Re: [Apbs-users] APBS, unable to parse ...

[Nathan B. <nat...@wu...>]

Without the offending PQR file, it's hard to say what the problem is.=20
Did you generate the PQR file from PDB2PQR or from within PyMOL?

Thanks,

Nathan

On 4/4/06, Minmin Yu <MY...@lb...> wrote:
> Hi all,
>
> After I loaded my pdb in pymol and used APBS plugin to click run APBS, I
> received the following message:
>
> Parsing input file pymol-generated.in...
> Parsed input file.
> Got PQR paths for 1 molecules
> Reading PQR-format atom data from pymol-generated.pqr.
> Valist_readPDB:  Unable to parse resSeq token (A) as int!
> Valist_readPDB:  Error while parsing residue name!
> Valist_readPQR:  Error parsing ATOM field!
> Error while reading molecule from pymol-generated.pqr
> Error reading molecules!
> ObjectMapLoadDXFile-Error: Unable to open file!
>
>
> It seems .pqr file has some problems to be created from the pdb file. I
> had a success to use another pdb file as a test. So it looks like this
> pdb file has some problems. Does anybody know why and can help me with
> this?  Thank you very much.
>
>
> M.
>
>
>
>
>
>
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--
Assistant Professor, Dept. of Biochemistry and Molecular Biophysics
Center for Computational Biology, Washington University in St. Louis
Web: http://cholla.wustl.edu/