VMD-L Mailing List

From: Andres Morales N (andresmoralesn2_at_hotmail.com)
Date: Thu Sep 03 2009 - 15:00:30 CDT

Dear Josh

 

I tried what you told.

I loaded the native in molid 0 and the mutant in molid 1 (Each dcd file contains 100 frames)

and changed the script to the following:

 

set outfile [open rmsd_min.txt w];
set sel1 [atomselect 0 "protein and backbone and noh"]
set nf1 [molinfo 0 get numframes]
set sel2 [atomselect 1 "protein and backbone and noh"]
 
for {set i 0 } {$i < $nf1 } { incr i } {
for {set j $i } {$j < $nf1 } { incr j } {

$sel1 frame $i
$sel2 frame $j

$sel2 move [measure fit $sel2 $sel1]
set rmsd_matrix($i,$j) [measure rmsd $sel2 $sel1]
rmsd_matrix($i,$j) [$rmsd_matrix($i,$j)]
}}
 
for { set i 0 } { $i < $nf1 } { incr i} {
for { set j 0 } { $j < $nf1 } { incr j } {
puts -nonewline $outfile "$rmsd_matrix($j,$i) "
}
puts $outfile ""
}
close $outfile

so I got a matrix that contains RMSD between native and mutant structures (100*100 matrix). but I need to calculate RMSD between native and mutat, and between themselves (200*200 matrix).

 

Do you have any suggestion else?

 

Thanks a lot

 

Andres

 

 

CC: andresmoralesn2_at_hotmail.com
From: jadelman_at_berkeley.edu
To: pachequin_at_gmail.com
Subject: Re: namd-l: Re: vmd-l: rmsd matrix
Date: Thu, 3 Sep 2009 11:23:15 -0700

Can't you just load the mutant file in one molid and the native into another? Then you just change the "top" command in the atomselect lines to the appropriate molid. This supposes that the two structures have the same number of atoms given the selections you made in the atomselect line. Also I believe the matrix should be symmetric so there is no need to do the calculation twice.

Josh

On Sep 3, 2009, at 9:23 AM, Cesar Millan wrote:
Hi andres, I'll recommend you to use Simulaid (free for academics) that is develop by Prof. Mihaly Mezei. (http://atlas.physbio.mssm.edu/~mezei/simulaid/). Simulaid can do the analysis that you want in a simple manner.

Best regards.

On Thu, Sep 3, 2009 at 7:45 AM, Andres Morales N <andresmoralesn2_at_hotmail.com> wrote:

Dear VMD users:
 
I was using script below to calculte a matrix that contains rmsd between structures from a dcd file:
 
set outfile [open rmsd_min.txt w];
set sel1 [atomselect top "protein and backbone and noh"]
set nf1 [molinfo top get numframes]
set sel2 [atomselect top "protein and backbone and noh"]
 
for {set i 0 } {$i < $nf1 } { incr i } {
for {set j $i } {$j < $nf1 } { incr j } {

$sel1 frame $i
$sel2 frame $j

$sel2 move [measure fit $sel2 $sel1]
set rmsd_matrix($i,$j) [measure rmsd $sel2 $sel1]
$sel2 move [measure fit $sel2 $sel1]
set rmsd_matrix($j,$i) [measure rmsd $sel2 $sel1]
}}
 
for { set i 0 } { $i < $nf1 } { incr i} {
for { set j 0 } { $j < $nf1 } { incr j } {
puts -nonewline $outfile "$rmsd_matrix($j,$i) "
}
puts $outfile ""
}
close $outfile
 
It was working well. I created a mutated structure and now I need to calculate RMSD matrix between structures from both dcd files (one of native structure and another from mutated structure), and I do not know how I should change the script above to do it. I wait somebody can help me.
 
Thanks for your suggestions
 
King regards
 
Andres
 
 
 

 

 
 
 

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