Hello –


We do not have parameters for iron-sulfur clusters available.  However, Marilyn Gunner and co-workers have published some excellent papers using implicit solvent models for predicting redox potentials and may have some parameters for these systems.





Nathan Baker

Laboratory Fellow and Technical Group Manager

Applied Statistics and Computational Modeling

Pacific Northwest National Laboratory




From: Jan Riehm [mailto:janriehm@gmail.com]
Sent: Wednesday, March 12, 2014 03:36
To: apbs-users@googlegroups.com
Subject: [apbs-users] APBS with CYP P450 enzymes or iron sulfur cluster proteins




I was wondering if it is possible to compute electrostatic potentials of CYP P450 enzymes or proteins that contain iron-sulfur clusters (like Adrenodoxin). The PDB2PQR tool was not able to cope with such clusters. So no further computation with the APBS plugin for VMD was possible (in my case). It was also not possible to compute electrostatics after manipulating my PQR file manually (adding charges, changing HETATM entries to ATM etc).


Is there a workaround or anything else for such proteins? Or has anybody advice or experience? 


Thank you very much and kind regards,


Jan Riehm