Hi Nikolay, Chimera has a Minimize Structure tool (in menu under Tools... Structure Editing). <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/minimize/minimize.h...> 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: <http://www.cgl.ucsf.edu/chimera/data/movie-howto-mar2012/movie_examples.html...> One possibility would be to freeze the protein atoms (move only the waters) during minimization. Best, Elaine 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