AMBER Archive (2008)

Subject: Re: AMBER: How to create average structure?

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Wed Jun 18 2008 - 23:52:35 CDT

these days you should use ptraj to create the average structure.
check the ptraj section of the manual for details.
then read the tutorials to find out about minimization if you
have not done that yet.
good luck

On Thu, Jun 19, 2008 at 12:44 AM, Shen, Lingling
<Lingling.Shen_at_pfizer.com> wrote:
> 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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