AMBER Archive (2003)

Subject: AMBER: Comparing PE of different conformations

From: Pratul K. Agarwal (pagarwal_at_linus.ornl.gov)
Date: Wed Aug 06 2003 - 11:14:03 CDT

Hello,

I am trying to compare potential energy (PE) of different
conformations of a small protein (Trp-cage). I have found
"unfolded" conformations which have lower PE than the NMR
structure. I am wondering what this means and if somebody
has seen something like this before.

The "unfolded" conformations were obtained by energy
minimizations (EM), is it meaningful to compare PE after EM
or does it make more sense to compare them after MD?
Another possibility could be -- the force-field (parm98) I
am using does not have global minimum at the NMR
conformation. Any discussion on this topic will be
appreciated.

Some details of simulations:
1. minimization performed with sander (v 7)
2. parm98 force-field used
3. implicit solvent (igb=1; "set default PBradii amber6")

Pratul

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