From: sajad falsafi (sajad.falsafi_at_yahoo.com)
Date: Mon Jul 04 2011 - 08:52:36 CDT
Hi
You can add this command in the script.
>> mol addfile solvated.pdb type pdb waitfor all
proc myrmsd { frame } {
global ref sel all
$all move [measure fit $sel $ref]
puts "$frame: [measure rmsd $sel $ref]"
}
set mol [mol new solvated.psf type psf waitfor all]
mol addfile solvated.pdb type pdb waitfor all
set all [atomselect $mol all]
set ref [atomselect $mol "name CA" frame 0]
set sel [atomselect $mol "name CA"]
bigdcd myrmsd dcd solvated_prod-01.dcd solvated_prod-02.dcd
solvated_prod-03.dcd
bigdcd_wait
quit
Hope this helps you
Sajad & Zahra
________________________________
From: "Cosseddu, Salvatore" <S.M.Cosseddu_at_warwick.ac.uk>
To: snoze pa <snoze.pa_at_gmail.com>; namd-l_at_ks.uiuc.edu
Sent: Mon, July 4, 2011 1:41:55 PM
Subject: RE: namd-l: bigdcd file help
RE: namd-l: bigdcd file help
I'm not an expert on bigdcd. But, because you are reading and removing from
memory the coordinate file, you are likely losing frame 0 coordinates.
try to load with the psf a pdb file or add something like
animate read dcd solvated_prod-01.dcd beg 0 end 0
after loading psf.
If I said something wrong please forgive me!
Regards
Tanti auguri di buona indipendenza
--
Salvatore Cosseddu
PhD student
Centre for Scientific Computing and School of Engineering
University of Warwick
Coventry CV4 7AL
United Kingdom
email: S.M.Cosseddu_at_warwick.ac.uk
-----Original Message-----
From: owner-namd-l_at_ks.uiuc.edu on behalf of snoze pa
Sent: Mon 04/07/2011 07:29
To: namd-l_at_ks.uiuc.edu
Subject: namd-l: bigdcd file help
Dear NamD users,
I am trying to calculate rmsd from my dcd files. the namd rmsd tcl script is
working fine. Unfortunately, My system size is big and I have multiple dcd
file for 1ns each.
I am trying big dcd file to get rmsd but somehow it is not working. Here is
my script
proc myrmsd { frame } {
global ref sel all
$all move [measure fit $sel $ref]
puts "$frame: [measure rmsd $sel $ref]"
}
set mol [mol new solvated.psf type psf waitfor all]
set all [atomselect $mol all]
set ref [atomselect $mol "name CA" frame 0]
set sel [atomselect $mol "name CA"]
bigdcd myrmsd dcd solvated_prod-01.dcd solvated_prod-02.dcd
solvated_prod-03.dcd
bigdcd_wait
quit
I will highly appreciate your help.
Thank you,
S
ps: Wish you all Happy 4th of July.
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