[Chimera-users] Charge calculations PDB2PQR

Nikolay Igorovich Rodionov nirodion at syr.edu
Fri Apr 20 09:57:06 PDT 2012

I've actually been talking with the developers of PDB2PQR about the problem and they've said that they that waters should be retained. One of the reasons I have been using PDB2PQR is that it optimizes hydrogen bonding and repositions waters accordingly, which gives me a sense of where hydrogen bonding between waters and protein occur. I should have asked about this in my previous email, does chimera optimize hydrogen bonds?

Nikolay Rodionov

-----Original Message-----
From: Elaine Meng [mailto:meng at cgl.ucsf.edu] 
Sent: Friday, April 20, 2012 9:52 AM
To: Conrad Huang
Cc: Nikolay Igorovich Rodionov; chimera-users at cgl.ucsf.edu
Subject: Re: [Chimera-users] Charge calculations PDB2PQR

I avoided the larger issues in my previous reply, trying to stick to Chimera information, but I suppose it needs to be said:

Since the PDB2PQR server is primarily for preparing structures for continuum electrostatics calculations, it only makes sense (to me) that it would remove all the water molecules.  I.e. these calculations are normally done without explicit waters; solvent is instead modeled as a high-dielectric continuum.

Perhaps Nikolay should ask the APBS and/or PDB2PQR people, if he wants a more direct discussion of whether his water molecules should be retained.  


On Apr 20, 2012, at 9:44 AM, Conrad Huang wrote:

> Hi,
> 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.
> Conrad
> 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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