Dear all

The original one was not calculated by APBS. The former one and the present one are not related to the same molecule. Thank you.

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 11:43:23 -0500
> To: coomteng@hotmail.com
>
> Hello --
>
> (see comments below)
>
> > 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
>
> This looks good...
>
> > 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
>
> ...but this second ELEC statement won't work unless you add a charge
> map to the READ statement above.
>
> > 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?
>
> Yes, you're correct -- the output is charge density. In fact, all
> right hand sides of PB-like equations are basically "densities"
> inasmuch as they're most meaningful inside an integral. The manual
> states that these maps are charge distributions/densities but gives
> the incorrect units. I'll fix this; thanks for bringing it to our
> attention.
>
> However, I was confused by the APBS output you showed the other day.
> When I read the oh.dx map back into APBS, I get output from APBS
> which reads:
>
> Got paths for 1 charge maps
> Reading charge map data from oh.dx:
> 65 x 65 x 65 grid
> (0.0283203, 0.0283203, 0.0283203) A spacings
> (-1.29575, -0.86425, -0.90625) A lower corner
> Charge map integral = -1.00e+00 e
> Preparing to run 1 PBE calculations.
>
> and thus gives the correct integrated charge density. The original e-
> mail you sent seemed to indicate that the integrated charge density
> was incorrect as well. Was that calculated by APBS?
>
> Thanks,
>
> Nathan
>
>
>
> > > 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
> > > >
> > > > 中国十大热门旅游景点 了解更多信息!
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> > > --
> > > Associate Professor, Dept. of Biochemistry and Molecular Biophysics
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> > > Web: http://cholla.wustl.edu/
> > >
> > >
> >
> > 中国十大热门旅游景点 了解更多信息!
>
> --
> Associate Professor, Dept. of Biochemistry and Molecular Biophysics
> Center for Computational Biology, Washington University in St. Louis
> Web: http://cholla.wustl.edu/
>
>


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