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

Elaine Meng meng at cgl.ucsf.edu
Fri Jul 17 13:25:40 PDT 2015


Dear Leila,
As I said before, you must add charges to the structure before running APBS, or else your map will not have values and the coloring will be black and white.

According to the error message, the pdb2pqr calculation did not run, so you did not have charges and your problem is exactly the same as before.

The pdb2pqr service changed its URL, so we had to change Chimera, and so to run that service you need to use a newer version of Chimera, the daily build:
<http://www.rbvi.ucsf.edu/chimera/download.html#daily>

OR, instead of using PDB2PQR you can use the other tools mentioned in the APBS manual page (link sent in previous message) for preparing the structure, for example Dock Prep (in menu under Tools… Structure Editing), which will in turn call AddH and AddCharge tools for adding hydrogens and charges.  However, the PDB2PQR charges may be better for Poisson-Boltzmann calculations, again as mentioned in the APBS manual page.

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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