AW: AW: save the last frame as a pdb file using dcd file

From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Thu Sep 22 2011 - 04:33:07 CDT

Yes you can use the final coor. But that’s not always the same as the last frame of dcd, what you have asked about. If simulation gets stopped before getting finished, you have no final coor, only a restart.coor if you have turned on restart files. This files can be much older than the last frame of the dcd. But you have to know what you want to have. Look to your namd.out when the last restart got written and when the last frame was put to the dcd. Then you see the difference.
 
Cheers
 
Norman Geist.
 
Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im Auftrag von Namd Namd
Gesendet: Donnerstag, 22. September 2011 10:33
An: namd-l_at_ks.uiuc.edu
Betreff: Re : AW: namd-l: save the last frame as a pdb file using dcd file
 
Thanks for your help. I've just found a way that is also easy. I think .coord file that includes final coordinates is a pdb file .So I can chance .coord with .pdb then use it . Am I right ?
 
All the best
 
  _____

Kimden: Norman Geist <norman.geist_at_uni-greifswald.de>
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Konu: AW: namd-l: save the last frame as a pdb file using dcd file

You can easily use vmd for that. Load your topology file. Load your DCD. Save coordinates as pdb for last frame through the menu. You can auto this with writing a little tcl script and call it with vmd. Or you can use the command “catDCD” for commandline which maybe fits your needs good also.
 
Good luck
 
Norman Geist.
 
Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im Auftrag von Namd Namd
Gesendet: Donnerstag, 22. September 2011 09:03
An: namd-l_at_ks.uiuc.edu
Betreff: namd-l: save the last frame as a pdb file using dcd file
 
Dear All,
 
How can I save the last frame as a pdb file using dcd file ?
 
Could you please help me to learn this procedure ?
 
Thanks for your help.
 
All the best.
 
 
 
 
 

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