AMBER Archive (2006)

Subject: AMBER: Curves and Average Structures

From: Lauren O'Neil (lhunter2_at_nd.edu)
Date: Mon Jun 26 2006 - 12:26:46 CDT

Dear All,

I have been using Amber to do MD simulations of DNA containing thymine
dimer(s). I know that this listserv is not for Curves, but I figure a
fair number of people must use it. I use Curves in the analysis of my
simulations and have noticed that it will only accept a snapshot, not an
average structure. I read a previous post that also said that this was
the case. Does anyone know why? I have used curves on snapshots from
my simulations from a time point where the RMSd seems "stable". Does
anyone have any other suggestions for picking time points? Would it be
possible to run multiple Curves analyses in some sort of automated
fashion (I'm sure anyone who has used it knows that there is significant
modification that has to be done to the pdb file)...I have a script that
modifies my .pdb files, but doing multiple (over 100 or so) structures
would be time consuming. Any suggestions would be much appreciated.

Lauren O'Neil
Wiest Group
University of Notre Dame
Notre Dame, IN
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