AMBER Archive (2008)

Subject: AMBER: ptraj average structure

From: Yunierkis Perez Castillo (
Date: Sat Oct 04 2008 - 08:25:42 CDT

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_at_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

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