Re: [Apbs-users] Problems reading files with no spaces between atom coordinates

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

Hi Ken --

This is a feature, not a bug. :)

As the APBS manual points out (http://apbs.sourceforge.net/doc/user-guide/index.html#pqr-flat-format 
), we require PQR files to have whitespace between the columns.   
Unfortunately, the PDB standard is pretty bad for large molecules and  
this whitespace requirement generally has to be enforced with some  
preprocessing.

Depending on how comfortable you are with sed or scripting languages,  
this should be pretty easy to fix.  Alternatively, you could run this  
through the command line version of PDB2PQR (I'd recommend using the  
developmental version from Subversion) with the --whitespace flag to  
add the necessary delimiters.  However, the easiest approach might  
just be to send your PQR file to me and we'll fix it.

Thanks,

Nathan

On Apr 22, 2008, at 1:00 PM, Ken Prehoda wrote:

> I've been trying to use apbs with some very elongated molecules
> (coiled-coils) and have been running into difficulties because many
> atoms in the pdb and pqr files have coordinates without spaces between
> them. This leads to problems because several of the parsing routines
> assume this type of demarcation. For example, psize.py uses the python
> split function:
>
> 	subline = string.replace(line[30:], "-", " -")
> 	words = string.split(subline)
>
> The first line tries to solve the problem but it doesn't work if the
> coordinate isn't negative. The "coulomb" program runs into the same
> problem and isn't able to parse lines like:
>
> ATOM   8847  N   GLU  1700      -4.377-368.118-167.786  0.00170000
> 1.824
>
> Error:
> Setting up atom list from cc.pqr.
> Valist_readPQR:  Error parsing atom 8847!
> Read 0 atoms
> Setting up Green's function object.
> Dielectric constant = 1 (vacuum)
> Distances in Angstroms
> Charges in electrons
> Allocating space for solution...
> VASSERT: ASSERTION FAILURE!  filename vmem.c, line 241, ((num > 0) &&
> (size > 0))
> Abort
>
> The main apbs program appears to just stall when attempting to read in
> files that include these lines. Is anyone aware of a workaround for
> this problem?
>
> Thanks for the help! -Ken
>
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--
Associate Professor, Dept. of Biochemistry and Molecular Biophysics
Center for Computational Biology, Washington University in St. Louis
Web: http://cholla.wustl.edu/