[Apbs-users] how to choose the grid

[Alfonso G. <alf...@po...>]

Hi all,
I am doing APBS calculation to get the interaction energy of two 
collagen molecule at different distances (I'd like to obtain a energy 
vs. distance plot) but I am new to this kind of calculations and I have 
some doubts.
My questions are:

1) how large should be the coarse and fine grids? In other words, how 
large should be the distance between the molecule and the coarse/fine 
grid edge?

2) I want to compare the binding energy for different intermolecular 
distances. This means that the grid length and dime must be the same in 
all calculations, even if the systems with smaller intermolecular 
distances are more compact? 


I attach my input file, in case it helps.

Thanks
alfonso


read
    mol pqr mol1.pqr  #
    mol pqr mol2.pqr  #
    mol pqr complex.pqr  #
end

elec name mol1               # BALANOL ENERGY CALCULATION
    mg-auto  
    dime 65 65 65            # Grid dimensions
    cglen 150 90 60          # Coarse grid lengths
    cgcent mol 3             # Coarse grid centered on the complex
    fglen 105 60 45          # Fine grid lengths
    fgcent mol 3             # Fine grid centered on the complex
    mol 1                   
    lpbe                     # Linearized PB
    bcfl sdh                 # Monopole boundary condition
    ion 1 0.000 2.0          # Zero ionic strength
    ion -1 0.000 2.0        
    pdie 2.0                 # Solute dielectric
    sdie 78.00               # Solvent dielectric
    chgm spl0                # Linear charge discretization
    srfm mol                # Smoothed molecular surface
    srad 0.0                 # Solvent probe radius
    swin 0.3                 # Surface spline window (not used)
    sdens 10.0               # Sphere density
    temp 298.15              # Temperature
    gamma 0.105              # Surface tension (not used)
    calcenergy total
    calcforce no
end

elec name mol2               # PROTEIN KINASE A CALCULATION
    mg-auto  
    dime 65 65 65             # Grid dimensions
    cglen 150 90 60          # Coarse grid lengths
    cgcent mol 3             # Coarse grid centered on the complex
    fglen 105 60 45          # Fine grid lengths
    fgcent mol 3             # Fine grid centered on the complex
    mol 2
    lpbe
    bcfl sdh
    ion 1 0.000 2.0
    ion -1 0.000 2.0        
    pdie 2.0      
    sdie 78.00    
    chgm spl0     
    srfm mol     
    srad 0.0      
    swin 0.3      
    sdens 10.0
    temp 298.15   
    gamma 0.105  
    calcenergy total
    calcforce no
end

elec name complex            # COMPLEX CALCULATION
    mg-auto  
    dime 65 65 65            # Grid dimensions
    cglen 150 90 60          # Coarse grid lengths
    cgcent mol 3             # Coarse grid centered on the complex
    fglen 105 60 45          # Fine grid lengths
    fgcent mol 3             # Fine grid centered on the complex
    mol 3
    lpbe
    bcfl sdh
    ion 1 0.000 2.0
    ion -1 0.000 2.0        
    pdie 2.0      
    sdie 78.00    
    chgm spl0     
    srfm mol     
    srad 0.0      
    swin 0.3  
    sdens 10.0   
    temp 298.15   
    gamma 0.105  
    calcenergy total
    calcforce no
end

print energy complex - mol1 - mol2 end

quit




-- 
Alfonso Gautieri
PhD Student
Bioengineering Dept. - Politecnico di Milano
P.zza Leondaro da Vinci, 32 - 20133 Milano - Italy
Phone +390223999501 - Fax +390223999508
www.biomed.polimi.it/cmb