AMBER Archive (2008)

Subject: AMBER: How to create average structure?

From: Shen, Lingling (Lingling.Shen_at_pfizer.com)
Date: Wed Jun 18 2008 - 23:44:03 CDT

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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