From: sajad falsafi (sajad.falsafi_at_yahoo.com)
Date: Thu Oct 27 2011 - 11:40:38 CDT

 >From: hamze rahimi <buksanbio_at_gmail.com> >To: vmd-l <vmd-l_at_ks.uiuc.edu> >Sent: Thursday, October 27, 2011 4:09 PM >Subject: vmd-l: average pdb from dcd file > >Dear expert > >I want find average pdb from pr.dcd file as final pdb for docking. I think following method be helpful: > 1- load pr.dcd file by using bigdcd > 2- convert dcd to pdb file >3- using mergepdb script > >Please let me know if there are other scripts or idea in this subject >many thanks in advance > >-- >Hamzeh Rahimi >PhD student in Medical Biotechnology >Pasteur institute   average positions of all atoms Hi, i assume you need to calculate average positions of all atoms. when you load a multi-frame PDB file OR dcd file in VMD you can use this script. so i wrote this script for your problem (calculate average positions of all atoms). set sel [atomselect top protein] set avg [measure avpos $sel] set coords [$sel get {x y z}] $sel set {x y z} $avg $sel writepdb avgpdb.pdb $sel set {x y z} $coords $sel delete Best of luck, Sajad Falsafi and Zahra Karimi Dept. of Genetics, Shahid Chamran University of Ahvaz Toxicology Research Center, Jondi-Shapour University of Medical Sciences