Are there ways to efficiently treat side chains in NMA without using all atoms?

[Manolo Plasencia]

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.

[Lars Skjærven]

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

[Lars Skjærven]

Adding this to the todo list

[Xinqiu Yao]

The task is moved to issue #287. Let me know if it should be reopened.