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

Elaine Meng meng at cgl.ucsf.edu
Fri Jul 17 14:03:46 PDT 2015


Hi Leila,
Here’s an image of your structure and dx map in Chimera, with status line showing the 4 values.  The ESP value is given as “nan”, meaning there is nothing useful in the map file because it was calculated without charges.
Elaine





On Jul 17, 2015, at 1:11 PM, leila karami <karami.leila1 at gmail.com> wrote:

> Dear Elaine,
> 
> 1) "report values" gives only 3 values (x coord, y coord, z coord)  and not 4 values.
> 
> 2) Based on your suggestion, I did following steps:
> 
> Tools... structure Editing... pdb2pqr
> 
> But I encountered with:
> 
> Service 'opal:pdb2pqr_1.8' is unavailable.
> 
> 3) Again, I tried the apbs in command line.
> 
> To have my dx and the PDB files, please check the following links:
> 
> https://www.dropbox.com/s/n4zv0lq7s4p1pz2/44.pdb?dl=0
> https://www.dropbox.com/s/w6dg4adb498178r/tmpiwv0lf.dx?dl=0
> 
> Again, electrostatic surface is as black and white instead of red and blue.
> 
> Thanks in advance,
> Leila
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