Re: DCD to PDB conversion

From: snoze pa (snoze.pa_at_gmail.com)
Date: Tue Jun 13 2006 - 17:10:37 CDT

Hi, I am looking similar script to calculate single residue rmsd. Any help

On 6/13/06, Jindal Shah <jindal.shah_at_gmail.com> wrote:
>
> Hi,
>
> If you are converting dcd into pdb on a remote machine (as I do). You can
> run following script to write out pdb files frame by frame.
>
> mol load psf *.psf dcd *.dcd
> set nf [molinfo top get numframes]
> for {set i 0 } {$i < $nf} {incr i} {
> [atomselect top all frame $i] writepdb frame_$i.pdb
> }
>
> Jindal
>
>
> On 6/8/06, Ay║e Ízlem Sezerman <asezerman_at_su.sabanciuniv.edu> wrote:
> >
> > Hi Miro,
> >
> > Yes,it is possible to convert DCD file to pdb ..
> > Load your psf file to VMD , then load the dcd trajectory file on to it
> > (without opening molecule file browser)
> > After loading click on the molecule in the VMD main window and from
> > file menu select "save coordinates"
> >
> > there you can choose the type of file you want to create..
> >
> > Good Luck!
> > Ozlem
> >
> > Edelmiro Moman wrote:
> >
> > > Hi,
> > >
> > > Is it possible to convert a DCD trajectory file to a PDB file or a
> > > collection/database of PDB files that can be analyzed in any
> > application?
> > >
> > > Cheers,
> > >
> > > Miro
> > >
> >
>
>

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