[Chimera-users] Charge calculations PDB2PQR
meng at cgl.ucsf.edu
Fri Apr 20 10:12:07 PDT 2012
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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