Re: Saving coordinates of each frame into one separate .pdb file from a 100-frame .dcd file.

From: Boyang Wang (pkuwangboyang_at_yahoo.com.cn)
Date: Sat Jan 21 2006 - 12:54:04 CST

Thanks. We also did another script yesterday, as follows, and I guess that there are other ways too.
 
 for {set i 1} {$i < 99} {incr i} {
         [atomselect top all frame $i] writepdb $i.pdb
 }
 
 
Carlos Simoes <caze.mailings_at_gmail.com> д Hi,
   I intended to do exactly the same, some time ago, and I found this
way, back then:
1- Load your entire trajectory on VMD (psf+dcd);
2- Use the "Save Coordinates" tool (here you can select a part or the
whole system to be saved);
3- Use the attached "splitmultiframepdb2files.tcl" script to split the
single multi-framed pdb file you obtain from the previous step (take a
look to the script to check its usage).

   I hope this helps...

carlos

On 1/20/06, Boyang Wang
 wrote:
> Hi all, I am wondering what is the best way to save the coordinates of each
> frame into one separate .pdb file from a 100-frame .dcd file.
>
> What I can do now is to save each frame as one pdb file using VMD, and I
> can only do this one frame by one frame. This is very slow.
>
> Thanks for all your time.
>
> Boyang.
>
>
> ________________________________
> Ż1Gٷְٷ
> Ż-ɱɧ
>
>

Boyang Wang,
Email - bwang9_at_uic.edu
Major - Phys. Chem.
dept Chemistry,
Univ Illinois, Chicago,
60607 IL US.
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