From: bora erdemli (boraerdemli_at_yahoo.com)
Date: Fri Oct 08 2004 - 12:29:22 CDT

Hi ;

I do not know exactly where your problem occured.
However, I can recommend you to use the following
script for rmsd calculation by using snapshots of your
simulation. I hope it will work for you....

best regards

Bora

set outfile [open rmsd.dat w]
 
set nf [molinfo top get numframes]

set frame0 [atomselect top "selection " frame 0]
 

# rmsd calculation loop

for { set i 1 } { $i <= $nf } { incr i } {
 
set sel [atomselect top "selection " frame $i]

#$sel move [measure fit $sel $frame0]

puts $outfile "[measure rmsd $sel $frame0]"

 
}
close $outfile
--- mashaojie163 <mashao_jie_at_163.com> wrote:

>
> ----- Original Message -----
> From: mashaojie163
> To: vmd-l
> Sent: Tuesday, September 28, 2004 12:12 PM
> Subject: vmd-l: measure fit error??
>
>
> Hello:
> I want to calculate the rmsd of protein by use of
> snopshots during MD simulation. when I regard the
> frame 0 as base strusture.
> for example:
>
>
> set sel0 [atomselect top "protein and backbone
> and noh" frame 0]
> set sel1 [atomselect top "protein and backbone
> and noh" frame 1]
> set sel2 [atomselect top "protein and backbone
> and noh" frame 2]
> measure fit $sel0 $sel1
> the return value is {1.0 0.0 0.0 1.#QNAN} {0.0
> 1.0 0.0 1.#QNAN} {0.0 0.0 1.0 1.#QNAN} {0.0 0.0 0.0
> 1.#QNAN}
> measure fit $sel1 $sel0
> the return value is -1.#IND -1.#IND -1.#IND
> -1.#IND} {-1.#IND -1.#IND -1.#IND -1.#IND} {-1.#IND
> -1.#IND -1.#IND -1.#IND} {-1.#IND -1.#IND -1.#IND
> -1.#IND}
> measure fit $sel2 $sel1
> the return value is right {0.999995708466
> 0.000757500936743 0.00282854191028 0.0485077947378}
> {-0.000757581554353 0.999999701977 2.7410878829e-005
> -0.0505107417703} {-0.00282852025703
> -2.95536119665e-005 0.999996006489 0.00872712116688}
> {0.0 0.0 0.0 1.0}
>
> I don not know what do "-1.#QNNA" and "-1.#IND"
> mean? why these appear when selection including
> frame 0?
>
> Best Regards
> Ma shaojie
>

                
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