Re: dcd to pdb conversion

From: Eric H. Lee (ericlee_at_ks.uiuc.edu)
Date: Mon Oct 27 2008 - 04:11:51 CDT

Save coordinates lets you save the current frame (1 pdb file) or your
entire trajectory file (for example, a dcd). It depends what kind of
output you want. From your original email, it sounded like you wanted
a bunch of separate pdb files so you might want to try the VMD animate
command, which will essentially scroll through all the frames in your
trajectory and let you write individual pdb files.

However, if you want to keep it in a convenient dcd format (you can
always load it into VMD later on for analysis), then catdcd will do
the trick.

-Eric

On Oct 27, 2008, at 3:58 AM, Ayşe Özlem Aykut wrote:

> 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>
>>
>>

Eric H. Lee
Medical Scholars Program
Theoretical and Computational Biophysics Group, UIUC
ericlee_at_ks.uiuc.edu

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