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