Hi All

The version I am using is APBS 0.5.0.

here is my input file
================================
read
  mol pqr oh.pqr
end

elec name solv # Electrostatics calculation on the solvated state
        mg-manual # Specify the mode for APBS to run
        dime 65 65 65 # The grid dimensions
        nlev 4 # Multigrid level parameter
        grid 2.832031e-02 2.832031e-02 2.832031e-02 # Grid spacing
        gcent -3.895000e-01 4.200000e-02 0.000000e+00 # Center the grid on molecule 1
        mol 1 # Perform the calculation on molecule 1
        lpbe # Solve the linearized Poisson-Boltzmann equation
        bcfl mdh # Use all multipole moments when calculating the potential
        pdie 1.0 # Solute dielectric
        sdie 78.5 # Solvent dielectric
        chgm spl2 # Spline-based discretization of the delta functions
        srfm mol # Molecular surface definition
        srad 1.4 # Solvent probe radius (for molecular surface)
        swin 0.3 # Solvent surface spline window (not used here)
        sdens 10.0 # Sphere density for accessibility object
        temp 300 # Temperature
        calcenergy total # Calculate energies
        calcforce no # Do not calculate forces
        write charge dx oh
end
elec name ref # Calculate potential for reference (vacuum) state
        mg-manual
        dime 65 65 65 # The grid dimensions
        nlev 4 # Multigrid level parameter
        grid 2.832031e-02 2.832031e-02 2.832031e-02 # Grid spacing
        gcent -3.895000e-01 4.200000e-02 0.000000e+00
        mol 1
        lpbe
        bcfl mdh
        pdie 1.0
        sdie 1.0
        chgm spl2
        srfm mol
        srad 1.4
        swin 0.3
        sdens 10.0
        temp 300
        calcenergy total
        calcforce no
   usemap charge 1
end

# Calculate solvation energy
print energy solv - ref end

quit
==============================

Here is my pqr file
==============================
ATOM      1     O OSP3_1   1   -0.027    0.301   -0.227   -0.803    1.660
ATOM      2     H OSP3_1   1   -0.752   -0.217    0.227   -0.197    1.330
==============================
then I have a charge map. When I sum up all the value in the oh.dx file, it should be -1, but I got -44025.668246, which is -1/(2.832031e-02)^3. I have no idea about what are values in oh.dx file. Is it the charge or the density?

I look forward to your reply at your earliest convenience. Thank you very much and best wishes from Zurich, Switzerland. Yours very faithfully, Zhou Ting coomteng@hotmail.com


> CC: apbs-users@lists.sourceforge.net
> From: baker@ccb.wustl.edu
> Subject: Re: [Apbs-users] misleading of the output of " Charge map integra"
> Date: Wed, 4 Apr 2007 07:38:37 -0500
> To: coomteng@hotmail.com
>
> Hello --
>
> I can't reproduce this behavior. Can you please provide more details
> about the version of APBS you're using and the specific PQR file
> that's causing the problem?
>
> Thanks,
>
> Nathan
>
> On Apr 4, 2007, at 5:02 AM, ZhouTing wrote:
>
> > Hi all,
> >
> > Reading charge map data from res47_o_lig011.dx:
> > 156 x 156 x 156 grid
> > (0.25, 0.25, 0.25) A spacings
> > (-22.48, -27.375, -24.059) A lower corner
> > Charge map integral = 4.69e-02 e
> > Preparing to run 2 PBE calculations.
> >
> >
> > According to manual the unit in dx file is electron charge. So if
> > write a dx file with +3 charge system, the sum of data in dx file
> > should be +3. But why here is 4.69e-02 e? It looks like 3*0.25^3,
> > but what's the meaning of this?
> >
> > I look forward to your reply at your earliest convenience. Thank
> > you very much and best wishes from Zurich, Switzerland. Yours very
> > faithfully, Zhou Ting coomteng@hotmail.com
> >
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