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

[Luis R. <lr...@la...>]

Hi,

The input file generated by the vmd plugin is attached on this mail
(apbs.in), I enclose also my pdb and psf files.


Thnks for your help,

Luis


On Wed, March 30, 2005 6:17, Nathan Baker said:
> Hello --
>
> It looks like there might be a problem with the grid size; can you send
> your input file?
>
> Thanks,
>
> Nathan
>
> Luis Rosales León wrote, On 3/29/2005 8:53 PM:
>> Hi all,
>>
>> My name is Luis and I am new to APBS and to the list too,
>> I have tried to run apbs from the available plugins from pymol and VMD,
>> however I have been unsuccesful to complete the calculations for my
>> protein.
>>
>> in VMD:
>> I am using apbs 0.3.2-1 (the binary compiled with RH-enterprise) and vmd
>> 1.8.3 on a fedora 3 system. I am starting my calculations for my pdb
>> with
>> both pdb and psf files loaded (hydrogens added and termini patches
>> applied).
>> When I run the calculation, after the starting message of APBS I got the
>> following message:
>>
>> This executable compiled on Nov 10 2004 at 10:51:17
>>
>> Parsing input file /home/lrl/4.0-Protease/apbs.in...
>> Parsed input file.
>> Got PQR paths for 1 molecules
>> Reading PQR-format atom data from /home/lrl/4.0-Protease/test.pqr.
>>   4786 atoms
>>   Centered at (-7.305e-01, 2.455e+01, 2.668e+01)
>>   Net charge 4.00e+00 e
>> Preparing to run 2 PBE calculations.
>> ----------------------------------------
>> CALCULATION #1: MULTIGRID
>>   Setting up problem...
>>   Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
>> apbsrun: error occurred while running APBS:
>>   parsePBE:  Warning -- parsed deprecated "bcfl 1" statement
>> parsePBE:  Please use "bcfl sdh" instead.
>> parsePBE:  Warning -- parsed deprecated "srfm 1" statement.
>> parsePBE:  Please use "srfm smol" instead.
>> NOsh:  Warning -- parsed deprecated statment "chgm 1".
>> NOsh:  Please use "chgm spl2" instead!
>> parsePBE:  Warning -- parsed deprecated "calcenergy 0" statement.
>> parsePBE:  Please use "calcenergy no" instead.
>> parsePBE:  Warning -- parsed deprecated "calcforce 0" statement.
>> parsePBE:  Please use "calcforce no" instead.
>> asc_getToken: Error occurred (bailing out).
>> Vio_scanf: Format problem with input.
>> VASSERT: ASSERTION FAILURE!  filename vmem.c, line 245, (ram != 0L)
>>
>> ********************************************************
>>
>> Pymol also complains about a VASSERT: ASSERTION FAILURE!:
>>
>> Got PQR paths for 1 molecules
>> Reading PQR-format atom data from pymol-generated.pqr.
>> asc_getToken: Error occurred (bailing out).
>> Vio_scanf: Format problem with input.
>>   4786 atoms
>>   Centered at (-7.305e-01, 2.455e+01, 2.668e+01)
>>   Net charge 4.15e+00 e
>> Preparing to run 2 PBE calculations.
>> ----------------------------------------
>> CALCULATION #1: MULTIGRID
>>   Setting up problem...
>>   Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
>> VASSERT: ASSERTION FAILURE!  filename vmem.c, line 245, (ram != 0L)
>> ObjectMapLoadDXFile-Error: Unable to open file!
>> ***************************************************************
>>
>> Could be the problem related to the use of a precompiled binary from
>> RH-enterprise on Fedora3 ??
>>
>> I would appreciate any help on the causes of this problem...
>>
>> Thanks,
>>
>>
>> Luis Rosales
>>
>> _______________________________________________
>> apbs-users mailing list
>> apb...@ch...
>> http://cholla.wustl.edu/mailman/listinfo/apbs-users
>
> --
> 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
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