.757597 130.386602 125.512701 # coarse mesh lengths (A)
    fglen   86.327998 96.698001 93.831000
    cgcent mol 2
    fgcent mol 2
    mol 3
    npbe
    bcfl mdh
    ion charge 1 conc 0.150 radius 2.0
    ion charge -1 conc 0.150 radius 2.0
    pdie 2.0000
    sdie 78.5400
    srfm smol
    chgm spl2
    sdens 10.00
    srad 1.40
    swin 0.30
    temp 298.15
    calcenergy total
    calcforce no
end

elec name ptn-ref
    mg-auto
    dime   161 193 161  # number of find grid points
    cglen   112.757597 130.386602 125.512701 # coarse mesh lengths (A)
    fglen   86.327998 96.698001 93.831000
    cgcent mol 2
    fgcent mol 2
    mol 3
    npbe
    bcfl mdh
    ion charge 1 conc 0.150 radius 2.0
    ion charge -1 conc 0.150 radius 2.0
    pdie 2.0000
    sdie 2.000
    srfm smol
    chgm spl2
    sdens 10.00
    srad 1.40
    swin 0.30
    temp 298.15
    calcenergy total
    calcforce no
end


# COMPLEX SOLVATION ENERGY
print elecEnergy complex-solv - complex-ref end

# DMSO SOLVATION ENERGY
print elecEnergy lig-solv - lig-ref end

# 1D7H SOLVATION ENERGY
print elecEnergy ptn-solv - ptn-ref end

# CHANGE IN SOLVATION ENERGY UPON BINDING
print elecEnergy complex-solv - complex-ref - lig-solv + lig-ref - ptn-solv + ptn-ref end

quit


--
-----------------------------------------------------------
Safwat Abdel-Azeim, PhD
Computational Chemistry
Laboratoire de Biologie et Pharmacologie Appliquées (LBPA)
Ecole Normale Supérieure de Cachan
61, avenue du Président Wilson
94235 Cachan cedex
Tel: +33(0)147407749
Cell phone: +33(0)6 29 68 18 71
WEB:http://www.lbpa.ens-cachan.fr/version-francaise/equipes/bioinformatique-modelisation-et-dynamique-moleculaire-bimodym-/