Are there ways to efficiently treat side chains in NMA without using all atoms?
Issue #250
resolved
Are there ways to efficiently treat side chains in NMA, perhaps combining C-alpha and COM pseudoatom for side-chains? I used the default Ca FF, which should be close when describing motions along amide backbone. A simple visualization using COM coordinates for reveals that these could be in different "environments" than the backbone.
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Hi Manolo, This is currently not implemented, but would be a very interesting extension. An example of this can be found in ref 16 in this paper: http://pubs.acs.org/doi/abs/10.1021/ct400399x. Sorry I can't say much more about this. Hopefully we'll find time to implement it, but its not a priority at the moment. Lars