Re: dcd to pdb conversion

From: L. Michel Espinoza-Fonseca (mef_at_ddt.biochem.umn.edu)
Date: Mon Oct 27 2008 - 04:05:12 CDT

Even easier. You can use the "animate" command:

set sel [atomselect top "protein and backbone"]
animate write pdb protein_backbone.pdb sel $sel

Cheers,
Michel

On Mon, Oct 27, 2008 at 9:39 AM, Eric H. Lee <ericlee_at_ks.uiuc.edu> wrote:
> You can use the tool catdcd to do this. Simply save the indices of your
> backbone atoms to a file, and use it as the input for catdcd along with your
> trajectory.
> http://www.ks.uiuc.edu/Development/MDTools/catdcd/
> -Eric
>
>
> On Oct 27, 2008, at 3:28 AM, Aye zlem Aykut wrote:
>
> Hello,
>
> I would like to save the coordinates of backbone atoms of a protein from a
> trajectory file in pdb format. I am trying to do this by using vmd unix
> command options.I tried to use writepdb command but it was unsuccesful as it
> won't append the frames but overwrite them . Does anyone have an idea?
>
> Thanks
>
> Ozlem
>
> Eric H. Lee
>
> Medical Scholars Program
>
> Theoretical and Computational Biophysics Group, UIUC
>
> ericlee_at_ks.uiuc.edu
>

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