AMBER Archive (2008)

Subject: AMBER: ptraj average structure

From: Yunierkis Perez Castillo (Yunierkis_at_uclv.edu.cu)
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
yunierkis

Servicio de Correos de la Universidad Central "Marta Abreu" de Las Villas. http://www.uclv.edu.cu
-VI Conferencia Internacional de Ciencias Empresariales, del 16 al 18 de octubre de 2008, Cayo Santa Mar?a, Cuba. http://economia-publica.uab.es/VIcubaCICE.doc
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