Re: Re: vmd-l: rmsd matrix

From: Mert Gür (gurmert_at_gmail.com)
Date: Fri Sep 04 2009 - 09:09:07 CDT

If I understood your problem correctly you want to evaluate the rmsd between
structure in two different dcd files.So the only think you have to do is to
load the two dcd files and defined the selections as follows

mol load psf protein.psf dcd notaligned.dcd
mol load psf protein.psf dcd aligned.dcd

#Select all atoms

#your aligned selection
set sel1 [atomselect 0 "all"]
#your not aligned selection
set sel2 [atomselect 1 "all"]

Best,
Mert

On Thu, Sep 3, 2009 at 7:23 PM, Cesar Millan <pachequin_at_gmail.com> 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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>
>
> --
> ############################
> César Millán Pacheco
> Facultad de Ciencias
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