From: <dkon_at_email.arizona.edu>
Date: Sun 16 Dec 2001 18:50:44 -0700

Dear AMBER folks,

I am trying to use the program quasih for statistical principal component
analysis of AMBER trajectories, but the documentation on it is rather short.

I have several questions to the experts:
1) How can you take out all the waters and probably hydrogens from
the trajectory (mine is an explicit-solvent simulation)
2) is there a way to average fluctuations over entire residues, since
a matrix of size 1500^2 is unwieldy; or alternatively, can the trajectory
be restricted to only backbone atoms
3) how does one create the "mass" input file - I have not found this
pdb_to_mass script and I have added a lot of water to the original pdb file

Thank you,
Received on Sun Dec 16 2001 - 17:50:44 PST
Custom Search