On May 13, 2011, at 4:00 PM, Tom J. Brett wrote:
On a similar extension to this topic, is there a good software out
there for doing these kinds of modifications and minimizations for
protein structures with chemicals entities (i.e., protein/inhibitor
complexes). What I am looking to do is take a protein/inhbitor
complex and add chemical modifications onto the inhibitor and see
how they fit. so a little minimization/relaxation of the surrounding
protein would be nice. It there a freely available software that
will allow something like this, if not what commercial packages are
cheapest/best at this? Thanks and sorry for hijacking this thread.
Chimera also has a tool (Build Structure) that can be used for simple
chemical modifications:
http://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/editing/editing.html
It's not as nice as some builders, but it can generally get the job
done. Chimera can compute the charges on your modified structure by
calling out to AmberTools/antechamber (included with the Chimera
download) and then perform minimization. Charge computation might
take awhile if the inhibitor is large-ish.
This isn't to say that you shouldn't follow the protocol outlined by
Saugata Hazra in another posting. It depends on your goals.
--Eric
Eric Pettersen
UCSF Computer Graphics Lab
http://www.cgl.ucsf.edu
