Re: How to "extract" coordinates from a DCD trajectory file?

From: Darren Anderson (danderso_at_chem.utoronto.ca)
Date: Tue Aug 09 2005 - 07:54:51 CDT

The basic approach you likely want is to write a PDB file for each frame
of your DCD trajectory. The following script shoul give you some
guidelines; first, load your psf and dcd file and remove any frames you
don't want, if you want to cut frames. If not, you can embed the command

mol load psf yourprotein.psf dcd yourprotein.dcd

into your script. The remainder of the script is as follows:

set nf [molinfo top get numframes]

for { set i 0 } {$i < $nf } { incr i } {
        set sel [atomselect top protein frame $i]
        $sel writepdb $i.pdb
}

This first finds the number of frames of your system, then sets up a loop
where for each frame it selects part of the system (the protein in this
case; if you wanted to include waters or ions, change the selection
appropriately), and writes a PDB file with the filename 'framenum.pdb'.

Darren
        

> Hello,
>
>
>
> As you can probably guess, I am new to NAMD.
>
>
>
> I would like to create a conformational database from the trajectory file in
> order to analyse the results with different programs.
>
>
>
> However, the DCD is a binary file.
>
>
>
> Is it possible to "extract" the coordinates data for every "snap shot" from
> that trajectory file?
>
>
>
> If so, how can I do it?
>
>
>
> Kind regards,
>
>
>
> Miro Moman
>
> (RCSI)
>
>

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