Hello --

Which of the molecules in your input file is the complex?  Are the coordinates for the components of the complex the same in all PDB files (i.e., a rigid body problem)?  If so, you should probably be centering all calculations on the complex PDB.

Thanks,

Nathan


On Nov 20, 2008, at 10:11 AM, Pinar KANLIKILICER wrote:

Hi All,
i am trying to calculate the solvation energy for protein complex that consists of  protein1.pqr + protein2.pqr (they combine into
0.pqr)

I am getting the following error for my unbound components :

Vpmg_fillco:  Atom #2283 at (-41.216, 18.857, 37.138) is off the mesh (ignoring):
Vpmg_fillco:  xmin = -36.1202, xmax = 66.9592
Vpmg_fillco:  ymin = -22.2223, ymax = 76.3623
Vpmg_fillco:  zmin = -4.33315, zmax = 106.998
Vpmg_fillco:  Atom #2284 at (-40.036, 19.940, 38.625) is off the mesh (ignoring):
Vpmg_fillco:  xmin = -36.1202, xmax = 66.9592
Vpmg_fillco:  ymin = -22.2223, ymax = 76.3623
Vpmg_fillco:  zmin = -4.33315, zmax = 106.998
Vpmg_fillco:  Atom #2285 at (-39.403, 19.044, 38.811) is off the mesh (ignoring):
Vpmg_fillco:  xmin = -36.1202, xmax = 66.9592
Vpmg_fillco:  ymin = -22.2223, ymax = 76.3623
Vpmg_fillco:  zmin = -4.33315, zmax = 106.998
.
.
.



I wonder if there is something wrong with my input file? I center all the grids on molecule 1 (0.pqr) . But when i center grid on molecule2 for molecule2 and molecule3 for molecule3 this error does not occur. Do you have any comment about the reasons of my problem?

Below is my .in file:

read
    mol pqr 0.pqr
    mol pqr 0_protein1.pqr
    mol pqr 0_protein2.pqr
end
elec name complex1
    mg-auto
    dime 161 129 161
    cglen 103.0795 98.5847 111.3313
    fglen 80.6350 77.9910 85.4890
    cgcent mol 1
    fgcent mol 1
    mol 1
    lpbe
    bcfl sdh
    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 pro1
    mg-auto
    dime 161 129 161
    cglen 103.0795 98.5847 111.3313
    fglen 80.6350 77.9910 85.4890
    cgcent mol 1
    fgcent mol 1
    mol 2
    lpbe
    bcfl sdh
    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 pro2
    mg-auto
    dime 161 129 161
    cglen 103.0795 98.5847 111.3313
    fglen 80.6350 77.9910 85.4890
    cgcent mol 1
    fgcent mol 1
    mol 3
    lpbe
    bcfl sdh
    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

print elecEnergy complex1 - pro1 - pro2 end
quit


Thanks in advance


Pinar Kanlikilicer
Bogazici University /Chemical Engineering Graduate Student
Istanbul/ TURKIYE
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--
Associate Professor, Dept. of Biochemistry and Molecular Biophysics
Center for Computational Biology, Washington University in St. Louis







--
Associate Professor, Dept. of Biochemistry and Molecular Biophysics
Center for Computational Biology, Washington University in St. Louis