[AMBER] Average structure over simulation

From: Olotu Odunayo <paxoo.nottingham.ac.uk>
Date: Mon, 27 Jul 2009 14:38:59 +0100


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!


This message has been checked for viruses but the contents of an attachment
may still contain software viruses, which could damage your computer system:
you are advised to perform your own checks. Email communications with the
University of Nottingham may be monitored as permitted by UK legislation.

AMBER mailing list
Received on Mon Jul 27 2009 - 10:09:36 PDT
Custom Search