[Chimera-users] Charge calculations PDB2PQR

Elaine Meng meng at cgl.ucsf.edu
Fri Apr 20 10:12:07 PDT 2012

Hi Nikolay,
Chimera has a Minimize Structure tool (in menu under Tools... Structure Editing).  

It is just a local minimization using the Amber force field (choices discussed previously), but you could try it and see if the amount of repositioning is sufficient for your purposes.  The H-bonds are not explicitly optimized but the force field will tend to improve H-bonds, especially in nonfrustrated systems.  

For example, here is a little video of improving H-bonds while minimizing a box of water here:

One possibility would be to freeze the protein atoms (move only the waters) during minimization.

On Apr 20, 2012, at 9:57 AM, Nikolay Igorovich Rodionov wrote:

> 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

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