RSMDTT keyword for nucleic acids

From: Aaron Larsen (
Date: Wed Feb 05 2014 - 14:43:13 CST


I am attempting to perform an RMSD analysis (using the RMSD trajectory
tool) on a trajectory file describing for the unrestrained simulation of a
nucleic acid. Most of the examples in manuals and online focus on
trajectory files describing simulation of proteins. The defualt keyword
works very well for such studies but I am unable to find literature
indicating what to replace this keyword with to evaluate nucleic acids or
any specific atom in particular. If someone could direct me to any resource
which may help or suggest an appropriate keyword to use, that would be very
much appreciated.



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