rams rams wrote:
Dear Users,
I tried to create a trajectory file from a set of pdb files (infact
several of them) starting from time frame 0 to lets say 100 with an
interval of 1ps each. If I use the following command,
trjconv -f 0.xtc 1.xtc ......100.xtc -o .xtc
its resuling only one frame (I think its not stiching them).
If I use "-settime" along with the above command, it is stiching all the
frames, but its asking for the start time for each frame. Its really
difficult to mention the start times for several hundred frames. Is
there any way we can handle this.
The best way to do this would be to develop a script to do it for you. Assuming
you have files named like frame_0.pdb, frame_1.pdb, etc:
#!/bin/bash
for file in `ls | grep frame`; do
temp=${file#frame_}
num=${temp%.pdb}
trjconv -f $file -s $file -o traj_$file -t0 $num
done
(Haven't tested that, so it might not be perfect)
Then they frames (now called, for example, traj_frame_0.pdb) can be assembled
with trjcat, without having to specify -settime, since trjconv will have
assigned them a time value.
-Justin
Thanks.
Ram.
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--
========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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