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Re: [Apbs-users] apbs error
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From: Nathan A. B. <ba...@ch...> - 2003-05-28 14:06:08
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Hello --
It sounds like your mess is too small. I would recommend using the
output from apbs/tools/manip/psize as a template for setting up input
files to prevent these types of errors.
Thanks,
Nathan
Prabal Maiti <ma...@wa...> (05-27-2003 14:35:16-0700):
>Hi,=20
>i am trying to calculate the solvation energy for a polymer with 4800=20
>atoms. I am getting the following message=20
>Vpmg_fillco: Atom #5787 at (9.648, 24.061, 8.825) is off the mesh=20
>(ignoring):
>Vpmg_fillco: xmin =3D 23.943, xmax =3D 45.063
>Vpmg_fillco: ymin =3D 21.3535, ymax =3D 42.4735
>Vpmg_fillco: zmin =3D 22.9365, zmax =3D 44.0565
>
>for lots of atoms. Can someone advise whats going on and whats the remedy.=
=20
>
>Below is my apbs.in file:
>read=20
> mol pqr test.pqr
>end
>elec
> mg-manual # Use the multigrid method
> dime 65 65 65 # Grid dimensions (c 2^(l+1) +1)
> # (in x, y, z)
> nlev 4 # Number of levels in multilevel
> # hierarchy (usually 'l' from abo=
ve
> # definition)
> grid 0.33 0.33 0.33 # Grid spacings (A)
> # glen 100 100 100 # You can EITHER specify the grid
> # lengths OR the grid spacing
> gcent mol 1 # This can either be 'mol n' to cen=
ter
> # on a specific molecule or (x, y=
, z)
> # coordinates
> mol 1 # Which molecule (1, 2, ...)
> lpbe # lpbe/npbe =3D linear/nonlinear PBE
> bcfl 2 # Boundary condition flag
> # 0 =3D> Zero
> # 1 =3D> Single DH sphere
> # 2 =3D> Multiple DH spheres
> # 4 =3D> Focusing
> ion 1 0.000 2.0 # Counterion declaration:
> ion -1 0.000 2.0 # ion <charge> <conc (M)> <radius>
> pdie 1.0 # Solute dielectric
> sdie 78.54 # Solvent dielectric
> chgm 1 # Charge disc method (linear)
> srfm 0 # Surface calculation method
> # 0 =3D> Mol surface for epsilon;
> # inflated VdW for kappa; no
> # smoothing
> # 1 =3D> As 0 with harmoic average
> # smoothing
> # 2 =3D> Cubic spline=20
> srad 1.4 # Solvent radius
> swin 0.3 # Surface cubic spline window
> temp 298.15 # Temperature
> gamma 0.105 # Surface tension (in kJ/mol/A^2)
> calcenergy 1 # Energy I/O (to stdout)
> # 0 =3D> don't write out energy
> # 1 =3D> write out total energy
> # 2 =3D> write out total energy an=
d all
> # components
> calcforce 0 # Atomic forces I/O (to stdout)
> # 0 =3D> don't write out forces
> # 1 =3D> write out net forces on m=
olecule
> # 2 =3D> write out atom-level forc=
es
>end
>elec
> mg-manual # Use the multigrid method
> dime 65 65 65 # Grid dimensions (c 2^(l+1) +1)
> # (in x, y, z)
> nlev 4 # Number of levels in multilevel
> # hierarchy (usually 'l' from abo=
ve
> # definition)
> grid 0.33 0.33 0.33 # Grid spacings (A)
> # glen 100 100 100 # You can EITHER specify the grid
> # lengths OR the grid spacing
> gcent mol 1 # This can either be 'mol n' to cen=
ter
> # on a specific molecule or (x, y=
, z)
> # coordinates
> mol 1 # Which molecule (1, 2, ...)
> lpbe # lpbe/npbe =3D linear/nonlinear PBE
> bcfl 2 # Boundary condition flag
> # 0 =3D> Zero
> # 1 =3D> Single DH sphere
> # 2 =3D> Multiple DH spheres
> # 4 =3D> Focusing
> ion 1 0.000 2.0 # Counterion declaration:
> ion -1 0.000 2.0 # ion <charge> <conc (M)> <radius>
> pdie 1.0 # Solute dielectric
> sdie 1.0 # Solvent dielectric
> chgm 1 # Charge disc method (linear)
> srfm 0 # Surface calculation method
> # 0 =3D> Mol surface for epsilon;
> # inflated VdW for kappa; no
> # smoothing
> # 1 =3D> As 0 with harmoic average
> # smoothing
> # 2 =3D> Cubic spline=20
> srad 1.4 # Solvent radius
> swin 0.3 # Surface cubic spline window
> temp 298.15 # Temperature
> gamma 0.105 # Surface tension (in kJ/mol/A^2)
> calcenergy 1 # Energy I/O (to stdout)
> # 0 =3D> don't write out energy
> # 1 =3D> write out total energy
> # 2 =3D> write out total energy an=
d all
> # components
> calcforce 0 # Atomic forces I/O (to stdout)
> # 0 =3D> don't write out forces
> # 1 =3D> write out net forces on m=
olecule
> # 2 =3D> write out atom-level forc=
es
>end
>
>print energy 1 - 2 end
>
>quit
>
>Thanks
>Prabal
>
>--=20
>------------------------------------------------------------------------
>Prabal K Maiti Email:ma...@wa...
>Beckman Institute (139-74) pk...@ya...
>California Institute of Technology Tel:626-395-8151 (O)
>400 South Wilson Avenue :626-744-1363 (H) =
=20
>Pasadena, CA 91125 Fax:626-585-0918
> Home add: 110 S. Michigan Ave.
>http://www.wag.caltech.edu/home/maiti Apt # 19, Pasadena, CA 91106
>------------------------------------------------------------------------
>
>_______________________________________________
>apbs-users mailing list
>apb...@ch...
>http://cholla.wustl.edu/mailman/listinfo/apbs-users
End of message from Prabal Maiti.
--=20
Nathan A. Baker, Assistant Professor
Washington University in St. Louis School of Medicine
Dept. of Biochemistry and Molecular Biophysics
Center for Computational Biology
700 S. Euclid Ave., Campus Box 8036, St. Louis, MO 63110
Phone: (314) 362-2040, Fax: (314) 362-0234
URL: http://www.biochem.wustl.edu/~baker
PGP key: http://cholla.wustl.edu/~baker/pubkey.asc
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