Re: vmd-l: rmsd matrix

From: Cesar Millan (pachequin_at_gmail.com)
Date: Thu Sep 03 2009 - 11:23:20 CDT

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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-- 
############################
César Millán Pacheco
Facultad de Ciencias
Universidad Autonoma del Estado de Morelos
Tel: 777 3297020
Fax: 777 3207040
email: cmp_at_uaem.mx
         pachequin_at_gmail.com

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