[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.

Elaine


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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