Hi Michael,

For the second problem, there is a whitespace option in PDB2PQR to handle occations like this, which inserts whitespaces between atom name and residue name, between x and y, and between y and z.

If you are using the PDB2PQR server (http://agave.wustl.edu/pdb2pqr), just check the last checkbox before "Submit"; if you are using the command line version, just add --whitespace to your command line.

Hope this helps.


On Thu, Jul 23, 2009 at 5:56 AM, Michael Nilges <nilges@pasteur.fr> wrote:

I have two problems with APBS, with a rather large PDB/ PQR file
(extent in z direction several hundred A, total net charge after
PDB2PQR -125). The two problems do not seem to be related.

The first problem appears with the VMD interface. The APBS calculation
runs through without any complaints, but the result is nonsense (very
strange and completely unrealistic charge distribution). I know this
sounds pretty vague but maybe somebody else has already had problems
with large, highly charged, very non-globular proteins.

Due to the strange results I used APBS stand-alone. The PQR file that
was treated without problems via VMD was not read (a "problem parsing
After some time I realized that the atom that was not parsed was the
first one exceeding -100, so there was no white space between the y
and z column. It seems that APBS cannot read PQR files that use the
full extent of the PDB format (without delimiters). I worked around
this by shifting the coordinates by 200 A.

In the end, the electrostatic potential/ surface looks realistic.

Workarounds used:
1) VMD interface not used
2) always whitspace between xyz in pdb/ pqr file


apbs-users mailing list

Yong Huang, D.Sc.

Center for Computational Biology
Washington University School of Medicine