Re: AMBER: Comparing PE of different conformations

From: Carlos Simmerling <>
Date: Wed, 6 Aug 2003 12:33:42 -0400

I suggest looking at some of recent publications
on potential energy comparisons, like

Okur, A., Strockbine, B., Hornak, V. and Simmerling, C., 'Using PC Clusters
to Evaluate the Transferability of Molecular Mechanics Force Fields for
Proteins", J. Comput. Chem.,
24:21, 2003.

You should also read our article and subsequent
ones about simulating trp-cage folding before
you get too far with it. I think you are seeing force
field artifacts. Parm98 is not a good choice (nor is
parm94 or 99).

Simmerling, C., Strockbine, B and Roitberg, A., 'All-Atom Structure
Prediction and Folding Simulations of a Stable Protein', J. Am. Chem. Soc,
124:11258, 2002.

Carlos L. Simmerling, Ph.D.
Assistant Professor Phone: (631) 632-1336
Center for Structural Biology Fax: (631) 632-1555
Stony Brook University Web:
Stony Brook, NY 11794-5115 E-mail:

----- Original Message -----
From: "Pratul K. Agarwal" <>
To: <>
Sent: Wednesday, August 06, 2003 12:14 PM
Subject: AMBER: Comparing PE of different conformations

> 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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Received on Wed Aug 06 2003 - 17:53:01 PDT
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