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

Elaine Meng meng at cgl.ucsf.edu
Sat Jul 18 11:36:44 PDT 2015


Dear Leila,
Your description does not make sense to me because you do not need to open the pqr file or the dx file yourself.  They will both open automatically when the calculations are done.

Otherwise it sounds OK, and it works fine when I do it.  Maybe (especially if you opened some files yourself) there are extra models and you are confused about which number is which.  You should always look in the Model Panel to make sure.  Otherwise I have no more ideas.
Elaine

On Jul 18, 2015, at 11:23 AM, leila karami <karami.leila1 at gmail.com> wrote:

> Dear Elaine,
> 
> I checked the useful link.
> 
> I opened pr.pdb file (#0).
> 
> I used pdb2pqr. Then, a new pdb file was created.
> 
> I opened this new file (#1). Then, I used apbs molecule #1.
> 
> Then, I opened created dx file.
> 
> Unfortunately, surface is black and white.
> 
> I confused. Which part of my steps is wrong?
> 
> Please guide me to resolve this problem.




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