Dear all:
I am trying to repeat the MD study of A->B DNA transition problem. The reference I am using is:
"Observation of theA-DNA toB-DNA Transition During Unrestrained Molecular Dynamics in Aqueous Solution", Cheatham, T.E., Kollman, P.A. J. Mol. Biol., 1996, 259, 434-444.
But I am confused by what said in the article:
"Creating average structures:
average structures from the trajectories were calculated using the
carnal module of AMBER 4.1 (Pearlman et al., 1995) to coordinate
average the RMS coordinate fit frames (over all DNA atoms)
taken at 1 ps intervals. These structures were then minimized to
a difference in the norm gradient of the energy of 1 kcal/mol-A° ,
which served to relax unrealistic bonds and angles (leading to an
overall RMSD change near 0.3 A° during the minimization).
".
What does this mean? Actually how I can create these initial average structures? And what is the purpose for this as well?
Thanks,
Lingling
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Received on Sun Jun 22 2008 - 06:07:24 PDT
