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.
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
-V Conferencia Cient?fica Internacional de Ingenier?a Mec?nica, COMEC 2008, del 4 al 6 de noviembre de 2008, UCLV, Cuba.
http://eventos.fim.uclv.edu.cu/comec
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Received on Sun Oct 05 2008 - 05:10:24 PDT
