[Chimera-users] Charge calculations PDB2PQR

Elaine Meng meng at cgl.ucsf.edu
Fri Apr 20 09:37:20 PDT 2012

Hi Nikolay,
The choices of force field are listed in the Add Charge manual page, but they are all versions from Amber:

Before charges are added, the user is prompted to add hydrogens with the AddH tool.  There is no choice of pH, sidechains are given their probable state near pH 7 (except histidine is determined by local environment, by default), but the user can control specific sidechains' protonation state as desired, as explained in the AddH manual page:

So Chimera does not provide PARSE charges, and does not do pKa prediction.  However, if you created an attribute definition file containing the PARSE charges (which could be a lot of work), you could use it to assign "custom" charges in Chimera. 
Also, you could run propKa yourself and then during hydrogen addition in Chimera, specify the protonation states individually to agree with propKa's predictions.  Probably more steps than you had in mind, and again, Chimera doesn't output PQR format.


On Apr 20, 2012, at 9:17 AM, Nikolay Igorovich Rodionov wrote:

> Does chimera allow you to define the force-field? I'm concentrating on using PARSE for most of my work. Also, I like how PDB2PQR uses proPKA as the model for predicting pKa values in the charge calculation. Does Chimera share this functionality? 
> Thank you,
> Nikolay Rodionov 

More information about the Chimera-users mailing list