AMBER Archive (2009)

Subject: RE: [AMBER] RE: Average structure over simulation

From: Olotu Odunayo (paxoo_at_nottingham.ac.uk)
Date: Mon Jul 27 2009 - 10:47:20 CDT

Thank you

O. Loyin Olotu

-----Original Message-----
From: amber-bounces_at_ambermd.org on behalf of Niel Henriksen
Sent: Mon 7/27/2009 15:56
To: AMBER Mailing List
Subject: [AMBER] RE: Average structure over simulation
 
This is normal. When you compute the average structure over a long time period, residues that
undergo a lot of motion will appear blurred. This occurs because the inter-atom distances are
shorter (due to the averaging) and your visualization program is "guessing" where bonds should be
based on those distances. Although they look messy, the structures can give you information about
which parts of your protein are moving compared to others.

--Niel
________________________________________
From: amber-bounces_at_ambermd.org [amber-bounces_at_ambermd.org] On Behalf Of Olotu Odunayo [paxoo_at_nottingham.ac.uk]
Sent: Monday, July 27, 2009 7:38 AM
To: amber_at_ambermd.org
Subject: [AMBER] Average structure over simulation

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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