Re: [Apbs-users] VASSERT: ASSERTION FAILURE!

[Nathan B. <ba...@cc...>]

Hello --

I would recommend using an automatic focusing (mg-auto) calculation
for this application.  Some examples are in the examples/hca-bind/
directory.  Please keep in mind that you'll need to modify the "dime",
"cglen", and "fglen" parameters to suit your particular system.
However, PDB2PQR can provide guidance for choosing these parameters by
creating input files for you.

Good luck,

Nathan

On Nov 8, 2007 10:54 AM, osmair oliveira <osm...@ho...> wrote:
>
> Hi,
>
> Ok, I am trying to obtain energy binding of a protein-ligand. As an intia=
l file, I am using the input file from APBS (apbs-mol-surf.in):
>
> read
>     mol pqr lig.pqr
>     mol pqr protein.pqr
>     mol pqr protein-lig.pqr
> end
>
> # LIGAND ENERGY (FOCUSING)
> elec name lig-coarse
>     mg-manual
>     dime 97 97 97
>     nlev 4
>     glen 70 70 70
>     gcent mol 3
>     mol 1
>     lpbe
>     bcfl sdh
>     ion 1 0.000 0
>     ion -1 0.000 0
>     pdie 2.0
>     sdie 78.00
>     chgm spl0
>     srfm mol
>     srad 1.4
>     swin 0.3
>     sdens 10.0
>     temp 298.15
>     calcenergy total
>     calcforce no
> end
> elec name lig-fine
>     mg-manual
>     dime 97 97 97
>     nlev 4
>     grid 0.25 0.25 0.25
>     gcent mol 1
>     mol 1
>     lpbe
>     bcfl focus
>     ion 1 0.000 0
>     ion -1 0.000 0
>     pdie 2.0
>     sdie 78.00
>     chgm spl0
>     srfm mol
>     srad 1.4
>     swin 0.3
>     sdens 10.0
>     temp 298.15
>     calcenergy total
>     calcforce no
> end
>  etc.......
>
>  My ligand (sugar) , protein and protein-lig were genered from pdb2pqr. H=
owever, the following error occur:
>
> CALCULATION #2 (lig-fine): MULTIGRID
>  Setting up problem...
>  Vpbe_ctor:  Using max ion radius (0 A) for exclusion function
> Vpmg::focusFillBound -- new mesh not contained in old!
> Vpmg::focusFillBound -- old mesh min =3D (21.7105, 0.41, -11.7365)
> Vpmg::focusFillBound -- old mesh max =3D (91.7105, 70.41, 58.2635)
> Vpmg::focusFillBound -- new mesh min =3D (49.631, -3.618, 6.1205)
> Vpmg::focusFillBound -- new mesh max =3D (73.631, 20.382, 30.1205)
> VASSERT: ASSERTION FAILURE!  filename vpmg.c, line 1790, (0)
> Abort
>
> Can I help me
> Thanks
>
> Osmair
>
>
>
> t>> Hello -->> We're going to need a bit more information than this (e.g.=
, the PQR
> > and input files) to help you with this problem.
> >> Thanks,>> Nathan
>
> > On Nov 7, 2007 3:30 PM, osmair oliveira  wrote:>>>> Hi>>>> I have been =
executed the apbs (version 0.5.1) and the following error occur:>>>> CALCUL=
ATION #2 (lig-fine): MULTIGRID>> Setting up problem...>> Vpbe_ctor: Using m=
ax ion radius (2 A) for exclusion function>> Vpmg::focusFillBound -- new me=
sh not contained in old!>> Vpmg::focusFillBound -- old mesh min =3D (21.420=
5, 0.4135, -11.727)>> Vpmg::focusFillBound -- old mesh max =3D (91.4205, 70=
.4135, 58.273)>> Vpmg::focusFillBound -- new mesh min =3D (28.021, -24.9495=
, -15.8275)>> Vpmg::focusFillBound -- new mesh max =3D (95.221, 42.2505, 51=
.3725)>> VASSERT: ASSERTION FAILURE! filename vpmg.c, line 1790, (0)>> Abor=
t>>>> Someone can I help me?>>>> Thanks>> _________________________________=
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--=20
Associate Professor, Dept. of Biochemistry and Molecular Biophysics
Center for Computational Biology, Washington University in St. Louis
Web: http://cholla.wustl.edu/