VMD-L Mailing List

From: Maxim Belkin (mbelkin_at_ks.uiuc.edu)
Date: Tue Sep 23 2014 - 06:23:31 CDT

So, you should be able to use "animatepdbs" from Tk Console of VMD like this:

  source animatepdbs.tcl
  animatepdbs 1 3 "%d.pdb"

Replace "3" with the number of pdb files in your folder.
Try that and let us know if you get any error.

Maxim

On Sep 23, 2014, at 2:07 AM, Aref Takiden <aref.takiden_at_mailbox.tu-berlin.de> wrote:

> Hallo Maxim,
> my pdbs are named like 1.pdb, 2.pdb etc..
>
> Aref
>
>
>
>
>
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> On 22 Sep 2014, at 20:04, Maxim Belkin <mbelkin_at_ks.uiuc.edu> wrote:
>
>> Aref, what are the names of the files you are trying to merge?
>>
>> Maxim
>>
>> On Sep 22, 2014, at 7:55 AM, Aref Takiden <aref.takiden_at_mailbox.tu-berlin.de> wrote:
>>
>>> Hi,
>>>
>>> I would like to merge several pdb-files into one dcd-like-file, in such away, that at the end, I could see for example the changes in the bond length of the different snapshots(pdb-files) as a graph in the label-window of vmd.
>>>
>>> I tried the script animatepdbs.tcl (link: http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/animatepdbs/animatepdbs.tcl), but it loaded only the first file in spit of that it read the names of the other files. I tested that by adding the command “puts $filename” at the end of the for-loop.
>>> So in other words I had only one frame in my main window of vmd.
>>>
>>> I am thankful for any help.
>>>
>>> Best regards,
>>>
>>> --
>>> M. Sc. Aref Takiden
>>> Technical University of Berlin
>>> Institute of Chemistry
>>> AG Mroginski
>>> Straße des 17. Juni 135
>>> D-10623 Berlin
>>>
>>>
>>>
>>>
>>>
>>>
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