Re: dcd to pdb conversion

From: Ayşe Özlem Aykut (asezerman_at_su.sabanciuniv.edu)
Date: Mon Oct 27 2008 - 03:58:58 CDT

Hello,
Thanks for your reply but I would like to save the trajectory
coordinates of the backbone atoms in each frame to a pdb file by using
unix command line. It is the same as doing the save coordinates form the
VMD menu bar.

Ozlem

Eric H. Lee 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, Ay�e �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 <mailto:ericlee_at_ks.uiuc.edu>
>
>

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:50:01 CST