[phenixbb] Electrostatic potential map/Delphi/PDB2PQR

Tim Gruene tg at shelx.uni-ac.gwdg.de
Tue Oct 21 10:40:56 PDT 2014

Dear Ivan,

as Pavel pointed out what appear to be errors to you are most likely
bugs or short-comings in the downstream programs. PDB2PQR is not greatly
sophisticated as it comes to PDB files (ANISOU records are for sure not
errors). Did you try, though, the online-server or the standalone
program? I have the impression that the server is more robust.


On 10/21/2014 05:20 PM, Ivan IVANOV wrote:
> Dear All, 
>   I am facing a problem. I have a protein-RNA complex at 2A resolution I
> refined using TLS in Phenix. Now in the pdb file I have ANISOU line for
> every atom and probably many other errors. This is the reason I am not
> able to run Delphi or PDB2PQR to create potential electrostatic map. 
>   I removed already all water molecules and all heteratoms and ANISOU
> lines and RNA molecule. The program creating the phi file for the
> potentials does not work at all. 
>    Do you know any server which can correct any errors in the pdb file
> in order to run properly the program to create electrostatic map ??
>    Thanks a lot, 
>  Ivan

Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen


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