Re: AMBER: ptraj average structure

From: Carlos Simmerling <>
Date: Sat, 4 Oct 2008 09:55:31 -0400

it's not ptraj, it's that you are calculating an average for something that
is moving, so it will always be this way. I suggest that you do one of

- minimize the average structure but be aware that the parts that are
flexible may look "ok" in the minimized version, but it's still not really
representative of the conformation. if you populate 2 rotamers, the average
probably doesn't look like either one.

- do cluster analysis and use the representative structure(s) instead of the
average one.

On Sat, Oct 4, 2008 at 9:25 AM, Yunierkis Perez Castillo <> wrote:

> Hi all.
> I have been trying to use ptraj in order to obtain an average structure of
> a 10 ns MD simulation of a protein. Here is my ptraj input file:
> trajin ../protein.crd
> center :1-634
> image center familiar
> rms first mass out 10ns_CA_rms.csv :1-635.CA
> average 10ns_aver_box.pdb :1-635 pdb
> After looking at the average structure I can see that some residues have
> very unrealistic geometries (overlapping atoms). By searching the amber
> mailing list I found that this is a common problem of calculating average
> structures with ptraj, mainly due to high flexibility residues. Is there any
> way a could obtain average structures from amber trajectories lacking this
> problems?
> Thanks in advance for any help
> yunierkis
> Servicio de Correos de la Universidad Central "Marta Abreu" de Las Villas.
> -VI Conferencia Internacional de Ciencias Empresariales, del 16 al 18 de
> octubre de 2008, Cayo Santa Mar?a, Cuba.
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> del 4 al 6 de noviembre de 2008, UCLV, Cuba.
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Received on Sun Oct 05 2008 - 05:10:27 PDT
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