[Chimera-users] Charge calculations PDB2PQR

Conrad Huang conrad at cgl.ucsf.edu
Fri Apr 20 09:44:19 PDT 2012


I'm actually working on interfacing Chimera with the pdb2pqr web service 
at NBCR.  I have something that works for a couple simple PDB entries. 
Would it be possible for me to get your data for testing?  If it works, 
the new tool should be in the Chimera daily builds by next week.


On 4/20/2012 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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