[Chimera-users] Electrostatic Potential based on Poisson-Boltzmann using APBS

Elaine Meng meng at cgl.ucsf.edu
Sat Jul 18 12:11:37 PDT 2015

If pdb2pqr runs successfully, it will open the file automatically.  It does not create a pdb file, it creates a pqr file.

Maybe you are looking at the Reply Log and seeing that there is a temp pdb file created.  This is NOT the output.  It is a temporary pdb file that is used as the input, and pdb files do not have charges in them.

So I can only guess either you didn’t wait long enough, or the pdb2pqr web service failed on your structure. We have not had this problem.


On Jul 18, 2015, at 11:43 AM, leila karami <karami.leila1 at gmail.com> wrote:

> Dear Elaine,
> I opened my original pdb file as #1 model.
> There is a important point:
> you said PQR file is automatically opened by PDB2PQR when it finishes running.
> But in my  case, generated PQR file is not opened automatically. Why?
> You are right. After finishing apbs, dx file is opened automatically .

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