VMD-L Mailing List

From: Ivan Gregoretti (ivangreg_at_gmail.com)
Date: Fri Mar 21 2014 - 07:31:32 CDT

Hi Adam,

If I understand your goal correctly, you want to go from an arbitrary
object instance to DCD. So, you want

adamformat -> DCD

I think that you can tackle the problem by doing it in two steps

1) adamformat -> PDB

2) PDB -> DCD

For step 1, your best friend is Biopython's Bio.PDB module.
http://biopython.org/wiki/The_Biopython_Structural_Bioinformatics_FAQ

For step 2, PDB to DCD, let us hear what the community is currently using.
It sounds like a routine task to me.

Ivan

Ivan Gregoretti, PhD
Bioinformatics

On Fri, Mar 21, 2014 at 3:51 AM, Norman Geist <
norman.geist_at_uni-greifswald.de> wrote:

> VMD Main->File->Save Coordinates and choose DCD as file type. Otherwise
> have a look at "catdcd".
>
>
>
> Norman Geist.
>
>
>
> *Von:* owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] *Im
> Auftrag von *Adam Goler
> *Gesendet:* Freitag, 21. März 2014 06:00
> *An:* Vmd l
> *Betreff:* vmd-l: Writing DCD from modified coordinates
>
>
>
> Hello,
>
> I have sets of modified xyz coordinate data (one set for each time step)
> from some python output that I would like to convert back into a DCD
> trajectory for further analysis in VMD.
>
> Can anyone offer suggestions on how to go about this?
>
> Thanks,
> Adam
>
>
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