Re: DCD to PDB conversion

From: Giovanni Bellesia (gbellesia_at_chem.ucsb.edu)
Date: Tue Jun 13 2006 - 18:47:01 CDT

Hi,
you can take a look at either the vmd user's guide or the namd tutorial.
You will find a detailed explanation of the algorithm for the
calculation of the RMSD on both the entire molecule and a restricted
selection of atoms/residues

Giovanni
> Hi, I am looking similar script to calculate single residue rmsd. Any help
>
> On 6/13/06, *Jindal Shah* <jindal.shah_at_gmail.com
> <mailto: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, *Ayşe Özlem Sezerman* < asezerman_at_su.sabanciuniv.edu
> <mailto: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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