AMBER Archive (2003)

Subject: Re: AMBER: Comparing PE of different conformations

From: Carlos Simmerling (carlos_at_csb.sunysb.edu)
Date: Thu Aug 07 2003 - 14:57:11 CDT

our low energy conformation
was nearly identical to the nmr one
so I didn't expect differences. you
can't really use the energy of the nmr ones
since there is a lot of variation in the family- ie
the structures are ill-determined in regions
so there is no experimental "structure".

you may have found something lower in energy
that we didn't see, but we have several million
structures and the nmr-like ones are lowest.
however, we didn't minimize structures, that
might help but also might hurt, some basins
minimize more than others. try looking at average
energies from MD if you don't have many snapshots
like in our JCC decoy paper.

carlos

----- Original Message -----
From: "Pratul K. Agarwal" <pagarwal_at_linus.ornl.gov>
To: <amber_at_scripps.edu>
Sent: Thursday, August 07, 2003 2:21 PM
Subject: Re: AMBER: Comparing PE of different conformations

> Dr. Simmerling,
>
> For the Trp-cage study you mentioned (or otherwise), did you
> compare energy of your minimum energy conformation with
> those of NMR structures?
>
> I am using parm99 with your corrections and still certain
> conformations have PE lower than NMR structures. I am
> wondering if I made a mistake while including your
> corrections.
>
> Thanks,
>
> Pratul
>
>
>
>
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