[Chimera-users] Charge calculations PDB2PQR

Nikolay Igorovich Rodionov nirodion at syr.edu
Fri Apr 20 09:17:18 PDT 2012

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 

-----Original Message-----
From: Elaine Meng [mailto:meng at cgl.ucsf.edu] 
Sent: Friday, April 20, 2012 9:13 AM
To: Nikolay Igorovich Rodionov
Cc: chimera-users at cgl.ucsf.edu
Subject: Re: [Chimera-users] Charge calculations PDB2PQR

Hi Nikolay,
Well, Chimera itself does charge assignments, see the Add Charge tool (in Chimera menu under Tools... Structure Editing).  It uses a lookup table for standard residues and Antechamber to calculate charges for other residues, as explained in the manual page:


However, Chimera does not write out the PQR format, it only reads it.

I can't answer anything specific about the PDB2PQR server...it's not part of Chimera and I haven't used it very much.
I hope this helps,
Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco

On Apr 20, 2012, at 7:53 AM, Nikolay Igorovich Rodionov wrote:

> Hi all,
>                 Does anyone knows any alternative charge calculating software packages to PDB2PQR. I need to calculate partial charge distribution but the local copy of PDB2PQR that I installed has some kind of glitch where it is scrapping all of the water molecules from my solvated protein while doing the analysis. I think it has something to do with the side of my PDB file since I am using about 30K atoms, at least, and everything goes perfectly when I work with less 10K atoms. So, I guess the second question is, has anyone else ever encountered this problem?
> Sincerely,
> Nikolay Rodionov

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