AMBER Archive (2009)

Subject: [AMBER] Average structure over simulation

From: Olotu Odunayo (paxoo_at_nottingham.ac.uk)
Date: Mon Jul 27 2009 - 08:38:59 CDT

Hi,

i'm using this ptraj input file to get an average structure over a period of simulation, some of the residues of my protein looks sewn together

trajin Equil.mdcrd
trajin Equil2.mdcrd
trajin Equil3.mdcrd
trajin Equil4.mdcrd
trajin Md.mdcrd
average W_Eq.pdb pdb nowrap

ptraj ddd.prmtop < ptraj.in

but if I create a pdb file from the .rst file, individually e.g below, it looks just fine

ambpdb -p ddd.prmtop < Md.rst > Md.pdb

Just want to check if this happens sometimes!

Thanks

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